format-version: 1.2 data-version: 4.1.142 date: 24:01:2024 10:23 saved-by: Eric Deutsch auto-generated-by: OBO-Edit 2.3.1 import: http://purl.obolibrary.org/obo/pato.obo import: http://purl.obolibrary.org/obo/stato.owl default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ remark: coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics remark: namespace: MS remark: namespace: PEFF remark: coverage: Mass spectrometer output files and spectra interpretation remark: creator: Yasset Perez-Riverol ebi.ac.uk> remark: creator: Matt Chambers vanderbilt.edu> remark: creator: Andreas Bertsch informatik.uni-tuebingen.de> remark: creator: Marius Kallhardt bdal.de> remark: creator: Eric Deutsch systemsbiology.org> remark: creator: Fredrik Levander immun.lth.se> remark: creator: Pierre-Alain Binz chuv.ch> remark: creator: Gerhard Mayer rub.de> remark: creator: Joshua Klein bu.edu> remark: creator: Chris Bielow fu-berlin.de> remark: creator: Wout Bittremieux health.ucsd.edu> remark: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de> remark: creator: Julian Uszkoreit ruhr-uni-bochum.de> remark: creator: Mathias Walzer ebi.ac.uk> remark: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html and http://mass-spec.lsu.edu/msterms/index.php/Main_Page remark: For any queries contact psidev-ms-vocab@lists.sourceforge.net remark: URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/ or send a letter to Creative Commons, 444 Castro Street, Suite 900, Mountain View, California, 94041, USA. ontology: ms [Typedef] id: has_regexp name: has regexp [Typedef] id: has_units name: has_units [Typedef] id: part_of name: part_of xref: BFO:0000050 is_transitive: true [Typedef] id: has_order name: has_order [Typedef] id: has_domain name: has_domain [Typedef] id: has_value_type name: has value type def: "'Entity A' has value type 'Entity B', such as xsd:float." [] [Typedef] id: has_structured_representation_in_format name: has structured representation in format def: "The term is encoded in the structure of the named file format rather than as an explicit parameter, and should not be used as one in that format." [] [Typedef] id: has_metric_category name: has_metric_category [Typedef] id: has_value_concept name: has_value_concept [Typedef] id: has_column name: has_column [Typedef] id: has_optional_column name: has_optional_column [Term] id: NCIT:C25330 name: Duration def: "The period of time during which something continues." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} is_a: NCIT:C21514 ! Temporal Qualifier [Term] id: NCIT:C45781 name: Density def: "The amount of something per unit size." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} is_a: NCIT:C25447 ! Characteristic [Term] id: NCIT:C68811 name: Cover def: "Span a region or interval of distance, space or time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} is_a: NCIT:C25404 ! Action [Term] id: NCIT:C79083 name: Outlier def: "An observation in a data set that is numerically distant from the rest of the data." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} is_a: NCIT:C20181 ! Conceptual Entity [Term] id: NCIT:C21514 name: Temporal Qualifier def: "Terms used to indicate units of time or other terms associated with time." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Temporal Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} is_a: NCIT:C41009 ! Qualifier [Term] id: NCIT:C41009 name: Qualifier def: "A term that helps define and render a concept unique." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} synonym: "Modifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Qualifier" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} is_a: NCIT:C20189 ! Property or Attribute [Term] id: NCIT:C25447 name: Characteristic def: "The distinguishing qualities or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} synonym: "Characteristic" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} synonym: "Characteristics" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Feature" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Features" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} is_a: NCIT:C20189 ! Property or Attribute [Term] id: NCIT:C20189 name: Property or Attribute def: "A distinguishing quality or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Property or Attribute" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NICHD"} [Term] id: NCIT:C25404 name: Action def: "A thing done." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} subset: NCIT:C105763 synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} synonym: "Generic Action" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} is_a: NCIT:C43431 ! Activity [Term] id: NCIT:C43431 name: Activity def: "An active process; excludes processes and mechanisms which fulfill biological functions." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 3.0.3"} synonym: "Activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="BRIDG 5.3"} synonym: "General activity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="SY", http://purl.obolibrary.org/obo/NCIT_P384="caDSR"} [Term] id: NCIT:C20181 name: Conceptual Entity def: "An organizational header for concepts representing mostly abstract entities." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} synonym: "Conceptual Entity" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} [Term] id: NCIT:C16847 name: Technique def: "A practiced and regimented skill or series of actions." [] {http://purl.obolibrary.org/obo/NCIT_C16847="NCI"} is_a: NCIT:C43431 ! Activity [Term] id: NCIT:C19044 name: Statistical Technique def: "A method of analyzing or representing statistical data; a procedure for calculating a statistic." [] {http://purl.obolibrary.org/obo/NCIT_C19044="NCI"} is_a: NCIT:C16847 ! Technique [Term] id: NCIT:C60694 name: Principal Component def: "One of the axes representing the projection of varience resulting from principal component analysis." [] {http://purl.obolibrary.org/obo/NCIT_C60694="NCI"} is_a: NCIT:C19044 ! Statistical Technique [Term] id: MS:0000000 name: Proteomics Standards Initiative Mass Spectrometry Vocabularies def: "Proteomics Standards Initiative Mass Spectrometry Vocabularies." [PSI:MS] [Term] id: MS:1000001 name: sample number def: "A reference number relevant to the sample under study." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000002 name: sample name def: "A reference string relevant to the sample under study." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000003 name: sample state def: "The chemical phase of a pure sample, or the state of a mixed sample." [PSI:MS] is_a: MS:1000548 ! sample attribute [Term] id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000021 ! gram relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000005 name: sample volume def: "Total volume of solution used." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000098 ! milliliter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000006 name: sample concentration def: "Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000175 ! gram per liter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000007 name: inlet type def: "The nature of the sample inlet." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000008 name: ionization type def: "The method by which gas phase ions are generated from the sample." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000009 name: ionization mode def: "OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer." [PSI:MS] comment: This term was made obsolete because it was replaced by scan polarity (MS:1000465). is_obsolete: true [Term] id: MS:1000010 name: analyzer type def: "OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000011 name: mass resolution def: "Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000012 name: resolution measurement method def: "Which of the available standard measures is used to define whether two peaks are separate." [PSI:MS] is_a: MS:1000596 ! measurement method [Term] id: MS:1000013 name: resolution type def: "OBSOLETE Specify the nature of resolution for the mass analyzer. Resolution is usually either constant with respect to m/z or proportional to m/z." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000014 name: accuracy def: "Accuracy is the degree of conformity of a measured mass to its actual value." [PSI:MS] is_a: MS:1000480 ! mass analyzer attribute relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000169 ! parts per million relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000015 name: scan rate def: "Rate in Th/sec for scanning analyzers." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units MS:1000807 ! Th/s relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000016 name: scan start time def: "The time that an analyzer started a scan, relative to the start of the MS run." [PSI:MS] is_a: MS:1000503 ! scan attribute is_a: MS:1002345 ! PSM-level attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000017 name: Scan Function def: "OBSOLETE Describes the type of mass analysis being performed. Two primary modes are: typical acquisition over a range of masses (Mass Scan), and Selected Ion Detection. The primary difference is that Selected Ion Detection produces a single value for the signal at the selected mass rather than producing a mass spectrum." [PSI:MS] comment: OBSOLETE This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000018 name: scan direction def: "Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low)." [PSI:MS] relationship: part_of MS:1000441 ! scan [Term] id: MS:1000019 name: scan law def: "Describes the function in control of the m/z scan (for scanning instruments). Commonly the scan function is linear, but in principle any function can be used." [PSI:MS] relationship: part_of MS:1000441 ! scan [Term] id: MS:1000020 name: scanning method def: "Describes the acquisition data type produced by a tandem mass spectrometry experiment." [PSI:MS] comment: OBSOLETE This former purgatory term was made obsolete. synonym: "Tandem Scanning Method" RELATED [] is_obsolete: true [Term] id: MS:1000021 name: reflectron state def: "Status of the reflectron, turned on or off." [PSI:MS] is_a: MS:1000480 ! mass analyzer attribute [Term] id: MS:1000022 name: TOF Total Path Length def: "The length of the field free drift space in a time of flight mass spectrometer." [PSI:MS] is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000008 ! meter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000023 name: isolation width def: "OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion." [PSI:MS] comment: This former purgatory term was made obsolete. relationship: has_units MS:1000040 ! m/z is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000024 name: final MS exponent def: "Final MS level achieved when performing PFF with the ion trap (e.g. MS E10)." [PSI:MS] is_a: MS:1000480 ! mass analyzer attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000025 name: magnetic field strength def: "A property of space that produces a force on a charged particle equal to qv x B where q is the particle charge and v its velocity." [PSI:MS] synonym: "B" EXACT [] synonym: "Magnetic Field" RELATED [] is_a: MS:1000480 ! mass analyzer attribute relationship: has_units UO:0000228 ! tesla relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000026 name: detector type def: "Type of detector used in the mass spectrometer." [PSI:MS] relationship: part_of MS:1000453 ! detector [Term] id: MS:1000027 name: detector acquisition mode def: "Method by which detector signal is acquired by the data system." [PSI:MS] relationship: part_of MS:1000453 ! detector [Term] id: MS:1000028 name: detector resolution def: "The resolving power of the detector to detect the smallest difference between two ions so that the valley between them is a specified fraction of the peak height." [PSI:MS] is_a: MS:1000481 ! detector attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000029 name: sampling frequency def: "The rate of signal sampling (measurement) with respect to time." [PSI:MS] synonym: "ADC Sampling Frequency" NARROW [] is_a: MS:1000481 ! detector attribute relationship: has_units UO:0000106 ! hertz relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000030 name: vendor def: "OBSOLETE Name of instrument vendor." [PSI:MS] comment: This term was made obsolete because it was replaced by instrument model (MS:1000031). is_obsolete: true [Term] id: MS:1000031 name: instrument model def: "Instrument model name not including the vendor's name." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000032 name: customization def: "Free text description of a single customization made to the instrument; for several modifications, use several entries." [PSI:MS] is_a: MS:1000496 ! instrument attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000033 name: deisotoping def: "The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000034 name: charge deconvolution def: "The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000035 name: peak picking def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000036 name: scan mode def: "OBSOLETE." [PSI:MS] comment: This term was made obsolete because . is_obsolete: true [Term] id: MS:1000037 name: polarity def: "OBSOLETE Terms to describe the polarity setting of the instrument." [PSI:MS] comment: This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186). is_obsolete: true [Term] id: MS:1000038 name: minute def: "OBSOLETE Acquisition time in minutes." [PSI:MS] comment: This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031). is_obsolete: true [Term] id: MS:1000039 name: second def: "OBSOLETE Acquisition time in seconds." [PSI:MS] comment: This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010). is_obsolete: true [Term] id: MS:1000040 name: m/z def: "Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated." [PSI:MS] synonym: "mass-to-charge ratio" EXACT [] synonym: "Th" EXACT [] synonym: "thomson" EXACT [] is_a: UO:0000000 ! unit [Term] id: MS:1000041 name: charge state def: "Number of net charges, positive or negative, on an ion." [PSI:MS] synonym: "z" EXACT [] is_a: MS:1000455 ! ion selection attribute is_a: MS:1000507 ! ion property relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000042 name: peak intensity def: "Intensity of ions as measured by the height or area of a peak in a mass spectrum." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: part_of MS:1000231 ! peak relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000043 name: intensity unit def: "Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors." [PSI:MS] is_a: UO:0000000 ! unit [Term] id: MS:1000044 name: dissociation method def: "Fragmentation method used for dissociation or fragmentation." [PSI:MS] synonym: "Activation Method" RELATED [] relationship: part_of MS:1000456 ! precursor activation [Term] id: MS:1000045 name: collision energy def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000046 name: energy unit def: "OBSOLETE Energy units are represented in either eV or Joules." [PSI:MS] comment: This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111). is_a: UO:0000000 ! unit is_obsolete: true [Term] id: MS:1000047 name: emulsion def: "State if the sample is in emulsion form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000048 name: gaseous sample state def: "State if the sample is in gaseous form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000049 name: liquid sample state def: "State if the sample is in liquid form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000050 name: solid sample state def: "State if the sample is in solid form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000051 name: solution def: "State if the sample is in solution form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000052 name: suspension def: "State if the sample is in suspension form." [PSI:MS] is_a: MS:1000003 ! sample state [Term] id: MS:1000053 name: sample batch def: "Sample batch lot identifier." [PSI:MS] is_a: MS:1000548 ! sample attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000054 name: chromatography def: "OBSOLETE Chromatographic conditions used to obtain the sample." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000055 name: continuous flow fast atom bombardment def: "Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix." [PSI:MS] synonym: "CF-FAB" EXACT [] is_a: MS:1000007 ! inlet type [Term] id: MS:1000056 name: direct inlet def: "The sample is directly inserted into the ion source, usually on the end of a heatable probe." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000057 name: electrospray inlet def: "Inlet used for introducing the liquid sample into an electrospray ionization source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000058 name: flow injection analysis def: "Sample is directly injected or infused into the ionization source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000059 name: inductively coupled plasma def: "A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000060 name: infusion def: "The continuous flow of solution of a sample into the ionization source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000061 name: jet separator def: "A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000062 name: membrane separator def: "A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000063 name: moving belt def: "Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000064 name: moving wire def: "Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000065 name: open split def: "A division of flowing stream of liquid into two streams." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000066 name: particle beam def: "Method for generating ions from a solution of an analyte." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000067 name: reservoir def: "A sample inlet method involving a reservoir." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000068 name: septum def: "A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000069 name: thermospray inlet def: "A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000070 name: atmospheric pressure chemical ionization def: "Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization." [PSI:MS] synonym: "APCI" EXACT [] is_a: MS:1000240 ! atmospheric pressure ionization [Term] id: MS:1000071 name: chemical ionization def: "The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization." [PSI:MS] synonym: "CI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000072 name: Electronic Ionization def: "OBSOLETE The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS] comment: This term was made obsolete because it was replaced by electron ionization (MS:1000389). synonym: "EI" EXACT [] is_obsolete: true [Term] id: MS:1000073 name: electrospray ionization def: "A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended." [PSI:MS] synonym: "ESI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000074 name: fast atom bombardment ionization def: "The ionization of any species by the interaction of a focused beam of neutral atoms having a translational energy of several thousand eV with a sample that is typically dissolved in a solvent matrix. See also secondary ionization." [PSI:MS] synonym: "FAB" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000075 name: matrix-assisted laser desorption ionization def: "The formation of gas-phase ions from molecules that are present in a solid or solvent matrix that is irradiated with a pulsed laser. See also laser desorption/ionization." [PSI:MS] synonym: "MALDI" EXACT [] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000076 name: negative ion mode def: "OBSOLETE." [PSI:MS] comment: This term was made obsolete because it was replaced by negative scan (MS:1000129). is_obsolete: true [Term] id: MS:1000077 name: positive ion mode def: "OBSOLETE." [PSI:MS] comment: This term was made obsolete because it was replaced by positive scan (MS:1000130). is_obsolete: true [Term] id: MS:1000078 name: axial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the axis of the analyzer." [PSI:MS] is_a: MS:1000291 ! linear ion trap [Term] id: MS:1000079 name: fourier transform ion cyclotron resonance mass spectrometer def: "A mass spectrometer based on the principle of ion cyclotron resonance in which an ion in a magnetic field moves in a circular orbit at a frequency characteristic of its m/z value. Ions are coherently excited to a larger radius orbit using a pulse of radio frequency energy and their image charge is detected on receiver plates as a time domain signal. Fourier transformation of the time domain signal results in a frequency domain signal which is converted to a mass spectrum based in the inverse relationship between frequency and m/z." [PSI:MS] synonym: "FT_ICR" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000080 name: magnetic sector def: "A device that produces a magnetic field perpendicular to a charged particle beam that deflects the beam to an extent that is proportional to the particle momentum per unit charge. For a monoenergetic beam, the deflection is proportional to m/z." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000081 name: quadrupole def: "A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000082 name: quadrupole ion trap def: "Quadrupole Ion Trap mass analyzer captures the ions in a three dimensional ion trap and then selectively ejects them by varying the RF and DC potentials." [PSI:MS] synonym: "Paul Ion trap" EXACT [] synonym: "QIT" EXACT [] synonym: "Quistor" EXACT [] is_a: MS:1000264 ! ion trap [Term] id: MS:1000083 name: radial ejection linear ion trap def: "A linear ion trap mass spectrometer where ions are ejected along the radius of the analyzer." [PSI:MS] is_a: MS:1000291 ! linear ion trap [Term] id: MS:1000084 name: time-of-flight def: "Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy." [PSI:MS] synonym: "TOF" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000085 name: baseline def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] is_a: MS:1000012 ! resolution measurement method [Term] id: MS:1000086 name: full width at half-maximum def: "A measure of resolution represented as width of the peak at half peak height." [PSI:MS] synonym: "FWHM" EXACT [] is_a: MS:1000012 ! resolution measurement method [Term] id: MS:1000087 name: ten percent valley def: "An attribute of resolution when the ratio between adjacent signals is 10% of the signal height." [PSI:MS] is_a: MS:1000012 ! resolution measurement method [Term] id: MS:1000088 name: constant def: "OBSOLETE When resolution is constant with respect to m/z." [PSI:MS] comment: This child of the former purgatory term resolution type was made obsolete. is_obsolete: true [Term] id: MS:1000089 name: proportional def: "OBSOLETE When resolution is proportional with respect to m/z." [PSI:MS] comment: This child of the former purgatory term resolution type was made obsolete. is_obsolete: true [Term] id: MS:1000090 name: mass scan def: "OBSOLETE A variation of instrument where a selected mass is scanned." [PSI:MS] comment: This child of the former purgatory term Scan Function was made obsolete. is_obsolete: true [Term] id: MS:1000091 name: selected ion detection def: "OBSOLETE Please see Single Ion Monitoring." [PSI:MS] comment: This child of the former purgatory term Scan Function was made obsolete. is_obsolete: true [Term] id: MS:1000092 name: decreasing m/z scan def: "High to low direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] is_a: MS:1000018 ! scan direction [Term] id: MS:1000093 name: increasing m/z scan def: "Low to high direction in terms of m/z of the scan for scanning analyzers." [PSI:MS] is_a: MS:1000018 ! scan direction [Term] id: MS:1000094 name: exponential def: "The mass scan is done in exponential mode." [PSI:MS] is_a: MS:1000019 ! scan law [Term] id: MS:1000095 name: linear def: "OBSOLETE The mass scan is done in linear mode." [PSI:MS] comment: This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199). is_a: MS:1000019 ! scan law is_obsolete: true [Term] id: MS:1000096 name: quadratic def: "The mass scan is done in quadratic mode." [PSI:MS] is_a: MS:1000019 ! scan law [Term] id: MS:1000097 name: constant neutral mass loss def: "OBSOLETE A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000098 name: multiple ion monitoring def: "OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000099 name: multiple reaction monitoring def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS] comment: This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206). synonym: "MRM" EXACT [] is_obsolete: true [Term] id: MS:1000100 name: precursor ion scan def: "OBSOLETE The specific scan function or process that will record a precursor ion spectrum." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000101 name: product ion scan def: "OBSOLETE The specific scan function or process that records product ion spectrum." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000102 name: single ion monitoring def: "OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum." [PSI:MS] comment: This term was made obsolete because it was replaced by single ion monitoring (MS:100205). is_obsolete: true [Term] id: MS:1000103 name: single reaction monitoring def: "OBSOLETE This term is not recommended. See Selected Reaction Monitoring." [PSI:MS] comment: This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206). is_obsolete: true [Term] id: MS:1000104 name: None ?? def: "OBSOLETE None." [PSI:MS] comment: This term was made obsolete because . is_obsolete: true [Term] id: MS:1000105 name: reflectron off def: "Reflectron is off." [PSI:MS] is_a: MS:1000021 ! reflectron state [Term] id: MS:1000106 name: reflectron on def: "Reflectron is on." [PSI:MS] is_a: MS:1000021 ! reflectron state [Term] id: MS:1000107 name: channeltron def: "A horn-shaped (or cone-shaped) continuous dynode particle multiplier. The ion strikes the inner surface of the device and induces the production of secondary electrons that in turn impinge on the inner surfaces to produce more secondary electrons. This avalanche effect produces an increase in signal in the final measured current pulse." [PSI:MS] synonym: "Channeltron Detector" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000108 name: conversion dynode electron multiplier def: "A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] is_a: MS:1000346 ! conversion dynode [Term] id: MS:1000109 name: conversion dynode photomultiplier def: "A detector in which ions strike a conversion dynode to produce electrons that in turn generate photons through a phosphorescent screen that are detected by a photomultiplier." [PSI:MS] synonym: "ion-to-photon detector" RELATED [] is_a: MS:1000346 ! conversion dynode [Term] id: MS:1000110 name: daly detector def: "Detector consisting of a conversion dynode, scintillator and photomultiplier. The metal knob at high potential emits secondary electrons when ions impinge on the surface. The secondary electrons are accelerated onto the scintillator that produces light that is then detected by the photomultiplier detector." [PSI:MS] synonym: "Daly" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000111 name: electron multiplier tube def: "A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons." [PSI:MS] synonym: "EMT" EXACT [] is_a: MS:1000253 ! electron multiplier [Term] id: MS:1000112 name: faraday cup def: "A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000113 name: focal plane array def: "An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] is_a: MS:1000348 ! focal plane collector [Term] id: MS:1000114 name: microchannel plate detector def: "A thin plate that contains a closely spaced array of channels that each act as a continuous dynode particle multiplier. A charged particle, fast neutral particle, or photon striking the plate causes a cascade of secondary electrons that ultimately exits the opposite side of the plate." [PSI:MS] synonym: "multichannel plate" EXACT [] is_a: MS:1000345 ! array detector [Term] id: MS:1000115 name: multi-collector def: "A detector system commonly used in inductively coupled plasma mass spectrometers." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000116 name: photomultiplier def: "A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected." [PSI:MS] synonym: "PMT" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000117 name: analog-digital converter def: "Analog-to-digital converter (abbreviated ADC, A/D or A to D) is an electronic integrated circuit (i/c) that converts continuous signals to discrete digital numbers." [PSI:MS] synonym: "ADC" EXACT [] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000118 name: pulse counting def: "Definition to do." [PSI:MS] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000119 name: time-digital converter def: "A device for converting a signal of sporadic pluses into a digital representation of their time indices." [PSI:MS] synonym: "TDC" EXACT [] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000120 name: transient recorder def: "A detector acquisition mode used for detecting transient signals." [PSI:MS] is_a: MS:1000027 ! detector acquisition mode [Term] id: MS:1000121 name: SCIEX instrument model def: "The brand of instruments from the joint venture between Applied Biosystems and MDS Analytical Technologies (formerly MDS SCIEX). Previously branded as \"Applied Biosystems|MDS SCIEX\"." [PSI:MS] synonym: "Applied Biosystems|MDS SCIEX" RELATED [] is_a: MS:1000031 ! instrument model [Term] id: MS:1000122 name: Bruker Daltonics instrument model def: "Bruker Daltonics' instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000123 name: IonSpec instrument model def: "IonSpec corporation instrument model." [PSI:MS] is_a: MS:1000489 ! Varian instrument model [Term] id: MS:1000124 name: Shimadzu instrument model def: "Shimadzu corporation instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000125 name: Thermo Finnigan instrument model def: "ThermoFinnigan from Thermo Electron Corporation instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000126 name: Waters instrument model def: "Waters Corporation instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000127 name: centroid spectrum def: "Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset." [PSI:MS] synonym: "Discrete Mass Spectrum" EXACT [] is_a: MS:1000525 ! spectrum representation [Term] id: MS:1000128 name: profile spectrum def: "A profile mass spectrum is created when data is recorded with ion current (counts per second) on one axis and mass/charge ratio on another axis." [PSI:MS] synonym: "continuous mass spectrum" EXACT [] synonym: "Continuum Mass Spectrum" EXACT [] is_a: MS:1000525 ! spectrum representation [Term] id: MS:1000129 name: negative scan def: "Polarity of the scan is negative." [PSI:MS] is_a: MS:1000465 ! scan polarity is_a: MS:1000808 ! chromatogram attribute [Term] id: MS:1000130 name: positive scan def: "Polarity of the scan is positive." [PSI:MS] is_a: MS:1000465 ! scan polarity is_a: MS:1000808 ! chromatogram attribute [Term] id: MS:1000131 name: number of detector counts def: "The number of counted events observed in one or a group of elements of a detector." [PSI:MS] is_a: MS:1000043 ! intensity unit [Term] id: MS:1000132 name: percent of base peak def: "The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity." [PSI:MS] is_a: MS:1000043 ! intensity unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000133 name: collision-induced dissociation def: "The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended." [PSI:MS] synonym: "CID" EXACT [] synonym: "CAD" EXACT [] synonym: "collisionally activated dissociation" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000134 name: plasma desorption def: "The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS] synonym: "PD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000135 name: post-source decay def: "A technique specific to reflectron time-of-flight mass spectrometers where product ions of metastable transitions or collision-induced dissociations generated in the drift tube prior to entering the reflectron are m/z separated to yield product ion spectra." [PSI:MS] synonym: "PSD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000136 name: surface-induced dissociation def: "Fragmentation that results from the collision of an ion with a surface." [PSI:MS] synonym: "SID" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000137 name: electron volt def: "OBSOLETE A non-SI unit of energy (eV) defined as the energy acquired by a particle containing one unit of charge through a potential difference of one volt. An electron-volt is equal to 1.602 176 53(14) x 10^-19 J." [PSI:MS] comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266). is_obsolete: true [Term] id: MS:1000138 name: normalized collision energy def: "Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions." [PSI:PI] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000187 ! percent relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000139 name: 4000 QTRAP def: "Applied Biosystems/MDS SCIEX Q 4000 TRAP MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000140 name: 4700 Proteomics Analyzer def: "Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000141 name: apex IV def: "Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] is_a: MS:1001556 ! Bruker Daltonics apex series [Term] id: MS:1000142 name: apex Q def: "Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] is_a: MS:1001556 ! Bruker Daltonics apex series [Term] id: MS:1000143 name: API 150EX def: "Applied Biosystems/MDS SCIEX API 150EX MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000144 name: API 150EX Prep def: "Applied Biosystems/MDS SCIEX API 150EX Prep MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000145 name: API 2000 def: "Applied Biosystems/MDS SCIEX API 2000 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000146 name: API 3000 def: "Applied Biosystems/MDS SCIEX API 3000 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000147 name: API 4000 def: "Applied Biosystems/MDS SCIEX API 4000 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000148 name: autoflex II def: "Bruker Daltonics' autoflex II: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000149 name: autoflex TOF/TOF def: "Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000150 name: Auto Spec Ultima NT def: "Waters magnetic sector based AutoSpec Ultima NT MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000151 name: BioTOF II def: "Bruker Daltonics' BioTOF II: ESI TOF." [PSI:MS] is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1000152 name: BioTOF-Q def: "Bruker Daltonics' BioTOF-Q: ESI Q-TOF." [PSI:MS] is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1000153 name: DELTA plusAdvantage def: "ThermoFinnigan DELTA plusAdvantage MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000154 name: DELTAplusXP def: "ThermoFinnigan DELTAplusXP MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000155 name: ELEMENT2 def: "OBSOLETE ThermoFinnigan ELEMENT2 MS." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000156 name: esquire 4000 def: "Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1001533 ! Bruker Daltonics esquire series [Term] id: MS:1000157 name: esquire 6000 def: "Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1001533 ! Bruker Daltonics esquire series [Term] id: MS:1000158 name: explorer def: "IonSpec Explorer MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000159 name: GCT def: "Waters oa-ToF based GCT." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000160 name: HCT def: "Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000161 name: HCTplus def: "Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000162 name: HiRes ESI def: "IonSpec HiResESI MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000163 name: HiRes MALDI def: "IonSpec HiResMALDI MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000164 name: IsoPrime def: "Waters IsoPrime MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000165 name: IsoProbe def: "Waters IsoProbe MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000166 name: IsoProbe T def: "Waters IsoProbe T MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000167 name: LCQ Advantage def: "ThermoFinnigan LCQ Advantage MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000168 name: LCQ Classic def: "ThermoFinnigan LCQ Classic MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000169 name: LCQ Deca XP Plus def: "ThermoFinnigan LCQ Deca XP Plus MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000170 name: M@LDI L def: "Waters oa-ToF based MALDI L." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000171 name: M@LDI LR def: "Waters oa-ToF based MALDI LR." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000172 name: MAT253 def: "ThermoFinnigan MAT253 MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000173 name: MAT900XP def: "ThermoFinnigan MAT900XP MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000174 name: MAT900XP Trap def: "ThermoFinnigan MAT900XP Trap MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000175 name: MAT95XP def: "ThermoFinnigan MAT95XP MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000176 name: MAT95XP Trap def: "ThermoFinnigan MAT95XP Trap MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000177 name: microflex def: "Bruker Daltonics' microflex: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000178 name: microTOF LC def: "Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000179 name: neptune def: "ThermoFinnigan NEPTUNE MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000180 name: NG-5400 def: "Waters NG-5400 MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000181 name: OMEGA def: "IonSpec OMEGA MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000182 name: OMEGA-2001 def: "IonSpec OMEGA-2001 MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000183 name: OmniFlex def: "Bruker Daltonics' OmniFlex: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000184 name: Platform ICP def: "Waters Platform ICP MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000185 name: PolarisQ def: "ThermoFinnigan PolarisQ MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000186 name: proteomics solution 1 def: "Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000187 name: Q TRAP def: "Applied Biosystems/MDS SCIEX Q TRAP MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000188 name: Q-Tof micro def: "Waters oa-ToF based Q-Tof micro." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000189 name: Q-Tof Ultima def: "Waters oa-ToF based Q-Tof Ultima." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000190 name: QSTAR def: "Applied Biosystems/MDS SCIEX QSTAR MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000191 name: quattro micro def: "Waters (triple) quadrupole based micro." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000192 name: Quattro Ultima def: "Waters (triple) quadrupole based Ultima." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000193 name: Surveyor MSQ def: "ThermoFinnigan Surveyor MSQ MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000194 name: SymBiot I def: "Applied Biosystems/MDS SCIEX SymBiot I MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000195 name: SymBiot XVI def: "Applied Biosystems/MDS SCIEX SymBiot XVI MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000196 name: TEMPUS TOF def: "ThermoFinnigan TEMPUS TOF MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000197 name: TRACE DSQ def: "ThermoFinnigan TRACE DSQ MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000198 name: TRITON def: "ThermoFinnigan TRITON MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000199 name: TSQ Quantum def: "ThermoFinnigan TSQ Quantum MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000200 name: ultima def: "IonSpec Ultima MS." [PSI:MS] is_a: MS:1000123 ! IonSpec instrument model [Term] id: MS:1000201 name: ultraflex def: "Bruker Daltonics' ultraflex: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000202 name: ultraflex TOF/TOF def: "Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000203 name: Voyager-DE PRO def: "Applied Biosystems/MDS SCIEX Voyager-DE PRO MS." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000204 name: Voyager-DE STR def: "Applied Biosystems/MDS SCIEX Voyager-DE STR MS." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000205 name: selected ion monitoring def: "The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum." [PSI:MS] synonym: "MIM" RELATED [] synonym: "Multiple Ion Monitoring" EXACT [] synonym: "SIM" EXACT [] is_a: MS:1003215 ! data-independent acquisition is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1000206 name: selected reaction monitoring def: "Data acquired from specific product ions corresponding to m/z selected precursor ions recorded via multiple stages of mass spectrometry. Selected reaction monitoring can be performed in time or in space." [PSI:MS] synonym: "MRM" RELATED [] synonym: "Multiple Reaction Monitoring" RELATED [] synonym: "SRM" EXACT [] is_a: MS:1003215 ! data-independent acquisition is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1000207 name: accurate mass def: "OBSOLETE An experimentally determined mass that is can be to determine a unique elemental formula. For ions less than 200 u, a measurement with 5 ppm accuracy is sufficient to determine the elemental composition." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000208 name: average mass def: "OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000209 name: appearance energy def: "OBSOLETE The minimum energy that must be imparted to an atom or molecule to produce a specified ion. The term appearance potential is not recommended." [PSI:MS] synonym: "AE" EXACT [] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000266 ! electronvolt is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000210 name: base peak def: "The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures." [PSI:MS] synonym: "BP" EXACT [] is_a: MS:1000231 ! peak [Term] id: MS:1000211 name: OBSOLETE charge number def: "OBSOLETE The total charge on an ion divided by the electron charge e. OBSOLETED 2009-10-27 since this was viewed as a duplication of 00041 charge state." [PSI:MS] is_obsolete: true relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000212 name: dalton def: "OBSOLETE A non-SI unit of mass (symbol Da) that is equal to the unified atomic mass unit: 1.660 538 86(28) x 10^-27 kg." [PSI:MS] comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221). is_obsolete: true [Term] id: MS:1000213 name: electron affinity def: "OBSOLETE The electron affinity of M is the minimum energy required for the process M- ? M + e where M- and M are in their ground rotational, vibrational and electronic states and the electron has zero kinetic energy." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. synonym: "EA" EXACT [] is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000214 name: electron energy obsolete def: "OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000215 name: exact mass def: "OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000216 name: field-free region def: "A section of a mass spectrometer in which there are no electric or magnetic fields." [PSI:MS] synonym: "FFR" EXACT [] is_a: MS:1000487 ! ion optics attribute [Term] id: MS:1000217 name: ionization cross section def: "OBSOLETE A measure of the probability that a given ionization process will occur when an atom or molecule interacts with a photon, electron, atom or molecule." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000218 name: ionization efficiency def: "OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392). is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000219 name: ionization energy def: "OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion." [PSI:MS] synonym: "IE" EXACT [] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000266 ! electronvolt is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000220 name: isotope dilution mass spectrometry def: "OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard." [PSI:MS] comment: This child of the former purgatory term mass spectrometry was made obsolete. synonym: "IDMS" EXACT [] is_obsolete: true [Term] id: MS:1000221 name: magnetic deflection def: "The deflection of charged particles in a magnetic field due to a force equal to qvxB where q is the particle charge, v its velocity and B the magnetic field. Magnetic deflection of an ion beam is used for m/z separation in a magnetic sector mass spectrometer." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000222 name: mass defect def: "OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000223 name: mass number def: "OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. is_obsolete: true relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000224 name: molecular mass def: "Mass of a molecule measured in unified atomic mass units (u or Da)." [https://en.wikipedia.org/wiki/Molecular_mass] is_a: MS:1000861 ! molecular entity property relationship: has_units UO:0000002 ! mass unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000225 name: monoisotopic mass def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000226 name: molecular beam mass spectrometry def: "OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "MBMS" EXACT [] is_obsolete: true [Term] id: MS:1000227 name: multiphoton ionization def: "Photoionization of an atom or molecule in which in two or more photons are absorbed." [PSI:MS] synonym: "MPI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000228 name: nitrogen rule def: "OBSOLETE An organic molecule containing the elements C, H, O, S, P, or halogen has an odd nominal mass if it contains an odd number of nitrogen atoms." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000229 name: nominal mass def: "OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element rounded to the nearest integer value." [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. relationship: has_units UO:0000002 ! mass unit is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000230 name: odd-electron rule def: "OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000231 name: peak def: "A localized region of relatively large ion signal in a mass spectrum. Although peaks are often associated with particular ions, the terms peak and ion should not be used interchangeably." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000232 name: peak intensity def: "OBSOLETE The height or area of a peak in a mass spectrum." [PSI:MS] comment: This term was made obsolete because it was replaced by base peak intensity (MS:1000505). is_obsolete: true [Term] id: MS:1000233 name: proton affinity def: "OBSOLETE The proton affinity of a species M is defined as the negative of the enthalpy change for the reaction M + H+ ->[M+H]+, where all species are in their ground rotational, vibrational and electronic states." [PSI:MS] synonym: "PA" EXACT [PSI:MS] comment: This child of the former purgatory term ion attribute was made obsolete. is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000234 name: mass resolving power def: "OBSOLETE In a mass spectrum, the observed mass divided by the difference between two masses that can be separated. The method by which delta m was obtained and the mass at which the measurement was made should be reported." [PSI:MS] comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800). is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000235 name: total ion current chromatogram def: "Representation of the total ion current detected in each of a series of mass spectra versus time." [PSI:MS] synonym: "TIC chromatogram" EXACT [] is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1000236 name: transmission def: "The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region." [PSI:MS] is_a: MS:1000496 ! instrument attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000237 name: unified atomic mass unit def: "OBSOLETE A non-SI unit of mass (u) defined as one twelfth of ^12 C in its ground state and equal to 1.660 538 86(28) x 10^-27 kg." [PSI:MS] comment: This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221). synonym: "u" EXACT [] is_obsolete: true [Term] id: MS:1000238 name: accelerator mass spectrometry def: "OBSOLETE A mass spectrometry technique in which atoms extracted from a sample are ionized, accelerated to MeV energies and separated according to their momentum, charge and energy." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "AMS" EXACT [] is_obsolete: true [Term] id: MS:1000239 name: atmospheric pressure matrix-assisted laser desorption ionization def: "Matrix-assisted laser desorption ionization in which the sample target is at atmospheric pressure and the ions formed by the pulsed laser are sampled through a small aperture into the mass spectrometer." [PSI:MS] synonym: "AP MALDI" EXACT [] is_a: MS:1000240 ! atmospheric pressure ionization [Term] id: MS:1000240 name: atmospheric pressure ionization def: "Any ionization process in which ions are formed in the gas phase at atmospheric pressure." [PSI:MS] synonym: "API" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000241 name: Atmostpheric Pressure Photoionization def: "OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS] comment: This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382). synonym: "APPI" EXACT [] is_obsolete: true [Term] id: MS:1000242 name: blackbody infrared radiative dissociation def: "A special case of infrared multiphoton dissociation wherein excitation of the reactant ion is caused by absorption of infrared photons radiating from heated blackbody surroundings, which are usually the walls of a vacuum chamber. See also infrared multiphoton dissociation." [PSI:MS] synonym: "BIRD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000243 name: charge-remote fragmentation def: "OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. synonym: "CRF" EXACT [] is_obsolete: true [Term] id: MS:1000244 name: consecutive reaction monitoring def: "OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] comment: This former purgatory term was made obsolete. synonym: "CRM" EXACT [] is_obsolete: true [Term] id: MS:1000245 name: charge stripping def: "The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion." [PSI:MS] synonym: "CS" EXACT [] is_a: MS:1000510 ! precursor activation attribute [Term] id: MS:1000246 name: delayed extraction def: "The application of the accelerating voltage pulse after a time delay in desorption ionization from a surface. The extraction delay can produce energy focusing in a time-of-flight mass spectrometer." [PSI:MS] synonym: "DE" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000247 name: desorption ionization def: "The formation of ions from a solid or liquid material after the rapid vaporization of that sample." [PSI:MS] synonym: "DI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000248 name: direct insertion probe def: "A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization." [PSI:MS] synonym: "DIP" EXACT [] is_a: MS:1000007 ! inlet type [Term] id: MS:1000249 name: direct liquid introduction def: "The delivery of a liquid sample into a mass spectrometer for spray or desorption ionization." [PSI:MS] synonym: "DLI" EXACT [] is_a: MS:1000007 ! inlet type [Term] id: MS:1000250 name: electron capture dissociation def: "A process in which a multiply protonated molecules interacts with a low energy electrons. Capture of the electron leads the liberation of energy and a reduction in charge state of the ion with the production of the (M + nH) (n-1)+ odd electron ion, which readily fragments." [PSI:MS] synonym: "ECD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000251 name: even-electron ion def: "OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. synonym: "EE" EXACT [] is_obsolete: true [Term] id: MS:1000252 name: electron-induced excitation in organics def: "OBSOLETE The reaction of an ion with an electron in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. synonym: "EIEIO" EXACT [] is_obsolete: true [Term] id: MS:1000253 name: electron multiplier def: "A device to amplify the current of a beam or packet of charged particles or photons by incidence upon the surface of an electrode to produce secondary electrons. The secondary electrons are then accelerated to other electrodes or parts of a continuous electrode to produce further secondary electrons." [PSI:MS] synonym: "EM" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000254 name: electrostatic energy analyzer def: "A device consisting of conducting parallel plates, concentric cylinders or concentric spheres that separates charged particles according to their kinetic energy by means of an electric field that is constant in time." [PSI:MS] synonym: "ESA" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000255 name: flowing afterglow def: "An ion source immersed in a flow of helium or other inert buffer gas that carries the ions through a meter-long reactor at pressures around 100 Pa." [PSI:MS] synonym: "FA" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000256 name: high-field asymmetric waveform ion mobility spectrometry def: "OBSOLETE The separation of ions between two concentric cylindrical electrodes due to application of a high voltage asymmetric waveform whereby ions migrate towards one of the two electrodes depending on the ratio of the high- to low-field mobility of the ion." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "FAIMS" EXACT [] is_obsolete: true [Term] id: MS:1000257 name: field desorption def: "The formation of gas-phase ions from a material deposited on a solid surface in the presence of a high electric field. Because this process may encompass ionization by field ionization or other mechanisms, it is not recommended as a synonym for field desorption ionization." [PSI:MS] synonym: "FD" EXACT [] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000258 name: field ionization def: "The removal of electrons from any species by interaction with a high electric field." [PSI:MS] synonym: "FI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000259 name: glow discharge ionization def: "The formation of ions in the gas phase and from solid samples at the cathode by application of a voltage to a low pressure gas." [PSI:MS] synonym: "GD-MS" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000260 name: ion kinetic energy spectrometry def: "OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "IKES" EXACT [] is_obsolete: true [Term] id: MS:1000261 name: ion mobility spectrometry def: "OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "IMS" EXACT [] is_obsolete: true [Term] id: MS:1000262 name: infrared multiphoton dissociation def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons." [PSI:MS] synonym: "IRMPD" EXACT [] is_a: MS:1000435 ! photodissociation [Term] id: MS:1000263 name: isotope ratio mass spectrometry def: "OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer." [PSI:MS] comment: This child of the former purgatory term mass spectrometry was made obsolete. synonym: "IRMS" EXACT [] is_obsolete: true [Term] id: MS:1000264 name: ion trap def: "A device for spatially confining ions using electric and magnetic fields alone or in combination." [PSI:MS] synonym: "IT" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000265 name: kinetic energy release distribution def: "OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. synonym: "KERD" EXACT [] is_obsolete: true [Term] id: MS:1000266 name: Laser Desorption def: "OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules." [PSI:MS] comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393). synonym: "Laser Ionization MERGE" EXACT [] synonym: "LD" EXACT [] is_obsolete: true replaced_by: MS:1000393 [Term] id: MS:1000267 name: mass analyzed ion kinetic energy spectrometry def: "OBSOLETE Spectra that are obtained from a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector in reverse geometry. The accelerating voltage, V, and the magnetic sector field, B, are set at fixed values to select the precursor ions, which are then allowed to dissociate or to react in a field free region between the two sectors. The kinetic energy product ions of m/z selected precursor ions is analyzed by scanning the electric sector field, E. The width of the product ion spectrum peaks is related to the kinetic energy release distribution (KERD) for the dissociation process." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "MIKES" EXACT [] is_obsolete: true [Term] id: MS:1000268 name: mass spectrometry def: "OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments." [PSI:MS] comment: This former purgatory term was made obsolete. synonym: "MS" EXACT [] is_obsolete: true [Term] id: MS:1000269 name: mass spectrometry/mass spectrometry def: "OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "MS/MS" EXACT [] is_obsolete: true [Term] id: MS:1000270 name: multiple stage mass spectrometry def: "OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. synonym: "MSn" EXACT [] is_obsolete: true [Term] id: MS:1000271 name: Negative Ion chemical ionization def: "Chemical ionization that results in the formation of negative ions." [PSI:MS] synonym: "NICI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000272 name: neutralization reionization mass spectrometry def: "With this technique, m/z selected ions form neutrals by charge transfer to a collision gas or by dissociation. The neutrals are separated from the remaining ions and ionized in collisions with a second gas. This method is used to investigate reaction intermediates and other unstable species." [PSI:MS] synonym: "NRMS" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000273 name: photoionization def: "The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended." [PSI:MS] synonym: "PI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000274 name: pyrolysis mass spectrometry def: "A mass spectrometry technique in which the sample is heated to the point of decomposition and the gaseous decomposition products are introduced into the ion source." [PSI:MS] synonym: "PyMS" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000275 name: collision quadrupole def: "A transmission quadrupole to which an oscillating potential is applied so as to focus a beam of ions through a collision gas with no m/z separation." [PSI:MS] synonym: "q" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000276 name: resonance enhanced multiphoton ionization def: "Multiphoton ionization in which the ionization cross section is significantly enhanced because the energy of the incident photons is resonant with an intermediate excited state of the neutral species." [PSI:MS] synonym: "REMPI" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000277 name: residual gas analyzer def: "OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "RGA" EXACT [] is_obsolete: true [Term] id: MS:1000278 name: surface enhanced laser desorption ionization def: "The formation of ionized species in the gas phase from analytes deposited on a particular surface substrate which is irradiated with a laser beam of which wavelength is absorbed by the surface. See also desorption/ionization on silicon and laser desorption/ionization." [PSI:MS] synonym: "SELDI" EXACT [] is_a: MS:1000406 ! surface ionization [Term] id: MS:1000279 name: surface enhanced neat desorption def: "Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface." [PSI:MS] synonym: "SEND" EXACT [] is_a: MS:1000406 ! surface ionization [Term] id: MS:1000280 name: suface ionization def: "OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS] comment: This term was made obsolete because it was replaced by surface ionization (MS:1000406). synonym: "SI" EXACT [] is_obsolete: true [Term] id: MS:1000281 name: selected ion flow tube def: "A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions." [PSI:MS] synonym: "SIFT" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000282 name: sustained off-resonance irradiation def: "A technique associated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry to carry out ion/neutral reactions such as low-energy collision-induced dissociation. A radio-frequency electric field of slightly off-resonance to the cyclotron frequency of the reactant ion cyclically accelerates and decelerates the reactant ion that is confined in the Penning ion trap. The ion's orbit does not exceed the dimensions of ion trap while the ion undergoes an ion/neutral species process that produces a high average translational energy for an extended time." [PSI:MS] synonym: "SORI" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000283 name: Spark Source Mass Spectrometry def: "OBSOLETE Mass spectrometry using spark ionization." [PSI:MS] comment: This term was made obsolete because it was replaced by spark ionization (MS:1000404). synonym: "SSMS" EXACT [] is_obsolete: true [Term] id: MS:1000284 name: stored waveform inverse fourier transform def: "A technique to create excitation waveforms for ions in FT-ICR mass spectrometer or Paul ion trap. An excitation waveform in the time-domain is generated by taking the inverse Fourier transform of an appropriate frequency-domain programmed excitation spectrum, in which the resonance frequencies of ions to be excited are included. This technique may be used for selection of precursor ions in MS2 experiments." [PSI:MS] synonym: "SWIFT" EXACT [] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000285 name: total ion current def: "The sum of all the separate ion currents carried by the ions of different m/z contributing to a complete mass spectrum or in a specified m/z range of a mass spectrum." [PSI:MS] synonym: "TIC" EXACT [] is_a: MS:1003058 ! spectrum property relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000286 name: time lag focusing def: "Energy focusing in a time-of-flight mass spectrometer that is accomplished by introducing a time delay between the formation of the ions and the application of the accelerating voltage pulse." [PSI:MS] synonym: "TLF" EXACT [] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000287 name: time-of-flight mass spectrometer def: "OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. synonym: "TOF-MS" EXACT [] is_obsolete: true [Term] id: MS:1000288 name: cyclotron def: "A device that uses an oscillating electric field and magnetic field to accelerate charged particles." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000289 name: double-focusing mass spectrometer def: "OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. is_obsolete: true [Term] id: MS:1000290 name: hybrid mass spectrometer def: "OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. is_obsolete: true [Term] id: MS:1000291 name: linear ion trap def: "A two dimensional Paul ion trap in which ions are confined in the axial dimension by means of an electric field at the ends of the trap." [PSI:MS] is_a: MS:1000264 ! ion trap [Term] id: MS:1000292 name: mass spectrograph obsolete def: "OBSOLETE An instrument that separates a beam of ions according to their mass-to-charge ratio in which the ions are directed onto a focal plane detector such as a photographic plate." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000293 name: mass spectrometer def: "OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000294 name: mass spectrum def: "A plot of the relative abundance of a beam or other collection of ions as a function of the mass-to-charge ratio (m/z)." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000295 name: mattauch-herzog geometry def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/(4 ?(2)) radians in a radial electric field is followed by a magnetic deflection of ?/2 radians." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000296 name: nier-johnson geometry def: "OBSOLETE An arrangement for a double-focusing mass spectrometer in which a deflection of ?/2 radians in a radial electric field analyzer is followed by a magnetic deflection of ?/3 radians." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000297 name: paul ion trap def: "OBSOLETE A device that permits the trapping of ions by means of an alternating current voltage. The ejection of ions with a m/z less than a prescribed value and retention of those with higher mass depends on the application of radio frequency voltages between a ring electrode and two end-cap electrodes to confine the ions in a circular path. The choice of these voltages determines the m/z below which ions are ejected." [PSI:MS] comment: This term was made obsolete because it is redundant to quadrupole ion trap. synonym: "quadrupole ion trap" RELATED [] is_obsolete: true [Term] id: MS:1000298 name: prolate traochoidal mass spectrometer def: "OBSOLETE A mass spectrometer in which the ions of different m/z are separated by means of crossed electric and magnetic fields in such a way that the selected ions follow a prolate trochoidal path." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. is_obsolete: true [Term] id: MS:1000299 name: quistor def: "OBSOLETE An abbreviation of quadrupole ion storage trap. This term is synonymous with Paul Ion Trap. If so then add a synonym to paul and obsolete this term." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000300 name: reflectron def: "A time-of-flight mass spectrometer that uses a static electric field to reverse the direction of travel of the ions entering it. A reflectron improves mass resolution by assuring that ions of the same m/z but different kinetic energy arrive at the detector at the same time." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000301 name: sector mass spectrometer def: "OBSOLETE A mass spectrometer consisting of one or more magnetic sectors for m/z selection in a beam of ions. Such instruments may also have one or more electric sectors for energy selection." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. is_obsolete: true [Term] id: MS:1000302 name: tandem mass spectrometer def: "OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. is_obsolete: true [Term] id: MS:1000303 name: transmission quadrupole mass spectrometer def: "OBSOLETE A mass spectrometer that consists of four parallel rods whose centers form the corners of a square and whose opposing poles are connected. The voltage applied to the rods is a superposition of a static potential and a sinusoidal radio frequency potential. The motion of an ion in the x and y dimensions is described by the Matthieu equation whose solutions show that ions in a particular m/z range can be transmitted along the z axis." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. is_obsolete: true [Term] id: MS:1000304 name: accelerating voltage def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] is_a: MS:1000487 ! ion optics attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000305 name: cyclotron motion def: "OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000306 name: dynamic mass spectrometry def: "OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time." [PSI:MS] comment: This child of the former purgatory term mass spectrometer was made obsolete. is_obsolete: true [Term] id: MS:1000307 name: einzel lens def: "Three element charged particle lens in which the first and third elements are held at the same voltage. Such a lens produces focusing without changing the translational energy of the particle." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000308 name: electric field strength def: "The magnitude of the force per unit charge at a given point in space." [PSI:MS] is_a: MS:1000487 ! ion optics attribute relationship: has_units UO:0000268 ! volt per meter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000309 name: first stability region def: "The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000310 name: fringing field def: "The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000311 name: kinetic energy analyzer def: "A device for measuring the kinetic energy of charged particles using a retarding field, time-of-flight, or the extent of deflection in an electric or magnetic field." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000312 name: mass limit def: "OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000313 name: scan m/z range? def: "OBSOLETE The limit of m/z over which a mass spectrometer can detect ions." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000314 name: mass selective axial ejection def: "OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000315 name: mass selective instability def: "OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000316 name: mathieu stability diagram def: "OBSOLETE A graphical representation expressed in terms of reduced coordinates that describes charged particle motion in a quadrupole mass filter or quadrupole ion trap mass spectrometer." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000317 name: orthogonal extraction def: "OBSOLETE The pulsed acceleration of ions perpendicular to their direction of travel into a time-of-flight mass spectrometer. Ions may be extracted from a directional ion source, drift tube or m/z separation stage." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000318 name: resonance ion ejection def: "OBSOLETE A mode of ion ejection in a quadrupole ion trap that relies on a auxiliary radio frequency voltage that is applied to the end-cap electrodes. The voltage is tuned to the secular frequency of a particular ion to eject it." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000319 name: space charge effect def: "The mutual repulsion of particles of like charge that limits the current in a charged-particle beam and causes beams or packets of charged particles to expand radially over time." [PSI:MS] is_a: MS:1000487 ! ion optics attribute [Term] id: MS:1000320 name: static field def: "An electric or magnetic field that does not change in time." [PSI:MS] is_a: MS:1000597 ! ion optics type [Term] id: MS:1000321 name: 2E Mass Spectrum def: "OBSOLETE A mass spectrum obtained by setting the electric sector field E to twice the value required to transmit the main ion-beam thereby allowing ions with a kinetic energy-to-charge ratio twice that of the main ion-beam to be transmitted. Product ions resulting from partial charge transfer reactions such as m^2+ + N ? m^+ + N^+ that occur in a collision cell (containing a gas, N) located in a field-free region preceding a magnetic and electric sector combination are detected. When the magnetic sector field B is scanned, a mass spectrum of singly charged product ions of doubly charged precursor ions is obtained." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000322 name: charge inversion mass spectrum def: "The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z." [PSI:MS] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000323 name: constant neutral loss scan def: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement." [PSI:MS] comment: This former purgatory term was made obsolete. synonym: "constant neutral mass loss scan" RELATED [] synonym: "fixed neutral fragment scan" RELATED [] is_obsolete: true [Term] id: MS:1000324 name: constant neutral gain scan def: "OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment." [PSI:MS] comment: This former purgatory term was made obsolete. synonym: "Constant Neutral Mass Gain Scan" EXACT [] is_obsolete: true [Term] id: MS:1000325 name: constant neutral gain spectrum def: "A spectrum formed of all product ions that have been produced by gain of a pre-selected neutral mass following the reaction with and addition of the gas in a collision cell." [PSI:MS] synonym: "constant neutral mass gain spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000326 name: constant neutral loss spectrum def: "A spectrum formed of all product ions that have been produced with a selected m/z decrement from any precursor ions. The spectrum shown correlates to the precursor ion spectrum. See also neutral loss spectrum." [PSI:MS] synonym: "constant neutral mass loss spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000327 name: consecutive reaction monitoring def: "OBSOLETE A type of MS2 experiments with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] comment: This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244). is_obsolete: true [Term] id: MS:1000328 name: e/2 mass spectrum def: "A mass spectrum obtained using a sector mass spectrometer in which the electric sector field E is set to half the value required to transmit the main ion-beam. This spectrum records the signal from doubly charged product ions of charge-stripping reactions." [PSI:MS] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000329 name: linked scan def: "OBSOLETE A scan in an instrument with two or more m/z analysers or in a sector mass spectrometer that incorporates at least one magnetic sector and one electric sector. Two or more of the analyzers are scanned simultaneously so as to preserve a predetermined relationship between scan parameters to produce a product ion, precursor ion or constant neutral loss spectrum." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000330 name: linked scan at constant b/e def: "OBSOLETE A linked scan at constant B/E may be performed on a sector mass spectrometer that incorporates at least one magnetic sector plus one electric sector. The magnetic field B and the electric field E are scanned simultaneously while the accelerating voltage V is held constant, so as to maintain the ratio of the two fields constant. This linked scan may record a product ion spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors." [PSI:MS] comment: This child of the former purgatory term linked scan was made obsolete. is_obsolete: true [Term] id: MS:1000331 name: Linked Scan at Constant E2/V def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector. The electric sector field, E, and the accelerating voltage, V, are scanned simultaneously, so as to maintain the ratio E2/V at a constant value. This linked scan recordss a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors." [PSI:MS] comment: This child of the former purgatory term linked scan was made obsolete. is_obsolete: true [Term] id: MS:1000332 name: Linked Scan at Constant B2/E def: "OBSOLETE A linked scan performed on a sector mass spectrometer that incorporates at least one electric sector plus one magnetic sector in either order. The accelerating voltage is fixed and the magnetic field, B, and the electric field, E, are scanned simultaneously so as to maintain the ratio B2/E at a constant value. This linked scan records a precursor ion spectrum of dissociation or other reactions occurring in the field free region preceding the two sectors. The term B2/E linked scan is not recommended." [PSI:MS] comment: This child of the former purgatory term linked scan was made obsolete. is_obsolete: true [Term] id: MS:1000333 name: Linked Scan at Constant B[1-(E/E0)]^1/2 / E def: "OBSOLETE A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan." [PSI:MS] comment: This child of the former purgatory term linked scan was made obsolete. is_obsolete: true [Term] id: MS:1000334 name: MS/MS in Time def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000335 name: MS/MS in Space def: "OBSOLETE A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition." [PSI:MS] comment: This child of the former purgatory term m/z Separation Method was made obsolete. is_obsolete: true [Term] id: MS:1000336 name: neutral loss def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] is_a: MS:1001055 ! modification parameters relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000337 name: nth generation product ion def: "OBSOLETE Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated." [PSI:MS] comment: This child of the former purgatory term product ion was made obsolete. synonym: "granddaughter ion" RELATED [] is_obsolete: true [Term] id: MS:1000338 name: nth generation product ion scan def: "OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000339 name: nth generation product ion spectrum def: "OBSOLETE The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions." [PSI:MS] comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580). is_obsolete: true [Term] id: MS:1000340 name: precursor ion def: "OBSOLETE An ion that reacts to form particular product ions. The reaction can be unimolecular dissociation, ion/molecule reaction, isomerization, or change in charge state. The term parent ion is deprecated." [PSI:MS] comment: This child of the former purgatory term ion role was made obsolete. synonym: "parent ion" RELATED [] is_obsolete: true [Term] id: MS:1000341 name: precursor ion spectrum def: "Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z." [PSI:MS] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000342 name: product ion def: "OBSOLETE An ion formed as the product of a reaction involving a particular precursor ion. The reaction can be unimolecular dissociation to form fragment ions, an ion/molecule reaction, or simply involve a change in the number of charges. The term fragment ion is deprecated. The term daughter ion is deprecated." [PSI:MS] comment: This child of the former purgatory term ion role was made obsolete. synonym: "daughter ion" RELATED [] is_obsolete: true [Term] id: MS:1000343 name: product ion spectrum def: "OBSOLETE A mass spectrum recorded from any spectrometer in which the appropriate m/z separation scan function is set to record the product ion or ions of selected precursor ions." [PSI:MS] comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580). is_a: MS:1000294 ! mass spectrum is_obsolete: true [Term] id: MS:1000344 name: progeny ion def: "OBSOLETE A charged product of a series of consecutive reactions that includes product ions, 1st generation product ions, 2nd generation product ions, etc. Given the sequential fragmentation scheme: M1+ -> M2+ -> M3+ -> M4+ -> M5+. M4+ is the precursor ion of M5+, a 1st generation product ion of M3+, a 2nd generation product ion of M2+ and a 3rd generation product ion of M1+." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. synonym: "Progeny Fragment Ion" EXACT [] is_obsolete: true [Term] id: MS:1000345 name: array detector def: "Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000346 name: conversion dynode def: "A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000347 name: dynode def: "One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000348 name: focal plane collector def: "A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000349 name: ion-to-photon detector def: "A detector in which ions strike a conversion dynode to produce electrons that in turn strike a phosphor and the resulting photons are detected by a photomultiplier." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000350 name: point collector def: "A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000351 name: postacceleration detector def: "A detector in which the charged particles are accelerated to a high velocity and impinge on a conversion dynode, emitting secondary electrons. The electrons are accelerated onto a phosphor screen, which emits photons that are in turn detected using a photomultiplier or other photon detector." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1000352 name: secondary electron def: "OBSOLETE Electrons that are ejected from a sample surface as a result of bombardment by a primary beam of atoms, ions or photons. WAS IN DETECTOR TYPE. Where should it go." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000353 name: adduct ion def: "Ion formed by the interaction of an ion with one or more atoms or molecules to form an ion containing all the constituent atoms of the precursor ion as well as the additional atoms from the associated atoms or molecules." [PSI:MS] is_a: MS:1003055 ! adduct [Term] id: MS:1000354 name: aromatic ion def: "OBSOLETE A planar cyclic ion that obeys the Hueckel (4n + 2) rule where n is a positive integer representing the number of conjugated Pi electrons. Charge delocalization leads to greater stability compared to a hypothetical localized structure." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000355 name: analog ion def: "OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000356 name: anti-aromatic ion def: "OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000357 name: cationized molecule def: "OBSOLETE An ion formed by the association of a cation with a neutral molecule, M, for example [M+ Na]+ and [M + K]+. The terms quasi-molecular ion and pseudo-molecular ion should not be used." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000358 name: cluster ion def: "OBSOLETE An ion formed by a multi-component atomic or molecular assembly of one or more ions with atoms or molecules, such as [(H20)nH]+, [(NaCl)nNa]+ and [(H3PO3)nHPO3]-." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000359 name: Conventional ion def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin are both formally located in the same atom or group of atoms, as opposed to the spatially separate electronic configuration of distonic ions. The radical cation of methanol, CH3OH+, in which the charge and spin sites are formally located at the O atom is an example of a conventional ion, whereas .CH2-OH2+ is a distonic ion." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000360 name: diagnostic ion def: "OBSOLETE A product ion whose formation reveals structural or compositional information of its precursor. For instance, the phenyl cation in an electron ionization mass spectrum is a diagnostic ion for benzene and derivatives." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000361 name: dimeric ion def: "OBSOLETE An ion formed by ionization of a dimer or by the association of an ion with its neutral counterpart such as [M2]+ or [M-H-M]+." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000362 name: distonic ion def: "OBSOLETE A radical cation or anion in which the charge site and the unpaired electron spin cannot be both formally located in the same atom or group of atoms as it can be with a conventional ion. For example, CH2-OH2+ is a distonic ion whereas the radical cation of methanol, CH3OH+ is a conventional ion." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000363 name: enium ion def: "OBSOLETE A positively charged lower-valency ion of the nonmetallic elements. The methenium ion is CH3+. Other examples are the oxenium, sulfenium, nitrenium, phosphenium, and halenium ions." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000364 name: fragment ion def: "OBSOLETE A product ion that results from the dissociation of a precursor ion." [PSI:MS] comment: This term was made obsolete because it was replaced by product ion (MS:1000342). is_obsolete: true [Term] id: MS:1000365 name: ion? def: "OBSOLETE An atomic or molecular species having a net positive or negative electric charge." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000366 name: Isotopologue ion def: "OBSOLETE An ion that differs only in the isotopic composition of one or more of its constituent atoms. For example CH4+ and CH3D+ or 10BF3 and 11BF3. The term isotopologue is a contraction of isotopic homologue." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000367 name: Isotopomeric ion def: "OBSOLETE Isomeric ion having the same numbers of each isotopic atom but differing in their positions. Isotopomeric ions can be either configurational isomers in which two atomic isotopes exchange positions or isotopic stereoisomers. The term isotopomer is a shortening of isotopic isomer." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000368 name: metastable ion def: "OBSOLETE An ion that is formed with internal energy higher than the threshold for dissociation but with a lifetime great enough to allow it to exit the ion source and enter the mass spectrometer where it dissociates before detection." [PSI:MS] comment: This child of the former purgatory term ion stability type was made obsolete. is_obsolete: true [Term] id: MS:1000369 name: molecular ion def: "OBSOLETE An ion formed by the removal of one or more electrons to form a positive ion or the addition off one or more electrons to form a negative ion." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000370 name: negative ion def: "OBSOLETE An atomic or molecular species having a net negative electric charge." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000371 name: non-classical ion def: "OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000372 name: onium ion def: "OBSOLETE A positively charged hypervalent ion of the nonmetallic elements. Examples are the methonium ion CH5+, the hydrogenonium ion H3+ and the hydronium ion H3O+. Other examples are the carbonium, oxonium, sulfonium, nitronium, diazonium, phosphonium, and halonium ions. Onium ions are not limited to monopositive ions; multiply-charged onium ions exist such as the gitonic (proximal) oxonium dication H4O2+ and the distonic oxonium dication H2O+-CH2-CH2-OH2+." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000373 name: principal ion def: "OBSOLETE Most abundant ion of an isotope cluster, such as the 11B79Br2 81Br+ ion of m/z 250 of the cluster of isotopologue molecular ions of BBr3. The term principal ion has also been used to describe ions that have been artificially isotopically enriched in one or more positions such as CH3 13CH3+ or CH2D2 +, but those are best defined as isotopologue ions." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000374 name: positive ion def: "OBSOLETE An atomic or molecular species having a net positive electric charge." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000375 name: protonated molecule def: "OBSOLETE An ion formed by interaction of a neutral molecule with a proton and represented by the symbol [M + H]+, where M is the neutral molecule. The term 'protonated molecular ion,' 'quasi-molecular ion' and 'pseudo-molecular ion' are not recommended." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000376 name: radical ion def: "OBSOLETE An ion, either a cation or anion, containing unpaired electrons in its ground state. The unpaired electron is denoted by a superscript dot alongside the superscript symbol for charge, such as for the molecular ion of a molecule M, that is, M+. Radical ions with more than one charge and/or more than one unpaired electron are denoted such as M(2+)(2). Unless the positions of the unpaired electron and charge can be associated with specific atoms, superscript charge designation should be placed before the superscript dot designation." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000377 name: reference ion def: "OBSOLETE A stable ion whose structure is known with certainty. These ions are usually formed by direct ionization of a neutral molecule of known structure and are used to verify by comparison the structure of an unknown ion." [PSI:MS] comment: This child of the former purgatory term ion chemical type was made obsolete. is_obsolete: true [Term] id: MS:1000378 name: stable ion def: "OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer." [PSI:MS] comment: This child of the former purgatory term ion stability type was made obsolete. is_obsolete: true [Term] id: MS:1000379 name: unstable ion def: "OBSOLETE An ion with sufficient energy to dissociate within the ion source." [PSI:MS] comment: This child of the former purgatory term ion stability type was made obsolete. is_obsolete: true [Term] id: MS:1000380 name: adiabatic ionization def: "A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000381 name: associative ionization def: "An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000382 name: atmospheric pressure photoionization def: "Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization." [PSI:MS] is_a: MS:1000240 ! atmospheric pressure ionization [Term] id: MS:1000383 name: autodetachment def: "The formation of a neutral when a negative ion in a discrete state with an energy greater than the detachment threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000384 name: autoionization def: "The formation of an ion when an atom or molecule in a discrete state with an energy greater than the ionization threshold loses an electron spontaneously without further interaction with an energy source." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000385 name: charge exchange ionization def: "The interaction of an ion with an atom or molecule in which the charge on the ion is transferred to the neutral without the dissociation of either. Synonymous with charge transfer ionization." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000386 name: chemi-ionization def: "The reaction of a neutral molecule with an internally excited molecule to form an ion. Note that this term is not synonymous with chemical ionization." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000387 name: desorption/ionization on silicon def: "The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface." [PSI:MS] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000388 name: dissociative ionization def: "The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000389 name: electron ionization def: "The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000390 name: ion desolvation def: "OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000391 name: ion-pair formation def: "OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000392 name: ionization efficiency def: "The ratio of the number of ions formed to the number of electrons, molecules or photons used." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000393 name: laser desorption ionization def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000395 name: liquid secondary ionization def: "The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000396 name: membrane inlet def: "A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source." [PSI:MS] is_a: MS:1000007 ! inlet type [Term] id: MS:1000397 name: microelectrospray def: "Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray." [PSI:MS] is_a: MS:1000073 ! electrospray ionization [Term] id: MS:1000398 name: nanoelectrospray def: "Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potenial on the tip of the electrospray needle and/or a gas presure to push the sample through the needle. See also electrospray ionization and microelectrospray." [PSI:MS] synonym: "nanospray" EXACT [] is_a: MS:1000073 ! electrospray ionization [Term] id: MS:1000399 name: penning ionization def: "Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000400 name: plasma desorption ionization def: "The ionization of material in a solid sample by bombarding it with ionic or neutral atoms formed as a result of the fission of a suitable nuclide, typically 252Cf. Synonymous with fission fragment ionization." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000401 name: pre-ionization state def: "OBSOLETE An electronic state capable of undergoing auto-Ionization." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000402 name: secondary ionization def: "The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000403 name: soft ionization def: "The formation of gas-phase ions without extensive fragmentation." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000404 name: spark ionization def: "The formation of ions from a solid material by an intermittent electrical discharge." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000405 name: surface-assisted laser desorption ionization def: "The formation of gas-phase ions from molecules that are deposited on a particular surface substrate that is irradiated with a pulsed laser. See also matrix-assisted laser desorption ionization." [PSI:MS] is_a: MS:1000247 ! desorption ionization [Term] id: MS:1000406 name: surface ionization def: "The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000407 name: thermal ionization def: "The ionization of a neutral species through contact with a high temperature surface." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000408 name: vertical ionization def: "A process in which an electron is removed from or added to a molecule without a change in the positions of the atoms. The resulting ion is typically in an excited vibrational state." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1000409 name: association reaction def: "OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000410 name: alpha-cleavage def: "OBSOLETE A homolytic cleavage where the bond fission occurs between at the atom adjacent to the atom at the apparent charge site and an atom removed from the aparent charge site by two bonds." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000411 name: beta-cleavage def: "OBSOLETE A homolytic cleavage where the bond fission occurs between at an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the aparent charge site by three bonds." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000412 name: buffer gas def: "An inert gas used for collisional deactivation of internally excited ions." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000413 name: charge-induced fragmentation def: "OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000414 name: charge inversion reaction def: "OBSOLETE Reaction of an ion with a neutral species in which the charge on the product ion is reversed in sign with respect to the reactant ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000415 name: charge permutation reaction def: "OBSOLETE The reaction of an ion with a neutral species with a resulting change in the magnitude or sign of the charge on the reactant ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000416 name: charge stripping reaction def: "OBSOLETE Reaction of a positive ion with a neutral species in which the positive charge on the product ion is greater than that on the reactant ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000417 name: charge transfer reaction def: "OBSOLETE The reaction of an ion with a neutral species in which some or all of the charge of the reactant ion is transferred to the neutral species." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000418 name: collisional excitation def: "OBSOLETE The reaction of an ion with a neutral species in which the translational energy of the collision is converted into internal energy of the ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000419 name: collision gas def: "An inert gas used for collisional excitation. The term target gas is not recommended." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000420 name: heterolytic cleavage def: "OBSOLETE Fragmentation of a molecule or ion in which both electrons forming the single bond that is broken remain on one of the atoms that were originally bonded. This term is synonymous with heterolysis." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. synonym: "heterolysis" RELATED [] is_obsolete: true [Term] id: MS:1000421 name: high energy collision def: "OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000422 name: beam-type collision-induced dissociation def: "A collision-induced dissociation process that occurs in a beam-type collision cell." [PSI:MS] synonym: "HCD" EXACT [] is_a: MS:1000133 ! collision-induced dissociation [Term] id: MS:1000423 name: homolytic cleavage def: "OBSOLETE Fragmentation of an odd electron ion that results from one of a pair of electrons that form a bond between two atoms moving to form a pair with the odd electron on the atom at the apparent charge site. Fragmentation results in the formation of an even electron ion and a radical. This reaction involves the movement of a single electron and is symbolized by a single-barbed arrow. Synonymous with Homolysis." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. synonym: "homolysis" RELATED [] is_obsolete: true [Term] id: MS:1000424 name: hydrogen/deuterium exchange def: "OBSOLETE Exchange of hydrogen atoms with deuterium atoms in a molecule or pre-formed ion in solution prior to introduction into a mass spectrometer, or by reaction of an ion with a deuterated collision gas inside a mass spectrometer." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000425 name: ion energy loss spectrum def: "OBSOLETE A plot of the relative abundance of a beam or other collection of ions as a function their loss of translational energy in reactions with neutral species." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000426 name: ionizing collision def: "OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000427 name: ion/molecule reaction def: "OBSOLETE The reaction of an ion with a neutral molecule. The term ion-molecule reaction is not recommended because the hyphen suggests a single species that is that is both an ion and a molecule." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000428 name: ion/neutral complex def: "OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000429 name: ion/neutral species reaction def: "OBSOLETE A process wherein a charged species interacts with a neutral reactant to produce either chemically different species or changes in the internal energy of one or both of the reactants." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000430 name: ion/neutral species exchange reaction def: "OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000431 name: kinetic method def: "OBSOLETE An approach to determination of ion thermodynamic quantities by a bracketing procedure in which the relative probabilities of competing ion fragmentations are measured via the relative abundances of the reaction products. The extended kinetic method takes the associated entropy changes into account." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000432 name: low energy collisions def: "OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000433 name: low-energy collision-induced dissociation def: "A collision-induced dissociation process wherein the precursor ion has the translational energy lower than approximately 1000 eV. This process typically requires multiple collisions and the collisional excitation is cumulative." [PSI:MS] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000434 name: McLafferty Rearrangement def: "OBSOLETE A dissociation reaction triggered by transfer of a hydrogen atom via a 6-member transition state to the formal radical/charge site from a carbon atom four atoms removed from the charge/radical site (the gamma-carbon); subsequent rearrangement of electron density leads to expulsion of an olefin molecule. This term was originally applied to ketone ions where the charge/radical site is the carbonyl oxygen, but it is now more widely applied." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000435 name: photodissociation def: "A process wherein the reactant ion is dissociated as a result of absorption of one or more photons." [PSI:MS] synonym: "multiphoton dissociation" EXACT [] synonym: "MPD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000436 name: partial charge transfer reaction def: "OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000437 name: ion reaction def: "OBSOLETE Chemical transformation involving an ion." [PSI:MS] comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] id: MS:1000438 name: superelastic collision def: "OBSOLETE Collision in which the translational energy of the fast-moving collision partner is increased at the expense of internal energy of one or both collision partners." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000439 name: surface-induced reaction def: "OBSOLETE A process wherein a reactant ion interacts with a surface to produce either chemically different species or a change in the internal energy of the reactant ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000440 name: unimolecular dissociation def: "OBSOLETE Fragmentation reaction in which the molecularity is treated as one, irrespective of whether the dissociative state is that of a metastable ion produced in the ion source or results from collisional excitation of a stable ion." [PSI:MS] comment: This child of the former purgatory term ion reaction was made obsolete. is_obsolete: true [Term] id: MS:1000441 name: scan def: "Function or process of the mass spectrometer where it records a spectrum." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000442 name: spectrum def: "Representation of intensity values corresponding to a range of measurement space." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000443 name: mass analyzer type def: "Mass analyzer separates the ions according to their mass-to-charge ratio." [PSI:MS] relationship: part_of MS:1000451 ! mass analyzer [Term] id: MS:1000444 name: m/z Separation Method def: "OBSOLETE Mass/charge separation Method." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000445 name: sequential m/z separation method def: "OBSOLETE Sequential m/z separation method." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000446 name: fast ion bombardment def: "The ionization of any species by the interaction of a focused beam of ions having a translational energy of several thousand eV with a solid sample." [PSI:MS] synonym: "FIB" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1000447 name: LTQ def: "Finnigan LTQ MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000448 name: LTQ FT def: "Finnigan LTQ FT MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000449 name: LTQ Orbitrap def: "Finnigan LTQ Orbitrap MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000450 name: LXQ def: "Finnigan LXQ MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000451 name: mass analyzer def: "Terms used to describe the Analyzer." [PSI:MS] synonym: "analyzer" EXACT [] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000452 name: data transformation def: "Terms used to describe types of data processing." [PSI:MS] synonym: "data processing" EXACT [] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000453 name: detector def: "The device that detects ions." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000454 name: instrument additional description def: "OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000455 name: ion selection attribute def: "Ion selection properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000456 name: precursor activation def: "Terms to describe the precursor activation." [PSI:MS] synonym: "activation" EXACT [] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000457 name: sample def: "Terms to describe the sample." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000458 name: source def: "Terms to describe the source." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000459 name: spectrum instrument description def: "OBSOLETE Terms used to describe the spectrum." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000460 name: unit def: "OBSOLETE Terms to describe units." [PSI:MS] comment: This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000). relationship: part_of MS:1001458 ! spectrum generation information is_obsolete: true [Term] id: MS:1000461 name: additional description def: "OBSOLETE Terms to describe Additional." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000462 name: ion optics def: "Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions." [PSI:MS] relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000463 name: instrument def: "Description of the instrument or the mass spectrometer." [PSI:MS] synonym: "instrument configuration" EXACT [] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000464 name: mass unit def: "OBSOLETE A unit of measurement for mass." [PSI:MS] comment: This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002). is_obsolete: true [Term] id: MS:1000465 name: scan polarity def: "Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer." [PSI:MS] relationship: part_of MS:1000441 ! scan [Term] id: MS:1000466 name: alternating def: "OBSOLETE Alternating." [PSI:MS] comment: This term was made obsolete because . is_obsolete: true [Term] id: MS:1000467 name: 1200 series LC/MSD SL def: "The 1200 Series LC/MSD SL ion trap belongs to the Agilent LC/MSD ion trap family. It provides fast polarity switching and multisignal data acquisition capabilities in a single run while also providing 5 stages of automated data dependent MS2 and 11 stages of manual MS2." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000468 name: 6110 Quadrupole LC/MS def: "The 6110 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with an entry level single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6110 Quadrupole mass spectrometer has m/z range of 10-1500 and 2500 u/s scan speed. It proves useful for wide range of SIM quantitative applications." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000469 name: 6120A Quadrupole LC/MS def: "The 6120A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers. 6120 quadrupole mass spectrometer has m/z range of 10-1500, 2500 u/s scan speed and utilizes multiple signal acquisition." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000470 name: 6130 Quadrupole LC/MS def: "The 6130 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 series of Agilent mass spectrometers. The 6130 quadrupole mass spectrometer has m/z range of 2-3000, 2500 u/s scan speed in standard mode and 5250 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000471 name: 6140 Quadrupole LC/MS def: "The 6140 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent quadrupole mass spectrometers. 6140 Quadrupole mass spectrometer has m/z range of 10-1350, 2500 u/s scan speed in standard mode and 10000 u/s speed in fast-scan mode. It also uses multiple signal acquisition." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000472 name: 6210 Time-of-Flight LC/MS def: "The 6210 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000473 name: 6310 Ion Trap LC/MS def: "The 6310 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.35 resolution and mass range of 200-4000 with resolution of 3-4. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000474 name: 6320 Ion Trap LC/MS def: "The 6320 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000475 name: 6330 Ion Trap LC/MS def: "The 6330 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000476 name: 6340 Ion Trap LC/MS def: "The 6340 Ion Trap LC/MS is a Agilent liquid chromatography instrument combined with a 6300 series Agilent ion trap. It has a mass range of 50-2200 between 0.6 to 0.25 resolution and mass range of 200-4000 with resolution of less than 3. The scan speed varies from 1650-27000 for the respective mass ranges." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000477 name: 6410 Triple Quadrupole LC/MS def: "The 6410 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. Mass range of the mass spectrometer is 15-1650 m/z, resolution is at three settings of 0.7 u (unit), 1.2 u (wide) and 2.5 u (widest). The mass accuracy for 6410 mass spectrometer is 0.1 across the mass range. The collision cell is a hexapole with linear acceleration." [PSI:MS] synonym: "6410 Triple Quad LC/MS" EXACT [] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000478 name: 1200 series LC/MSD VL def: "The LC/MSD VL ion trap is part of the family of Agilent ion trap mass spectrometers. It has ESI, APCI and APPI ion sources and is a useful ion trap when the amount of sample is not the limiting factor." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000479 name: purgatory def: "OBSOLETE Terms that will likely become obsolete unless there are wails of dissent." [PSI:MS] comment: The whole branch purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000480 name: mass analyzer attribute def: "Analyzer properties that are associated with a value." [PSI:MS] relationship: part_of MS:1000451 ! mass analyzer [Term] id: MS:1000481 name: detector attribute def: "Detector attribute recognized as a value." [PSI:MS] relationship: part_of MS:1000453 ! detector [Term] id: MS:1000482 name: source attribute def: "Property of a source device that need a value." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1000483 name: Thermo Fisher Scientific instrument model def: "Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific." [PSI:MS] synonym: "Thermo Scientific" RELATED [] is_a: MS:1000031 ! instrument model [Term] id: MS:1000484 name: orbitrap def: "An ion trapping device that consists of an outer barrel-like electrode and a coaxial inner spindle-like electrode that form an electrostatic field with quadro-logarithmic potential distribution. The frequency of harmonic oscillations of the orbitally trapped ions along the axis of the electrostatic field is independent of the ion velocity and is inversely proportional to the square root of m/z so that the trap can be used as a mass analyzer." [PSI:MS] is_a: MS:1000443 ! mass analyzer type [Term] id: MS:1000485 name: nanospray inlet def: "Nanospray Inlet." [PSI:MS] is_a: MS:1000057 ! electrospray inlet [Term] id: MS:1000486 name: source potential def: "Potential difference at the MS source in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000487 name: ion optics attribute def: "Ion optics involves components that help focus ion streams in mass spectrometry." [PSI:MS] is_a: MS:1000462 ! ion optics [Term] id: MS:1000488 name: Hitachi instrument model def: "Hitachi instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000489 name: Varian instrument model def: "Varian instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000490 name: Agilent instrument model def: "Agilent instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000491 name: Dionex instrument model def: "Dionex instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1000492 name: Thermo Electron instrument model def: "Thermo Electron Corporation instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000493 name: Finnigan MAT instrument model def: "Finnigan MAT instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000494 name: Thermo Scientific instrument model def: "Thermo Scientific instrument model." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1000495 name: Applied Biosystems instrument model def: "Applied Biosystems instrument model." [PSI:MS] synonym: "ABI" EXACT [] is_a: MS:1000031 ! instrument model [Term] id: MS:1000496 name: instrument attribute def: "Instrument properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000463 ! instrument [Term] id: MS:1000497 name: zoom scan def: "Special scan mode where data with improved resolution is acquired. This is typically achieved by scanning a more narrow m/z window or scanning with a lower scan rate." [PSI:MS] synonym: "enhanced resolution scan" EXACT [] is_a: MS:1000503 ! scan attribute [Term] id: MS:1000498 name: full scan def: "OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000499 name: spectrum attribute def: "Nonphysical characteristic attributed to a spectrum." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000500 name: scan window upper limit def: "The lower m/z bound of a mass spectrometer scan window." [PSI:MS] synonym: "mzRangeStop" RELATED [] is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000501 name: scan window lower limit def: "The upper m/z bound of a mass spectrometer scan window." [PSI:MS] synonym: "mzRangeStart" RELATED [] is_a: MS:1000549 ! selection window attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000502 name: dwell time def: "The time spent gathering data across a peak." [PSI:MS] synonym: "Scan Duration" RELATED [] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000503 name: scan attribute def: "Nonphysical characteristic attributed to a spectrum acquisition scan." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000441 ! scan [Term] id: MS:1000504 name: base peak m/z def: "M/z value of the signal of highest intensity in the mass spectrum." [PSI:MS] is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000505 name: base peak intensity def: "The intensity of the greatest peak in the mass spectrum." [PSI:MS] is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000506 name: ion role def: "OBSOLETE Ion Role." [PSI:MS] comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] id: MS:1000507 name: ion property def: "Nonphysical characteristic attributed to an ion." [PSI:MS] relationship: part_of MS:1002806 ! ion [Term] id: MS:1000508 name: ion chemical type def: "OBSOLETE Ion Type." [PSI:MS] comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] id: MS:1000509 name: activation energy def: "Activation Energy." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000510 name: precursor activation attribute def: "Precursor Activation Attribute." [PSI:MS] relationship: part_of MS:1000456 ! precursor activation [Term] id: MS:1000511 name: ms level def: "Stage number achieved in a multi stage mass spectrometry acquisition." [PSI:MS] is_a: MS:1000499 ! spectrum attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000512 name: filter string def: "A string unique to Thermo instrument describing instrument settings for the scan." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000513 name: binary data array def: "A data array of values." [PSI:MS] relationship: part_of MS:1000442 ! spectrum relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000514 name: m/z array def: "A data array of m/z values." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000515 name: intensity array def: "A data array of intensity values." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit [Term] id: MS:1000516 name: charge array def: "A data array of charge values." [PSI:MS] xref: binary-data-type:MS\:1000519 "32-bit integer" is_a: MS:1000513 ! binary data array [Term] id: MS:1000517 name: signal to noise array def: "A data array of signal-to-noise values." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array [Term] id: MS:1000518 name: binary data type def: "Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float." [PSI:MS] relationship: part_of MS:1000442 ! spectrum relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000519 name: 32-bit integer def: "Signed 32-bit little-endian integer." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000520 name: 16-bit float def: "OBSOLETE Signed 16-bit float." [PSI:MS] is_a: MS:1000518 ! binary data type is_obsolete: true [Term] id: MS:1000521 name: 32-bit float def: "32-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000522 name: 64-bit integer def: "Signed 64-bit little-endian integer." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000523 name: 64-bit float def: "64-bit precision little-endian floating point conforming to IEEE-754." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1000524 name: data file content def: "Describes the data content on the file." [PSI:MS] relationship: part_of MS:1000577 ! source data file [Term] id: MS:1000525 name: spectrum representation def: "Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000526 name: Waters raw format def: "Waters data file format found in a Waters RAW directory, generated from an MS acquisition." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000527 name: highest observed m/z def: "Highest m/z value observed in the m/z array." [PSI:MS] is_a: MS:1000808 ! chromatogram attribute is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000528 name: lowest observed m/z def: "Lowest m/z value observed in the m/z array." [PSI:MS] is_a: MS:1000808 ! chromatogram attribute is_a: MS:1003058 ! spectrum property relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000529 name: instrument serial number def: "Serial Number of the instrument." [PSI:MS] is_a: MS:1000496 ! instrument attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000530 name: file format conversion def: "Conversion of one file format to another." [PSI:MS] is_a: MS:1000452 ! data transformation [Term] id: MS:1000531 name: software def: "Software related to the recording or transformation of spectra." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1000532 name: Xcalibur def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000533 name: Bioworks def: "Thermo Finnigan software for data analysis of peptides and proteins." [PSI:MS] synonym: "Bioworks Browser" RELATED [] is_a: MS:1000693 ! Thermo Finnigan software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000534 name: MassLynx def: "Micromass software for data acquisition and analysis." [PSI:MS] is_a: MS:1000694 ! Waters software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000535 name: FlexAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000536 name: Data Explorer def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000691 ! Applied Biosystems software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000537 name: 4700 Explorer def: "Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000691 ! Applied Biosystems software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000538 name: massWolf def: "A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology." [PSI:MS] synonym: "wolf" EXACT [] is_a: MS:1001457 ! data processing software [Term] id: MS:1000539 name: Voyager Biospectrometry Workstation System def: "Applied Biosystems MALDI-TOF data acquisition and analysis system." [PSI:MS] is_a: MS:1000691 ! Applied Biosystems software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000540 name: FlexControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000541 name: ReAdW def: "A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced \"readraw\"." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1000542 name: MzStar def: "A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1000543 name: data processing action def: "Data processing attribute used to describe the type of data processing performed on the data file." [PSI:MS] is_a: MS:1000452 ! data transformation [Term] id: MS:1000544 name: Conversion to mzML def: "Conversion of a file format to Proteomics Standards Initiative mzML file format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000545 name: Conversion to mzXML def: "Conversion of a file format to Institute of Systems Biology mzXML file format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000546 name: Conversion to mzData def: "Conversion of a file format to Proteomics Standards Initiative mzData file format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000547 name: object attribute def: "Object Attribute." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000548 name: sample attribute def: "Sample properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000457 ! sample [Term] id: MS:1000549 name: selection window attribute def: "Selection window properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000441 ! scan [Term] id: MS:1000550 name: time unit def: "OBSOLETE Time Unit." [PSI:MS] comment: This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003). is_obsolete: true [Term] id: MS:1000551 name: Analyst def: "SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000552 name: maldi spot identifier def: "OBSOLETE Maldi Spot Identifier." [PSI:MS] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1000553 name: Trapper def: "A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1000554 name: LCQ Deca def: "ThermoFinnigan LCQ Deca." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000555 name: LTQ Orbitrap Discovery def: "LTQ Orbitrap Discovery." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000556 name: LTQ Orbitrap XL def: "LTQ Orbitrap XL." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000557 name: LTQ FT Ultra def: "LTQ FT Ultra." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000558 name: GC Quantum def: "GC Quantum." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000559 name: spectrum type def: "Spectrum type." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000560 name: mass spectrometer file format def: "The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:MS] is_a: MS:1001459 ! file format [Term] id: MS:1000561 name: data file checksum type def: "Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data." [PSI:MS] relationship: part_of MS:1000577 ! source data file [Term] id: MS:1000562 name: ABI WIFF format def: "Applied Biosystems WIFF file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000563 name: Thermo RAW format def: "Thermo Scientific RAW file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000564 name: PSI mzData format def: "Proteomics Standards Inititative mzData file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000565 name: Micromass PKL format def: "Micromass PKL file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000566 name: ISB mzXML format def: "Institute of Systems Biology mzXML file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000567 name: Bruker/Agilent YEP format def: "Bruker/Agilent YEP file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000568 name: MD5 def: "MD5 (Message-Digest algorithm 5) is a (now deprecated) cryptographic hash function with a 128-bit hash value used to check the integrity of files." [PSI:MS] is_a: MS:1000561 ! data file checksum type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000569 name: SHA-1 def: "SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA). It is also used to verify file integrity. Since 2011 it has been deprecated by the NIST as a U. S. government standard." [PSI:MS] is_a: MS:1000561 ! data file checksum type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000570 name: spectra combination def: "Method used to combine the mass spectra." [PSI:MS] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1000571 name: sum of spectra def: "Spectra Sum." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000572 name: binary data compression type def: "Compression Type." [PSI:MS] relationship: part_of MS:1000442 ! spectrum relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000573 name: median of spectra def: "Spectra is combined by calculating the median of the spectra." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000574 name: zlib compression def: "Zlib." [PSI:MS] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1000575 name: mean of spectra def: "Spectra is combined by calculating the mean of the spectra." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000576 name: no compression def: "No Compression." [PSI:MS] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1000577 name: source data file def: "Data file from which an entity is sourced." [PSI:MS] synonym: "source file" EXACT [] relationship: part_of MS:1001458 ! spectrum generation information is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1000578 name: LCQ Fleet def: "LCQ Fleet." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000579 name: MS1 spectrum def: "Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment." [PSI:MS] synonym: "full spectrum" EXACT [] synonym: "Q1 spectrum" EXACT [] synonym: "Q3 spectrum" EXACT [] synonym: "Single-Stage Mass Spectrometry" EXACT [] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000580 name: MSn spectrum def: "MSn refers to multi-stage MS2 experiments designed to record product ion spectra where n is the number of product ion stages (progeny ions). For ion traps, sequential MS/MS experiments can be undertaken where n > 2 whereas for a simple triple quadrupole system n=2. Use the term ms level (MS:1000511) for specifying n." [PSI:MS] synonym: "multiple-stage mass spectrometry spectrum" EXACT [] synonym: "nth generation product ion spectrum" EXACT [] synonym: "product ion spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000581 name: CRM spectrum def: "Spectrum generated from MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored." [PSI:MS] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000582 name: SIM spectrum def: "Spectrum obtained with the operation of a mass spectrometer in which the abundances of one ion or several ions of specific m/z values are recorded rather than the entire mass spectrum (Selected Ion Monitoring)." [PSI:MS] synonym: "MIM spectrum" EXACT [] synonym: "multiple ion monitoring spectrum" EXACT [] synonym: "selected ion monitoring spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000583 name: SRM spectrum def: "Spectrum obtained when data are acquired from specific product ions corresponding to m/z values of selected precursor ions a recorded via two or more stages of mass spectrometry. The precursor/product ion pair is called a transition pair. Data can be obtained for a single transition pair or multiple transition pairs. Multiple time segments of different transition pairs can exist in a single file. Single precursor ions can have multiple product ions consitituting multiple transition pairs. Selected reaction monitoring can be performed as tandem mass spectrometry in time or tandem mass spectrometry in space." [PSI:MS] synonym: "MRM spectrum" EXACT [] synonym: "multiple reaction monitoring spectrum" EXACT [] synonym: "selected reaction monitoring spectrum" EXACT [] is_a: MS:1000294 ! mass spectrum [Term] id: MS:1000584 name: mzML format def: "Proteomics Standards Inititative mzML file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000585 name: contact attribute def: "Details about a person or organization to contact in case of concern or discussion about the file." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1000586 name: contact name def: "Name of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000587 name: contact address def: "Postal address of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000588 name: contact URL def: "Uniform Resource Locator related to the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000589 name: contact email def: "Email address of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000590 name: contact affiliation def: "Home institution of the contact person." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000591 name: MzWiff def: "A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1000592 name: smoothing def: "A process of reducing spikes of intensity in order to reduce noise while preserving real peak signal. Many algorithms can be applied for this process." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000593 name: baseline reduction def: "A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparision between intensities of m/z values." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000594 name: low intensity data point removal def: "The removal of very low intensity data points that are likely to be spurious noise rather than real signal." [PSI:MS] synonym: "thresholding" EXACT [] is_a: MS:1001486 ! data filtering [Term] id: MS:1000595 name: time array def: "A data array of relative time offset values from a reference time." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute [Term] id: MS:1000596 name: measurement method def: "An attribute of resolution when recording the detector response in absence of the analyte." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000597 name: ion optics type def: "The electrical potential used to impart kinetic energy to ions in a mass spectrometer." [PSI:MS] is_a: MS:1000462 ! ion optics [Term] id: MS:1000598 name: electron transfer dissociation def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of cations (e.g. peptides or proteins) by transferring electrons from radical-anions." [DOI:10.1073/pnas.0402700101, PMID:15210983, PSI:MS] synonym: "ETD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000599 name: pulsed q dissociation def: "A process that involves precursor ion activation at high Q, a time delay to allow the precursor to fragment, then a rapid pulse to low Q where all fragment ions are trapped. The product ions can then be scanned out of the ion trap and detected." [PSI:MS] synonym: "PQD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1000600 name: Proteios def: "Database application and analysis platform for proteomics." [PSI:MS, source:http://www.proteios.org] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000601 name: ProteinLynx Global Server def: "Waters software for data analysis." [PSI:MS] is_a: MS:1000694 ! Waters software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000602 name: Shimadzu MALDI-TOF instrument model def: "Shimadzu MALDI-TOF instrument model." [PSI:MS] is_a: MS:1000124 ! Shimadzu instrument model [Term] id: MS:1000603 name: Shimadzu Scientific Instruments instrument model def: "Shimadzu Scientific Instruments instrument model." [PSI:MS] is_a: MS:1000124 ! Shimadzu instrument model [Term] id: MS:1000604 name: LCMS-IT-TOF def: "Shimadzu Scientific Instruments LCMS-IT-TOF MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000605 name: LCMS-2010EV def: "Shimadzu Scientific Instruments LCMS-2010EV MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000606 name: LCMS-2010A def: "Shimadzu Scientific Instruments LCMS-2010A MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1000607 name: AXIMA CFR MALDI-TOF def: "Shimadzu Biotech AXIMA CFR MALDI-TOF MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000608 name: AXIMA-QIT def: "Shimadzu Biotech AXIMA-QIT MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000609 name: AXIMA-CFR plus def: "Shimadzu Biotech AXIMA-CFR plus MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000610 name: AXIMA Performance MALDI-TOF/TOF def: "Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000611 name: AXIMA Confidence MALDI-TOF def: "Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000612 name: AXIMA Assurance Linear MALDI-TOF def: "Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS." [PSI:MS] is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1000613 name: DTA format def: "SEQUEST DTA file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000614 name: ProteinLynx Global Server mass spectrum XML format def: "Peak list file format used by ProteinLynx Global Server." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000615 name: ProteoWizard software def: "ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb." [PSI:MS] synonym: "pwiz" EXACT [] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000616 name: preset scan configuration def: "A user-defined scan configuration that specifies the instrumental settings in which a spectrum is acquired. An instrument may cycle through a list of preset scan configurations to acquire data. This is a more generic term for the Thermo \"scan event\", which is defined in the Thermo Xcalibur glossary as: a mass spectrometer scan that is defined by choosing the necessary scan parameter settings. Multiple scan events can be defined for each segment of time." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000617 name: wavelength array def: "A data array of electromagnetic radiation wavelength values." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units UO:0000018 ! nanometer [Term] id: MS:1000618 name: highest observed wavelength def: "Highest wavelength observed in an EMR spectrum." [PSI:MS] is_a: MS:1003058 ! spectrum property is_a: MS:1000808 ! chromatogram attribute relationship: has_units UO:0000018 ! nanometer relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000619 name: lowest observed wavelength def: "Lowest wavelength observed in an EMR spectrum." [PSI:MS] is_a: MS:1003058 ! spectrum property is_a: MS:1000808 ! chromatogram attribute relationship: has_units UO:0000018 ! nanometer relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000620 name: PDA spectrum def: "OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum)." [PSI:MS] comment: This term was made obsolete because it was replaced by absorption spectrum (MS:1000806). is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type is_obsolete: true [Term] id: MS:1000621 name: photodiode array detector def: "An array detector used to record spectra in the ultraviolet and visible region of light." [PSI:MS] synonym: "PDA" EXACT [] is_a: MS:1000345 ! array detector [Term] id: MS:1000622 name: Surveyor PDA def: "Surveyor PDA." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000623 name: Accela PDA def: "Accela PDA." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000624 name: inductive detector def: "Inductive detector." [PSI:MS] synonym: "image current detector" EXACT [] is_a: MS:1000026 ! detector type [Term] id: MS:1000625 name: chromatogram def: "Representation of a chromatographic separation attribute measurement versus time." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000626 name: chromatogram type def: "Type of chromatogram measurement being represented." [PSI:MS] relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000627 name: selected ion current chromatogram def: "Representation of an array of the measurements of a specific single ion current versus time." [PSI:MS] synonym: "SIC chromatogram" EXACT [] is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1000628 name: basepeak chromatogram def: "Representation of an array of the most intense peaks versus time." [PSI:MS] is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1000629 name: low intensity threshold def: "Threshold below which some action is taken." [PSI:MS] is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000630 name: data processing parameter def: "Data processing parameter used in the data processing performed on the data file." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000631 name: high intensity threshold def: "Threshold above which some action is taken." [PSI:MS] is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000632 name: Q-Tof Premier def: "Waters oa-ToF based Q-Tof Premier." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1000633 name: possible charge state def: "A possible charge state of the ion in a situation where the charge of an ion is known to be one of several possible values rather than a completely unknown value or determined to be a specific charge with reasonable certainty." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1000634 name: DSQ def: "ThermoFinnigan DSQ GC-MS." [PSI:MS] is_a: MS:1000125 ! Thermo Finnigan instrument model [Term] id: MS:1000635 name: ITQ 700 def: "Thermo Scientific ITQ 700 GC-MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000636 name: ITQ 900 def: "Thermo Scientific ITQ 900 GC-MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000637 name: ITQ 1100 def: "Thermo Scientific ITQ 1100 GC-MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000638 name: LTQ XL ETD def: "Thermo Scientific LTQ XL MS with ETD." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000639 name: LTQ Orbitrap XL ETD def: "Thermo Scientific LTQ Orbitrap XL MS with ETD." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000640 name: DFS def: "Thermo Scientific DFS HR GC-MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000641 name: DSQ II def: "Thermo Scientific DSQ II GC-MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000642 name: MALDI LTQ XL def: "Thermo Scientific MALDI LTQ XL MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000643 name: MALDI LTQ Orbitrap def: "Thermo Scientific MALDI LTQ Orbitrap MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000644 name: TSQ Quantum Access def: "Thermo Scientific TSQ Quantum Access MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000645 name: Element XR def: "Thermo Scientific Element XR HR-ICP-MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000646 name: Element 2 def: "Thermo Scientific Element 2 HR-ICP-MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000647 name: Element GD def: "Thermo Scientific Element GD Glow Discharge MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000648 name: GC IsoLink def: "Thermo Scientific GC IsoLink Isotope Ratio MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000649 name: Exactive def: "Thermo Scientific Exactive MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000650 name: Proteome Discoverer def: "Thermo Scientific software for data analysis of peptides and proteins." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000651 name: 3200 QTRAP def: "SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000652 name: 4800 Plus MALDI TOF/TOF def: "SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000653 name: API 3200 def: "SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000654 name: API 5000 def: "SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000655 name: QSTAR Elite def: "SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000656 name: QSTAR Pulsar def: "Applied Biosystems|MDS SCIEX QSTAR Pulsar." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000657 name: QSTAR XL def: "Applied Biosystems|MDS SCIEX QSTAR XL." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000658 name: 4800 Proteomics Analyzer def: "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer." [PSI:MS] is_a: MS:1000495 ! Applied Biosystems instrument model [Term] id: MS:1000659 name: 4000 Series Explorer Software def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000661 name: GPS Explorer def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000662 name: LightSight Software def: "SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000663 name: ProteinPilot Software def: "SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000664 name: TissueView Software def: "Applied Biosystems|MDS SCIEX software for tissue imaging." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000665 name: MarkerView Software def: "Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000666 name: MRMPilot Software def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000667 name: BioAnalyst def: "Applied Biosystems|MDS SCIEX software for bio-related data exploration." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000668 name: Pro ID def: "Applied Biosystems|MDS SCIEX software for protein identification." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000669 name: Pro ICAT def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000670 name: Pro Quant def: "Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000671 name: Pro BLAST def: "Applied Biosystems|MDS SCIEX software for MS-BLAST identification." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000672 name: Cliquid def: "SCIEX Cliquid software for data analysis and quantitation." [PSI:MS] is_a: MS:1000690 ! SCIEX software [Term] id: MS:1000673 name: MIDAS Workflow Designer def: "Applied Biosystems|MDS SCIEX software for MRM assay development." [PSI:MS] is_a: MS:1000690 ! SCIEX software [Term] id: MS:1000674 name: MultiQuant def: "Applied Biosystems|MDS SCIEX software for MRM-based quantitation." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000675 name: 6220 Time-of-Flight LC/MS def: "The 6220 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000676 name: 6510 Quadrupole Time-of-Flight LC/MS def: "The 6510 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 13,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000677 name: 6520A Quadrupole Time-of-Flight LC/MS def: "The 6520A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer. This time of flight mass spectrometer has a m/z range of 50-12000, mass accuracy of less than 2 ppm and resolution greater than 26,000 at m/z 2722. It has multiple ion sources and can be used with multimode ion sources." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000678 name: MassHunter Data Acquisition def: "Software for data acquisition of 6000 series instruments." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000679 name: MassHunter Easy Access def: "Software for open access data acquisition." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000680 name: MassHunter Qualitative Analysis def: "Software for data analysis of data from 6000 series instruments." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000681 name: MassHunter Quantitative Analysis def: "Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000682 name: MassHunter Metabolite ID def: "Software for identification of metabolites." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000683 name: MassHunter BioConfirm def: "Software for protein characterization." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000684 name: Genespring MS def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000685 name: MassHunter Mass Profiler def: "Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000686 name: METLIN def: "Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000687 name: Spectrum Mill for MassHunter Workstation def: "Software for protein identification and characterization of complex protein digest mixtures." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000688 name: 6300 Series Ion Trap Data Analysis Software def: "Software for data analysis of 6300 series ion trap mass spectrometers." [PSI:MS] is_a: MS:1000689 ! Agilent software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000689 name: Agilent software def: "Agilent software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000690 name: SCIEX software def: "SCIEX or Applied Biosystems software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000691 name: Applied Biosystems software def: "Applied Biosystems|MDS SCIEX software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000692 name: Bruker software def: "Bruker software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000693 name: Thermo Finnigan software def: "Thermo Finnigan software for data acquisition and analysis." [PSI:MS] synonym: "Bioworks Browser" RELATED [] is_a: MS:1000531 ! software [Term] id: MS:1000694 name: Waters software def: "Waters software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000695 name: apex ultra def: "Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR." [PSI:MS] is_a: MS:1001556 ! Bruker Daltonics apex series [Term] id: MS:1000696 name: autoflex III smartbeam def: "Bruker Daltonics' autoflex III smartbeam: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000697 name: Bruker Daltonics HCT Series def: "Bruker Daltonics' HCT Series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1000698 name: HCTultra def: "Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000699 name: HCTultra PTM def: "Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR." [PSI:MS] is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000700 name: HCTultra ETD II def: "Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD." [PSI:MS] is_a: MS:1000697 ! Bruker Daltonics HCT Series [Term] id: MS:1000701 name: microflex LT def: "Bruker Daltonics' microflex LT: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000702 name: micrOTOF def: "Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000703 name: micrOTOF-Q def: "Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000704 name: micrOTOF-Q II def: "Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1000705 name: ultraflex III TOF/TOF def: "Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1000706 name: apexControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000707 name: BioTools def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000708 name: CLINPROT def: "Bruker CLINPROT software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000709 name: CLINPROT micro def: "Bruker CLINPROT micro software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000710 name: CLINPROT robot def: "Bruker CLINPROT robot software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000711 name: ClinProTools def: "Bruker ClinProTools software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000712 name: Compass def: "Bruker Compass software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000713 name: Compass for HCT/esquire def: "Bruker Compass for HCT/esquire software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000714 name: Compass for micrOTOF def: "Bruker Compass for micrOTOF software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000715 name: Compass OpenAccess def: "Bruker compass OpenAccess software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000716 name: Compass Security Pack def: "Bruker compass Security Pack software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000717 name: CompassXport def: "Bruker stand-alone software for data conversion." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001457 ! data processing software [Term] id: MS:1000718 name: CompassXtract def: "Bruker software library for data access." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001457 ! data processing software [Term] id: MS:1000719 name: DataAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000720 name: dpControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000721 name: esquireControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000722 name: flexImaging def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000723 name: GENOLINK def: "Bruker GENOLINK software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000724 name: GenoTools def: "Bruker GenoTools software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000725 name: HCTcontrol def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000726 name: micrOTOFcontrol def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000727 name: PolyTools def: "Bruker PolyTools software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000728 name: ProfileAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000729 name: PROTEINEER def: "Bruker PROTEINEER software." [PSI:PI] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000730 name: PROTEINEER dp def: "Bruker PROTEINEER dp software." [PSI:PI] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000731 name: PROTEINEER fc def: "Bruker PROTEINEER fc software." [PSI:PI] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000732 name: PROTEINEER spII def: "Bruker PROTEINEER spII software." [PSI:PI] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000733 name: PROTEINEER-LC def: "Bruker PROTEINEER-LC software." [PSI:PI] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000734 name: ProteinScape def: "Bruker ProteinScape software." [PSI:PI] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software [Term] id: MS:1000735 name: PureDisk def: "BrukerPureDisk software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000736 name: QuantAnalysis def: "Bruker software for data analysis." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000737 name: spControl def: "Bruker software for data acquisition." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001455 ! acquisition software [Term] id: MS:1000738 name: TargetAnalysis def: "Bruker TargetAnalysis software." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000739 name: WARP-LC def: "Bruker WARP-LC software." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001139 ! quantitation software name [Term] id: MS:1000740 name: parameter file def: "Parameter file used to configure the acquisition of raw data on the instrument." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000741 name: Conversion to dta def: "Conversion to dta format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1000742 name: Bioworks SRF format def: "Thermo Finnigan SRF file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1000743 name: TSQ Quantum Ultra AM def: "Thermo Scientific TSQ Quantum Ultra AM." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000744 name: selected ion m/z def: "Mass-to-charge ratio of an selected ion." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000745 name: retention time alignment def: "The correction of the spectrum scan times, as used e.g. in label-free proteomics." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000746 name: high intensity data point removal def: "The removal of very high intensity data points." [PSI:MS] is_a: MS:1001486 ! data filtering [Term] id: MS:1000747 name: completion time def: "The time that a data processing action was finished." [PSI:MS] is_a: MS:1000630 ! data processing parameter relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term [Term] id: MS:1000748 name: SSQ 7000 def: "ThermoFinnigan SSQ 7000 MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000749 name: TSQ 7000 def: "ThermoFinnigan TSQ 7000 MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000750 name: TSQ def: "ThermoFinnigan TSQ MS." [PSI:MS] is_a: MS:1000493 ! Finnigan MAT instrument model [Term] id: MS:1000751 name: TSQ Quantum Ultra def: "Thermo Scientific TSQ Quantum Ultra." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000752 name: TOPP software def: "TOPP (The OpenMS proteomics pipeline) software." [PSI:MS] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1000753 name: BaselineFilter def: "Removes the baseline from profile spectra using a top-hat filter." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000754 name: DBExporter def: "Exports data from an OpenMS database to a file." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000755 name: DBImporter def: "Imports data to an OpenMS database." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000756 name: FileConverter def: "Converts between different MS file formats." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000757 name: FileFilter def: "Extracts or manipulates portions of data from peak, feature or consensus feature files." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000758 name: FileMerger def: "Merges several MS files into one file." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000759 name: InternalCalibration def: "Applies an internal calibration." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000760 name: MapAligner def: "OBSOLETE Corrects retention time distortions between maps." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000761 name: MapNormalizer def: "Normalizes peak intensities in an MS run." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000762 name: NoiseFilter def: "OBSOLETE Removes noise from profile spectra by using different smoothing techniques." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000763 name: PeakPicker def: "OBSOLETE Finds mass spectrometric peaks in profile mass spectra." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000764 name: Resampler def: "Transforms an LC/MS map into a resampled map or a png image." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000765 name: SpectraFilter def: "OBSOLETE Applies a filter to peak spectra." [PSI:MS] comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch. is_a: MS:1000752 ! TOPP software is_obsolete: true [Term] id: MS:1000766 name: TOFCalibration def: "Applies time of flight calibration." [PSI:MS] is_a: MS:1000752 ! TOPP software [Term] id: MS:1000767 name: native spectrum identifier format def: "Describes how the native spectrum identifiers are formated." [PSI:MS] synonym: "nativeID format" EXACT [] relationship: part_of MS:1000577 ! source data file [Term] id: MS:1000768 name: Thermo nativeID format def: "Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000769 name: Waters nativeID format def: "Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000770 name: WIFF nativeID format def: "Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000771 name: Bruker/Agilent YEP nativeID format def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000772 name: Bruker BAF nativeID format def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000773 name: Bruker FID nativeID format def: "Native format defined by file=xsd:IDREF." [PSI:MS] comment: The nativeID must be the same as the source file ID. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000774 name: multiple peak list nativeID format def: "Native format defined by index=xsd:nonNegativeInteger." [PSI:MS] comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000775 name: single peak list nativeID format def: "Native format defined by file=xsd:IDREF." [PSI:MS] comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000776 name: scan number only nativeID format def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:MS] comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000777 name: spectrum identifier nativeID format def: "Native format defined by spectrum=xsd:nonNegativeInteger." [PSI:MS] comment: Used for conversion from mzData. The spectrum id attribute is referenced. is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000778 name: charge state calculation def: "A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000779 name: below precursor intensity dominance charge state calculation def: "Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z." [PSI:MS] is_a: MS:1000778 ! charge state calculation [Term] id: MS:1000780 name: precursor recalculation def: "A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1000781 name: msPrefix precursor recalculation def: "Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans." [PSI:MS] is_a: MS:1000780 ! precursor recalculation [Term] id: MS:1000782 name: Savitzky-Golay smoothing def: "Reduces intensity spikes by applying local polynomial regression (of degree k) on a distribution (of at least k+1 equally spaced points) to determine the smoothed value for each point. It tends to preserve features of the distribution such as relative maxima, minima and width, which are usually 'flattened' by other adjacent averaging techniques." [PSI:MS] is_a: MS:1000592 ! smoothing [Term] id: MS:1000783 name: LOWESS smoothing def: "Reduces intensity spikes by applying a modelling method known as locally weighted polynomial regression. At each point in the data set a low-degree polynomial is fit to a subset of the data, with explanatory variable values near the point whose response is being estimated. The polynomial is fit using weighted least squares, giving more weight to points near the point whose response is being estimated and less weight to points further away. The value of the regression function for the point is then obtained by evaluating the local polynomial using the explanatory variable values for that data point. The LOESS fit is complete after regression function values have been computed for each of the n data points. Many of the details of this method, such as the degree of the polynomial model and the weights, are flexible." [PSI:MS] is_a: MS:1000592 ! smoothing [Term] id: MS:1000784 name: Gaussian smoothing def: "Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function." [PSI:MS] synonym: "binomial smoothing" EXACT [] synonym: "Weierstrass transform" EXACT [] is_a: MS:1000592 ! smoothing [Term] id: MS:1000785 name: moving average smoothing def: "Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect." [PSI:MS] synonym: "box smoothing" EXACT [] synonym: "boxcar smoothing" EXACT [] synonym: "sliding average smoothing" EXACT [] is_a: MS:1000592 ! smoothing [Term] id: MS:1000786 name: non-standard data array def: "A data array that contains data not covered by any other term in this group. Please do not use this term, if the binary data array type might be commonly used - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] xref: binary-data-type:MS\:1000519 "32-bit integer" xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000522 "64-bit integer" xref: binary-data-type:MS\:1000523 "64-bit float" xref: binary-data-type:MS\:1001479 "null-terminated ASCII string" is_a: MS:1000513 ! binary data array relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000787 name: inclusive low intensity threshold def: "Threshold at or below which some action is taken." [PSI:MS] is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000788 name: inclusive high intensity threshold def: "Threshold at or above which some action is taken." [PSI:MS] is_a: MS:1000630 ! data processing parameter relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 relationship: has_units UO:0000269 ! absorbance unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000789 name: enhanced multiply charged spectrum def: "MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions." [PSI:MS] is_a: MS:1000579 ! MS1 spectrum [Term] id: MS:1000790 name: time-delayed fragmentation spectrum def: "MSn spectrum in which the product ions are collected after a time delay, which allows the observation of lower energy fragmentation processes after precursor ion activation." [PSI:MS] is_a: MS:1000580 ! MSn spectrum [Term] id: MS:1000791 name: enhanced resolution scan def: "OBSOLETE Scan with enhanced resolution." [PSI:MS] comment: This term was made obsolete because it was merged with zoom scan (MS:1000497). is_obsolete: true [Term] id: MS:1000792 name: isolation window attribute def: "Isolation window parameter." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000441 ! scan [Term] id: MS:1000793 name: isolation window upper limit def: "OBSOLETE The highest m/z being isolated in an isolation window." [PSI:MS] comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000794 name: isolation window lower limit def: "OBSOLETE The lowest m/z being isolated in an isolation window." [PSI:MS] comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829. is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000795 name: no combination def: "Use this term if only one scan was recorded or there is no information about scans available." [PSI:MS] is_a: MS:1000570 ! spectra combination [Term] id: MS:1000796 name: spectrum title def: "Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file." [PSI:MS] comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list. is_a: MS:1001405 ! spectrum identification result details is_a: MS:1000499 ! spectrum attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000797 name: peak list scans def: "A list of scan numbers and or scan ranges associated with a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list. is_a: MS:1001405 ! spectrum identification result details is_a: MS:1003058 ! spectrum property relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000798 name: peak list raw scans def: "A list of raw scans and or scan ranges used to generate a peak list. If possible the list of scans should be converted to native spectrum identifiers instead of using this term." [PSI:MS] comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list. is_a: MS:1001405 ! spectrum identification result details is_a: MS:1003058 ! spectrum property relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000799 name: custom unreleased software tool def: "A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added." [PSI:MS] is_a: MS:1000531 ! software relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000800 name: mass resolving power def: "The observed mass divided by the difference between two masses that can be separated: m/dm. The procedure by which dm was obtained and the mass at which the measurement was made should be reported." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000801 name: area peak picking def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The area defined by all raw data points that belong to the peak is reported." [PSI:MS] synonym: "sum peak picking" EXACT [] is_a: MS:1000035 ! peak picking [Term] id: MS:1000802 name: height peak picking def: "Spectral peak processing conducted on the acquired data to convert profile data to centroided data. The maximum intensity of all raw data points that belong to the peak is reported." [PSI:MS] synonym: "max peak picking" EXACT [] is_a: MS:1000035 ! peak picking [Term] id: MS:1000803 name: analyzer scan offset def: "Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000804 name: electromagnetic radiation spectrum def: "A plot of the relative intensity of electromagnetic radiation as a function of the wavelength." [PSI:MS] synonym: "EMR spectrum" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000805 name: emission spectrum def: "A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000806 name: absorption spectrum def: "A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000559 ! spectrum type [Term] id: MS:1000807 name: Th/s def: "Unit describing the scan rate of a spectrum in Thomson per second." [PSI:MS] is_a: UO:0000000 ! unit [Term] id: MS:1000808 name: chromatogram attribute def: "Chromatogram properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1000809 name: chromatogram title def: "A free-form text title describing a chromatogram." [PSI:MS] comment: This is the preferred storage place for the spectrum title. is_a: MS:1000808 ! chromatogram attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000810 name: ion current chromatogram def: "Representation of the current of ions versus time." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1000626 ! chromatogram type [Term] id: MS:1000811 name: electromagnetic radiation chromatogram def: "Representation of electromagnetic properties versus time." [PSI:MS] synonym: "EMR radiation chromatogram" EXACT [] is_a: MS:1000524 ! data file content is_a: MS:1000626 ! chromatogram type [Term] id: MS:1000812 name: absorption chromatogram def: "Representation of light absorbed by the sample versus time." [PSI:MS] is_a: MS:1000811 ! electromagnetic radiation chromatogram [Term] id: MS:1000813 name: emission chromatogram def: "Representation of light emitted by the sample versus time." [PSI:MS] is_a: MS:1000811 ! electromagnetic radiation chromatogram [Term] id: MS:1000814 name: counts per second def: "The number of counted events observed per second in one or a group of elements of a detector." [PSI:MS] is_a: MS:1000043 ! intensity unit [Term] id: MS:1000815 name: Bruker BAF format def: "Bruker BAF raw file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000816 name: Bruker U2 format def: "Bruker HyStar U2 file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000817 name: HyStar def: "Bruker software for hyphenated experiments." [PSI:MS] is_a: MS:1000692 ! Bruker software [Term] id: MS:1000818 name: Acquity UPLC PDA def: "Acquity UPLC Photodiode Array Detector." [PSI:MS] is_a: MS:1000126 ! Waters instrument model is_a: MS:1000621 ! photodiode array detector [Term] id: MS:1000819 name: Acquity UPLC FLR def: "Acquity UPLC Fluorescence Detector." [PSI:MS] is_a: MS:1000126 ! Waters instrument model is_a: MS:1002308 ! fluorescence detector [Term] id: MS:1000820 name: flow rate array def: "A data array of flow rate measurements." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units UO:0000271 ! microliters per minute [Term] id: MS:1000821 name: pressure array def: "A data array of pressure measurements." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units UO:0000110 ! pascal [Term] id: MS:1000822 name: temperature array def: "A data array of temperature measurements." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units UO:0000012 ! kelvin [Term] id: MS:1000823 name: Bruker U2 nativeID format def: "Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000824 name: no nativeID format def: "No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000825 name: Bruker FID format def: "Bruker FID file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000826 name: elution time def: "The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000827 name: isolation window target m/z def: "The primary or reference m/z about which the isolation window is defined." [PSI:MS] is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000828 name: isolation window lower offset def: "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000829 name: isolation window upper offset def: "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z." [PSI:MS] is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000831 name: sample preparation def: "Properties of the preparation steps which took place before the measurement was performed." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000548 ! sample attribute [Term] id: MS:1000832 name: MALDI matrix application def: "Attributes to describe the technique how the sample is prepared with the matrix solution." [PSI:MS] relationship: part_of MS:1000831 ! sample preparation [Term] id: MS:1000833 name: matrix application type def: "Describes the technique how the matrix is put on the sample target." [PSI:MS] relationship: part_of MS:1000832 ! MALDI matrix application [Term] id: MS:1000834 name: matrix solution def: "Describes the chemical solution used as matrix." [PSI:MS] is_a: MS:1000832 ! MALDI matrix application relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000835 name: matrix solution concentration def: "Concentration of the chemical solution used as matrix." [PSI:MS] is_a: MS:1000832 ! MALDI matrix application relationship: has_units UO:0000175 ! gram per liter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000836 name: dried droplet MALDI matrix preparation def: "Dried droplet in MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type [Term] id: MS:1000837 name: printed MALDI matrix preparation def: "Printed MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type [Term] id: MS:1000838 name: sprayed MALDI matrix preparation def: "Sprayed MALDI matrix preparation." [PSI:MS] is_a: MS:1000833 ! matrix application type [Term] id: MS:1000839 name: precoated MALDI sample plate def: "Precoated MALDI sample plate." [PSI:MS] is_a: MS:1000833 ! matrix application type is_a: MS:1001938 ! sample plate type [Term] id: MS:1000840 name: laser def: "Device that emits light (electromagnetic radiation) through a process called stimulated emission. The term is an acronym for Light Amplification by Stimulated Emission of Radiation." [PSI:MS] relationship: part_of MS:1000482 ! source attribute [Term] id: MS:1000841 name: laser attribute def: "Laser properties that are associated with a value." [PSI:MS] relationship: part_of MS:1000840 ! laser [Term] id: MS:1000842 name: laser type def: "Type of laser used for desorption purpose." [PSI:MS] relationship: part_of MS:1000840 ! laser [Term] id: MS:1000843 name: wavelength def: "OBSOLETE The distance between two peaks of the emitted laser beam." [PSI:MS] comment: This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242). is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000018 ! nanometer is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000844 name: focus diameter x def: "Describes the diameter of the laser beam in x direction." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000017 ! micrometer relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000845 name: focus diameter y def: "Describes the diameter of the laser beam in y direction." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000017 ! micrometer relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000846 name: pulse energy def: "Describes output energy of the laser system. May be attenuated by filters or other means." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000112 ! joule relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000847 name: pulse duration def: "Describes how long the laser beam was emitted from the laser device." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000150 ! nanosecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000848 name: attenuation def: "Describes the reduction of the intensity of the laser beam energy." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000187 ! percent relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000849 name: impact angle def: "Describes the angle between the laser beam and the sample target." [PSI:MS] is_a: MS:1000841 ! laser attribute relationship: has_units UO:0000185 ! degree relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000850 name: gas laser def: "Laser which is powered by a gaseous medium." [PSI:MS] is_a: MS:1000842 ! laser type [Term] id: MS:1000851 name: solid-state laser def: "Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states." [PSI:MS] is_a: MS:1000842 ! laser type [Term] id: MS:1000852 name: dye-laser def: "Dye lasers use an organic dye as the gain medium." [PSI:MS] is_a: MS:1000842 ! laser type [Term] id: MS:1000853 name: free electron laser def: "Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term." [PSI:MS] is_a: MS:1000842 ! laser type [Term] id: MS:1000854 name: LTQ XL def: "Thermo Scientific LTQ XL MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000855 name: LTQ Velos def: "Thermo Scientific LTQ Velos MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000856 name: LTQ Velos ETD def: "Thermo Scientific LTQ Velos MS with ETD." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1000857 name: run attribute def: "Properties of the described run." [PSI:MS] is_a: MS:1000547 ! object attribute [Term] id: MS:1000858 name: fraction identifier def: "Identier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information." [PSI:MS] is_a: MS:1000857 ! run attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000859 name: molecule def: "Group of two or more atoms held together by chemical bonds." [https://en.wikipedia.org/wiki/Molecule] is_a: MS:1000881 ! molecular entity [Term] id: MS:1000860 name: peptide def: "A molecule of low molecular weight that is composed of two or more amino acid residues." [PSI:MS] is_a: MS:1000859 ! molecule [Term] id: MS:1000861 name: molecular entity property def: "A physical characteristic of a molecular entity." [PSI:MS] relationship: part_of MS:1000881 ! molecular entity [Term] id: MS:1000862 name: isoelectric point def: "The pH of a solution at which a charged molecule does not migrate in an electric field." [PSI:MS] synonym: "pI" EXACT [] is_a: MS:1000861 ! molecular entity property relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000863 name: predicted isoelectric point def: "The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm." [PSI:MS] synonym: "predicted pI" EXACT [] is_a: MS:1000862 ! isoelectric point relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000864 name: chemical formula def: "A combination of symbols used to express the chemical composition of a molecule." [EDAM:0846] is_a: MS:1003033 ! molecular entity attribute [Term] id: MS:1000865 name: empirical formula def: "A chemical formula which expresses the proportions of the elements present in a substance." [PSI:MS] is_a: MS:1000864 ! chemical formula relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000866 name: molecular formula def: "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked." [PSI:MS] is_a: MS:1000864 ! chemical formula relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000867 name: structural formula def: "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other." [PSI:MS] is_a: MS:1000864 ! chemical formula relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000868 name: SMILES string def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301] is_a: MS:1000867 ! structural formula relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000869 name: collision gas pressure def: "The gas pressure of the collision gas used for collisional excitation." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000110 ! pascal relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000870 name: 4000 QTRAP def: "OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000." [PSI:MS] comment: This term was obsoleted because was redundant to MS:1000139. is_a: MS:1000121 ! SCIEX instrument model is_obsolete: true [Term] id: MS:1000871 name: SRM software def: "Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000872 name: MaRiMba def: "Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba] is_a: MS:1000871 ! SRM software [Term] id: MS:1000873 name: peptide attribute calculation software def: "Software used to predict or calculate numerical attributes of peptides." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1000874 name: SSRCalc def: "Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence." [http://hs2.proteome.ca/SSRCalc/SSRCalc.html] is_a: MS:1000873 ! peptide attribute calculation software [Term] id: MS:1000875 name: declustering potential def: "Potential difference between the orifice and the skimmer in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000876 name: cone voltage def: "Potential difference between the sampling cone/orifice in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000877 name: tube lens voltage def: "Potential difference setting of the tube lens in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000878 name: external reference identifier def: "An identifier/accession number to an external reference database." [PSI:MS] is_a: MS:1002840 ! external reference data [Term] id: MS:1000879 name: PubMed identifier def: "A unique identifier for a publication in the PubMed database (MIR:00000015)." [PSI:MS] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1000880 name: interchannel delay def: "The duration of intervals between scanning, during which the instrument configuration is switched." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000881 name: molecular entity def: "Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity." [https://en.wikipedia.org/wiki/Molecular_entity] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1000882 name: protein def: "A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA of a gene." [PSI:MS] is_a: MS:1000859 ! molecule [Term] id: MS:1000883 name: protein short name def: "A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN)." [PSI:MS] is_a: MS:1000884 ! protein attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000884 name: protein attribute def: "An nonphysical characterstic attributed to a specific protein." [PSI:MS] relationship: part_of MS:1000882 ! protein is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1000885 name: protein accession def: "Identifier for a specific protein in a database." [PSI:MS] is_a: MS:1000884 ! protein attribute is_a: MS:1003046 ! peptide-to-protein mapping attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000886 name: protein name def: "A long name describing the function of the protein." [PSI:MS] is_a: MS:1000884 ! protein attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000887 name: peptide attribute def: "Nonphysical characteristic attributed to a peptide." [PSI:MS] relationship: part_of MS:1000860 ! peptide [Term] id: MS:1000888 name: stripped peptide sequence def: "Sequence of letter symbols denoting the order of amino acids that compose the peptide, with any amino acid mass modifications that might be present having been stripped away." [PSI:MS] is_a: MS:1003050 ! peptidoform attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000889 name: peptidoform sequence def: "Sequence of letter symbols denoting the order of amino acid residues that compose the peptidoform including the encoding of any residue modifications that are present." [PSI:MS] comment: Make it more general as there are actually many other ways to display a modified peptide sequence. is_a: MS:1003050 ! peptidoform attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000890 name: peptidoform labeling state def: "A state description of how a peptide might be isotopically or isobarically labelled." [PSI:MS] is_a: MS:1003050 ! peptidoform attribute [Term] id: MS:1000891 name: heavy labeled peptidoform def: "A peptide that has been created or labelled with some heavier-than-usual isotopes." [PSI:MS] is_a: MS:1000890 ! peptidoform labeling state [Term] id: MS:1000892 name: unlabeled peptidoform def: "A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:MS] synonym: "light labeled peptide" EXACT [] is_a: MS:1000890 ! peptidoform labeling state [Term] id: MS:1000893 name: peptidoform group label def: "An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label." [PSI:MS] is_a: MS:1003050 ! peptidoform attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000894 name: retention time def: "A time interval from the start of chromatography when an analyte exits a chromatographic column." [PSI:MS] is_a: MS:1003050 ! peptidoform attribute is_a: MS:1003295 ! summary statistics of replicates relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000895 name: local retention time def: "A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup." [PSI:MS] is_a: MS:1000894 ! retention time relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000896 name: normalized retention time def: "A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup." [PSI:MS] is_a: MS:1000894 ! retention time is_a: MS:1003295 ! summary statistics of replicates relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000897 name: predicted retention time def: "A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application." [PSI:MS] is_a: MS:1000894 ! retention time relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000898 name: standard def: "Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1000899 name: de facto standard def: "A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard." [PSI:MS] is_a: MS:1000898 ! standard [Term] id: MS:1000900 name: minimum information standard def: "A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result." [PSI:MS] is_a: MS:1000898 ! standard [Term] id: MS:1000901 name: retention time normalization standard def: "A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column." [PSI:MS] is_a: MS:1000898 ! standard [Term] id: MS:1000902 name: H-PINS retention time normalization standard def: "The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column." [DOI:10.1074/mcp.M800569-MCP200, PMID:19411281] is_a: MS:1000901 ! retention time normalization standard [Term] id: MS:1000903 name: product ion series ordinal def: "The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion)." [PSI:PI] is_a: MS:1001221 ! product ion attribute relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000904 name: product ion m/z delta def: "The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z." [PSI:PI] is_a: MS:1001221 ! product ion attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1000905 name: percent of base peak times 100 def: "The magnitude of a peak expressed in terms of the percentage of the magnitude of the base peak intensity multiplied by 100. The base peak is therefore 10000. This unit is common in normalized spectrum libraries." [PSI:MS] is_a: MS:1000043 ! intensity unit relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000906 name: peak intensity rank def: "Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: part_of MS:1000231 ! peak relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000907 name: peak targeting suitability rank def: "Ordinal specifying the rank of a peak in a spectrum in terms of suitability for targeting. The most suitable peak is 1. The next most suitability peak is 2, etc. Suitability is algorithm and context dependant." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: part_of MS:1000231 ! peak relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000908 name: transition def: "A set of two m/z values corresponding to the precursor m/z and a fragment m/z that in combination can be used to identify or quantify a specific ion, although not necessarily uniquely." [PSI:MS] synonym: "reaction" EXACT [] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000909 name: transition validation method def: "The strategy used to validate that a transition is effective." [PSI:MS] relationship: part_of MS:1000908 ! transition [Term] id: MS:1000910 name: transition optimized on specified instrument def: "The transition has been optimized by direct injection of the peptide into an instrument specified in a separate term, and the optimum voltages and fragmentation energies have been determined." [PSI:MS] is_a: MS:1000909 ! transition validation method [Term] id: MS:1000911 name: transition validated with an MS/MS spectrum on specified instrument def: "The transition has been validated by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term." [PSI:MS] is_a: MS:1000909 ! transition validation method [Term] id: MS:1000912 name: transition purported from an MS/MS spectrum on a different, specified instrument def: "The transition has been purported by obtaining an MS2 spectrum and demonstrating that the peak is detectable on the instrument specified with a separate term. However, the detecting instrument is of a different type (e.g. ion trap) than the instrument that the transition will eventually be used on (e.g. triple quad)." [PSI:MS] is_a: MS:1000909 ! transition validation method [Term] id: MS:1000913 name: transition predicted by informatic analysis def: "The transition has been predicted by informatics software without any direct spectral evidence." [PSI:MS] is_a: MS:1000909 ! transition validation method [Term] id: MS:1000914 name: tab delimited text format def: "A file format that has two or more columns of tabular data where each column is separated by a TAB character." [PSI:MS] is_a: MS:1001459 ! file format is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1000915 name: retention time window attribute def: "An attribute of a window in time about which a peptide might elute from the column." [PSI:MS] relationship: part_of MS:1000894 ! retention time [Term] id: MS:1000916 name: retention time window lower offset def: "The extent of the retention time window in time units below the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000917 name: retention time window upper offset def: "The extent of the retention time window in time units above the target retention time. The lower and upper offsets may be asymmetric about the target time." [PSI:MS] is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000918 name: target list def: "A list of peptides or compounds and their expected m/z coordinates that can be used to cause a mass spectrometry to obtain spectra of those molecules specifically." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information [Term] id: MS:1000919 name: target inclusion exclusion priority def: "A priority setting specifying whether included or excluded targets have priority over the other." [PSI:MS] relationship: part_of MS:1000918 ! target list [Term] id: MS:1000920 name: includes supersede excludes def: "A priority setting specifying that included targets have priority over the excluded targets if there is a conflict." [PSI:MS] is_a: MS:1000919 ! target inclusion exclusion priority [Term] id: MS:1000921 name: excludes supersede includes def: "A priority setting specifying that excluded targets have priority over the included targets if there is a conflict." [PSI:MS] is_a: MS:1000919 ! target inclusion exclusion priority [Term] id: MS:1000922 name: Skyline def: "Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington." [https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default] is_a: MS:1000871 ! SRM software is_a: MS:1001139 ! quantitation software name [Term] id: MS:1000923 name: TIQAM def: "Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/TIQAM/TIQAM.html] is_a: MS:1000871 ! SRM software [Term] id: MS:1000924 name: MaRiMba def: "OBSOLETE Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology." [http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP-MaRiMba] comment: This term was made obsolete because it was redundant with an existing term (MS:1000872). is_obsolete: true replaced_by: MS:1000872 [Term] id: MS:1000925 name: ATAQS def: "Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology." [PSI:MS] is_a: MS:1000871 ! SRM software [Term] id: MS:1000926 name: product interpretation rank def: "The integer rank given an interpretation of an observed product ion. For example, if y8 is selected as the most likely interpretation of a peak, then it is assigned a rank of 1." [PSI:MS] is_a: MS:1001221 ! product ion attribute relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1000927 name: ion injection time def: "The length of time spent filling an ion trapping device." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1000928 name: calibration spectrum def: "A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample." [PSI:MS] is_a: MS:1000559 ! spectrum type [Term] id: MS:1000929 name: Shimadzu Biotech nativeID format def: "Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1000930 name: Shimadzu Biotech database entity def: "Shimadzu Biotech format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1000931 name: QTRAP 5500 def: "Applied Biosystems|MDS SCIEX QTRAP 5500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000932 name: TripleTOF 5600 def: "SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1000933 name: protein modifications def: "Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation." [PSI:MS] is_a: MS:1000884 ! protein attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000934 name: gene name def: "Name of the gene from which the protein is translated." [PSI:MS] is_a: MS:1000884 ! protein attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1000935 name: 6470A Triple Quadrupole LC/MS def: "The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000936 name: 6470B Triple Quadrupole LC/MS def: "The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1000937 name: 6495C Triple Quadrupole LC/MS def: "The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1001000 name: spectrum interpretation def: "Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra." [PSI:PI] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1001005 name: SEQUEST:CleavesAt is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001006 name: SEQUEST:ViewCV def: "SEQUEST View Input Parameters." [PSI:PI] is_a: MS:1002096 ! SEQUEST input parameter [Term] id: MS:1001007 name: SEQUEST:OutputLines def: "Number of peptide results to show." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001009 name: SEQUEST:DescriptionLines def: "Number of full protein descriptions to show for top N peptides." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001010 name: de novo search def: "A de novo sequencing search (without database)." [PSI:PI] is_a: MS:1001080 ! search type [Term] id: MS:1001011 name: search database details def: "Details about the database searched." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001012 name: database source def: "The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other)." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001013 name: database name def: "The name of the search database (nr, SwissProt or est_human)." [PSI:PI] is_a: MS:1001011 ! search database details [Term] id: MS:1001014 name: database local file path def: "OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view." [PSI:PI] is_a: MS:1001011 ! search database details is_obsolete: true [Term] id: MS:1001015 name: database original uri def: "URI, from where the search database was originally downloaded." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001016 name: database version def: "Version of the search database. In mzIdentML use the attribute instead." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001017 name: release date def: "Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term." [PSI:PI] is_a: MS:1001011 ! search database details is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:dateTime relationship: has_structured_representation_in_format MS:1002073 ! mzIdentML format [Term] id: MS:1001018 name: database type def: "Database containing amino acid or nucleic acid sequences." [PSI:PI] is_a: MS:1001011 ! search database details [Term] id: MS:1001019 name: database filtering def: "Was there filtering used on the database." [PSI:PI] is_a: MS:1001011 ! search database details [Term] id: MS:1001020 name: DB filter taxonomy def: "A taxonomy filter was to the database search." [PSI:PI] is_a: MS:1001511 ! Sequence database filter types [Term] id: MS:1001021 name: DB filter on accession numbers def: "Filtering applied specifically by accession number pattern." [PSI:PI] is_a: MS:1001511 ! Sequence database filter types [Term] id: MS:1001022 name: DB MW filter def: "Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value." [PSI:PI] is_a: MS:1001511 ! Sequence database filter types [Term] id: MS:1001023 name: DB PI filter def: "Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value." [PSI:PI] is_a: MS:1001511 ! Sequence database filter types [Term] id: MS:1001024 name: translation frame def: "The translated open reading frames from a nucleotide database considered in the search (range: 1-6)." [PSI:PI] is_a: MS:1001011 ! search database details [Term] id: MS:1001025 name: translation table def: "The translation table used to translate the nucleotides to amino acids." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001026 name: SEQUEST:NormalizeXCorrValues is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001027 name: DB filter on sequence pattern def: "Filtering applied specifically by amino acid sequence pattern." [PSI:PI] is_a: MS:1001511 ! Sequence database filter types [Term] id: MS:1001028 name: SEQUEST:SequenceHeaderFilter def: "String in the header of a sequence entry for that entry to be searched." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001029 name: number of sequences searched def: "The number of sequences (proteins / nucleotides) from the database search after filtering." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001030 name: number of peptide seqs compared to each spectrum def: "Number of peptide seqs compared to each spectrum." [PSI:PI] is_a: MS:1001011 ! search database details is_a: MS:1001405 ! spectrum identification result details relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001031 name: spectral library search def: "A search using a library of spectra." [PSI:PI] is_a: MS:1001080 ! search type [Term] id: MS:1001032 name: SEQUEST:SequencePartialFilter is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001035 name: date / time search performed def: "OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run." [PSI:PI] is_a: MS:1001184 ! search statistics is_obsolete: true [Term] id: MS:1001036 name: search time taken def: "The time taken to complete the search in seconds." [PSI:PI] is_a: MS:1001184 ! search statistics relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001037 name: SEQUEST:ShowFragmentIons def: "Flag indicating that fragment ions should be shown." [PSI:MS] is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001038 name: SEQUEST:Consensus def: "Specify depth as value of the CVParam." [PSI:PI] is_a: MS:1001006 ! SEQUEST:ViewCV relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001040 name: intermediate analysis format def: "Type of the source file, the mzIdentML was created from." [PSI:PI] is_a: MS:1001459 ! file format [Term] id: MS:1001041 name: SEQUEST:sortCV def: "SEQUEST View / Sort Input Parameters." [PSI:PI] is_a: MS:1001006 ! SEQUEST:ViewCV [Term] id: MS:1001042 name: SEQUEST:LimitTo def: "Specify \"number of dtas shown\" as value of the CVParam." [PSI:PI] is_a: MS:1002096 ! SEQUEST input parameter relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001044 name: cleavage agent details def: "Details of cleavage agent (enzyme)." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001045 name: cleavage agent name def: "The name of the cleavage agent." [PSI:PI] is_a: MS:1001044 ! cleavage agent details [Term] id: MS:1001046 name: SEQUEST:sort by dCn def: "Sort order of SEQUEST search results by the delta of the normalized correlation score." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001047 name: SEQUEST:sort by dM def: "Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001048 name: SEQUEST:sort by Ions def: "Sort order of SEQUEST search results given by the ions." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001049 name: SEQUEST:sort by MH+ def: "Sort order of SEQUEST search results given by the mass of the protonated ion." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001050 name: SEQUEST:sort by P def: "Sort order of SEQUEST search results given by the probability." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001051 name: multiple enzyme combination rules def: "OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any." [PSI:PI] is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001052 name: SEQUEST:sort by PreviousAminoAcid def: "Sort order of SEQUEST search results given by the previous amino acid." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001053 name: SEQUEST:sort by Ref def: "Sort order of SEQUEST search results given by the reference." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001055 name: modification parameters def: "Modification parameters for the search engine run." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001056 name: modification specificity rule def: "The specificity rules for the modifications applied by the search engine." [PSI:PI] is_a: MS:1001055 ! modification parameters [Term] id: MS:1001057 name: tolerance on types def: "OBSOLETE: Tolerance on types." [PSI:PI] is_a: MS:1001055 ! modification parameters is_obsolete: true [Term] id: MS:1001058 name: quality estimation by manual validation def: "The quality estimation was done manually." [PSI:PI] is_a: MS:1001060 ! quality estimation method details [Term] id: MS:1001059 name: SEQUEST:sort by RSp def: "Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide)." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001060 name: quality estimation method details def: "Method for quality estimation (manually or with decoy database)." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001061 name: neutral loss def: "OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD." [PSI:PI] is_a: MS:1001055 ! modification parameters is_obsolete: true replaced_by: MS:1000336 [Term] id: MS:1001062 name: Mascot MGF format def: "Mascot MGF file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001065 name: TODOscoring model def: "OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms." [PSI:PI] comment: This term was made obsolete and is replaced by the term (MS:1001961). is_a: MS:1001249 ! search input details is_obsolete: true replaced_by: MS:1001961 [Term] id: MS:1001066 name: ions series considered in search def: "The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001068 name: SEQUEST:sort by Sp def: "Sort order of SEQUEST search results by the Sp score." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001069 name: SEQUEST:sort by TIC def: "Sort order of SEQUEST search results given by the total ion current." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001070 name: SEQUEST:sort by Scan def: "Sort order of SEQUEST search results given by the scan number." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001071 name: SEQUEST:sort by Sequence def: "Sort order of SEQUEST search results given by the sequence." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001072 name: SEQUEST:sort by Sf def: "Sort order of SEQUEST search results given by the SEQUEST result 'Sf'." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001073 name: database type amino acid def: "Database contains amino acid sequences." [PSI:PI] is_a: MS:1001018 ! database type [Term] id: MS:1001079 name: database type nucleotide def: "Database contains nucleic acid sequences." [PSI:PI] is_a: MS:1001018 ! database type [Term] id: MS:1001080 name: search type def: "Enumeration of type of search value (i.e. from PMF, sequence tag, MS2)." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001081 name: pmf search def: "A peptide mass fingerprint search." [PSI:PI] is_a: MS:1001080 ! search type [Term] id: MS:1001082 name: tag search def: "A sequence tag search." [PSI:PI] is_a: MS:1001080 ! search type [Term] id: MS:1001083 name: ms-ms search def: "An MS2 search (with fragment ions)." [PSI:PI] is_a: MS:1001080 ! search type [Term] id: MS:1001084 name: database nr def: "Non-redundant GenBank sequence database." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001085 name: protein-level identification attribute def: "Protein level information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1001086 name: SEQUEST:sort by XCorr def: "Sort order of SEQUEST search results by the correlation score." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001087 name: SEQUEST:ProcessCV def: "SEQUEST View / Process Input Parameters." [PSI:PI] is_a: MS:1002096 ! SEQUEST input parameter [Term] id: MS:1001088 name: protein description def: "The protein description line from the sequence entry in the source database FASTA file." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute is_a: MS:1001342 ! database sequence details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001089 name: molecule taxonomy def: "The taxonomy of the resultant molecule from the search." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute is_a: MS:1001342 ! database sequence details is_a: MS:1001512 ! Sequence database filters relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001090 name: taxonomy nomenclature def: "OBSOLETE: The system used to indicate taxonomy. There should be an enumerated list of options: latin name, NCBI TaxID, common name, Swiss-Prot species ID (ex. RABIT from the full protein ID ALBU_RABIT)." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy is_obsolete: true replaced_by: MS:1001467 replaced_by: MS:1001468 replaced_by: MS:1001469 replaced_by: MS:1001470 [Term] id: MS:1001091 name: NoEnzyme is_a: MS:1001045 ! cleavage agent name comment: This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956). is_obsolete: true [Term] id: MS:1001092 name: peptide sequence-level identification statistic def: "Identification confidence metric for a peptide." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute [Term] id: MS:1001093 name: sequence coverage def: "The percent coverage for the protein based upon the matched peptide sequences (can be calculated)." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute relationship: has_value_type xsd:decimal ! The allowed value-type for this CV term [Term] id: MS:1001094 name: SEQUEST:sort by z def: "Sort order of SEQUEST search results given by the charge." [PSI:PI] is_a: MS:1001041 ! SEQUEST:sortCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001095 name: SEQUEST:ProcessAll is_a: MS:1001087 ! SEQUEST:ProcessCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001096 name: SEQUEST:TopPercentMostIntense def: "Specify \"percentage\" as value of the CVParam." [PSI:PI] is_a: MS:1001087 ! SEQUEST:ProcessCV relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001097 name: distinct peptide sequences def: "This counts distinct sequences hitting the protein without regard to a minimal confidence threshold." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001098 name: confident distinct peptide sequences def: "This counts the number of distinct peptide sequences. Multiple charge states and multiple modification states do NOT count as multiple sequences. The definition of 'confident' must be qualified elsewhere." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001099 name: confident peptide qualification def: "The point of this entry is to define what is meant by confident for the term Confident distinct peptide sequence and/or Confident peptides. Example 1 - metric=Paragon:Confidence value=95 sense=greater than Example 2 - metric=Mascot:Eval value=0.05 sense=less than." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001100 name: confident peptide sequence number def: "This counts the number of peptide sequences without regard to whether they are distinct. Multiple charges states and multiple modification states DO count as multiple peptides. The definition of 'confident' must be qualified elsewhere." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001101 name: protein group or subset relationship def: "Protein group or subset relationships." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute [Term] id: MS:1001102 name: SEQUEST:Chromatogram is_a: MS:1001006 ! SEQUEST:ViewCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001103 name: SEQUEST:InfoAndLog is_a: MS:1001006 ! SEQUEST:ViewCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001104 name: database UniProtKB/Swiss-Prot def: "The name of the UniProtKB/Swiss-Prot knowledgebase." [PSI:PI] is_a: MS:1002126 ! database UniProtKB [Term] id: MS:1001105 name: peptide sequence-level identification attribute def: "Peptide level information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1001106 name: SEQUEST:TopNumber def: "Specify \"number\" as value of the CVParam." [PSI:PI] is_a: MS:1001087 ! SEQUEST:ProcessCV relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001107 name: data stored in database def: "Source file for this mzIdentML was a data set in a database." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001108 name: param: a ion def: "Parameter information, type of product: a ion with charge on the N-terminal side." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001109 name: SEQUEST:CullTo def: "Specify cull string as value of the CVParam." [PSI:PI] is_a: MS:1001087 ! SEQUEST:ProcessCV relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001110 name: SEQUEST:modeCV def: "SEQUEST Mode Input Parameters." [PSI:PI] is_a: MS:1002096 ! SEQUEST input parameter [Term] id: MS:1001111 name: SEQUEST:Full is_a: MS:1001110 ! SEQUEST:modeCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001112 name: n-terminal flanking residue def: "Residue preceding the first amino acid in the peptide sequence as it occurs in the protein. Use 'N-term' to denote if the peptide starts at the N terminus of the protein." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001113 name: c-terminal flanking residue def: "Residue following the last amino acid in the peptide sequence as it occurs in the protein. Use 'C-term' to denote if the peptide ends at the C terminus of the protein." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001114 name: retention time(s) def: "OBSOLETE Retention time of the spectrum from the source file." [PSI:PI] comment: This term was made obsolete because scan start time (MS:1000016) should be used instead. is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001115 name: scan number(s) def: "OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData." [PSI:PI] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1001116 name: single protein identification statistic def: "Results specific for one protein as part of a protein ambiguity group (a result not valid for all the other proteins in the protein ambiguity group)." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute [Term] id: MS:1001117 name: theoretical mass def: "The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001118 name: param: b ion def: "Parameter information, type of product: b ion with charge on the N-terminal side." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001119 name: param: c ion def: "Parameter information, type of product: c ion with charge on the N-terminal side." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001120 name: SEQUEST:FormatAndLinks is_a: MS:1001110 ! SEQUEST:modeCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001121 name: number of matched peaks def: "The number of peaks that were matched as qualified by the ion series considered field. If a peak matches multiple ions then only 1 would be added the count." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001122 name: ions series considered def: "The ion series that were used during the calculation of the count (e.g. a, b, c, d, v, w, x, y, z, a-H2O, a-NH3, b-H2O, b-NH3, y-H2O, y-NH3, b-H20, b+, z-, z+1, z+2, b-H3PO4, y-H3PO4, immonium, internal ya, internal yb)." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute [Term] id: MS:1001123 name: number of peaks used def: "The number of peaks from the original peak list that are used to calculate the scores for a particular search engine. All ions that have the opportunity to match or be counted even if they don't." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001124 name: number of peaks submitted def: "The number of peaks from the original peaks listed that were submitted to the search engine." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001125 name: manual validation def: "Result of quality estimation: decision of a manual validation." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001126 name: SEQUEST:Fast is_a: MS:1001110 ! SEQUEST:modeCV relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001127 name: peptide sharing details def: "Accessions Containing Sequence - Accessions for each protein containing this peptide." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute [Term] id: MS:1001128 name: SEQUEST:selectCV def: "SEQUEST Select Input Parameters." [PSI:PI] is_a: MS:1002096 ! SEQUEST input parameter [Term] id: MS:1001129 name: quantification information def: "Quantification information." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001130 name: peptide raw area def: "OBSOLETE Peptide raw area." [PSI:PI] comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844). is_a: MS:1002737 ! peptide-level quantification datatype is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001131 name: error on peptide area def: "Error on peptide area." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001132 name: peptide ratio def: "Peptide ratio." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001133 name: error on peptide ratio def: "Error on peptide ratio." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001134 name: protein ratio def: "Protein ratio." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001135 name: error on protein ratio def: "Error on protein ratio." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001136 name: p-value (protein diff from 1 randomly) def: "OBSOLETE P-value (protein diff from 1 randomly)." [PSI:PI] comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855). is_a: MS:1002738 ! protein-level quantification datatype is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001137 name: absolute quantity def: "Absolute quantity in terms of real concentration or molecule copy number in sample." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001138 name: error on absolute quantity def: "Error on absolute quantity." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001139 name: quantitation software name def: "Quantitation software name." [PSI:PI] is_a: MS:1000531 ! software is_a: MS:1001129 ! quantification information [Term] id: MS:1001140 name: quantitation software version def: "OBSOLETE Quantitation software version." [PSI:PI] comment: This term was made obsolete because part of mzQuantML schema. is_a: MS:1001129 ! quantification information is_obsolete: true [Term] id: MS:1001141 name: intensity of precursor ion def: "The intensity of the precursor ion." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001142 name: database IPI_human def: "International Protein Index database for Homo sapiens sequences." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001143 name: PSM-level search engine specific statistic def: "Search engine specific peptide spectrum match scores." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic [Term] id: MS:1001144 name: SEQUEST:SelectDefault is_a: MS:1001128 ! SEQUEST:selectCV [Term] id: MS:1001145 name: SEQUEST:SelectAdvancedCV def: "SEQUEST Select Advanced Input Parameters." [PSI:PI] is_a: MS:1001128 ! SEQUEST:selectCV [Term] id: MS:1001146 name: param: a ion-NH3 DEPRECATED def: "Ion a-NH3 parameter information, type of product: a ion with lost ammonia." [PSI:PI] is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1001147 name: protein ambiguity group result details is_a: MS:1001085 ! protein-level identification attribute is_a: MS:1001153 ! search engine specific score [Term] id: MS:1001148 name: param: a ion-H2O DEPRECATED def: "Ion a-H2O if a significant and fragment includes STED." [PSI:PI] is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1001149 name: param: b ion-NH3 DEPRECATED def: "Ion b-NH3 parameter information, type of product: b ion with lost ammonia." [PSI:PI] is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1001150 name: param: b ion-H2O DEPRECATED def: "Ion b-H2O if b significant and fragment includes STED." [PSI:PI] is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1001151 name: param: y ion-NH3 DEPRECATED def: "Ion y-NH3 parameter information, type of product: y ion with lost ammonia." [PSI:PI] is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1001152 name: param: y ion-H2O DEPRECATED comment: This term was made obsolete - use MS:1001262 and MS:1002455 instead. is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1001153 name: search engine specific score def: "Search engine specific scores." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1001154 name: SEQUEST:probability def: "The SEQUEST result 'Probability'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001155 name: SEQUEST:xcorr def: "The SEQUEST result 'XCorr'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001156 name: SEQUEST:deltacn def: "The SEQUEST result 'DeltaCn'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001157 name: SEQUEST:sp def: "The SEQUEST result 'Sp' (protein)." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001158 name: SEQUEST:Uniq is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001159 name: SEQUEST:expectation value def: "The SEQUEST result 'Expectation value'." [PSI:PI] is_a: MS:1001153 ! search engine specific score relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001160 name: SEQUEST:sf def: "The SEQUEST result 'Sf'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001161 name: SEQUEST:matched ions def: "The SEQUEST result 'Matched Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001162 name: SEQUEST:total ions def: "The SEQUEST result 'Total Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001163 name: SEQUEST:consensus score def: "The SEQUEST result 'Consensus Score'." [PSI:PI] is_a: MS:1001153 ! search engine specific score relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001164 name: Paragon:unused protscore def: "The Paragon result 'Unused ProtScore'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001165 name: Paragon:total protscore def: "The Paragon result 'Total ProtScore'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001166 name: Paragon:score def: "The Paragon result 'Score'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001167 name: Paragon:confidence def: "The Paragon result 'Confidence'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001168 name: Paragon:expression error factor def: "The Paragon result 'Expression Error Factor'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001169 name: Paragon:expression change p-value def: "The Paragon result 'Expression change P-value'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001170 name: Paragon:contrib def: "The Paragon result 'Contrib'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001171 name: Mascot:score def: "The Mascot result 'Score'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001172 name: Mascot:expectation value def: "The Mascot result 'expectation value'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001173 name: Mascot:matched ions def: "The Mascot result 'Matched ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001174 name: Mascot:total ions def: "The Mascot result 'Total ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001175 name: peptide shared in multiple proteins def: "A peptide matching multiple proteins." [PSI:PI] is_a: MS:1001127 ! peptide sharing details [Term] id: MS:1001176 name: (?<=[KR])(?\!P) def: "Regular expression for Trypsin." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001177 name: number of molecular hypothesis considered def: "Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search." [PSI:PI] is_a: MS:1001184 ! search statistics relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001178 name: database EST def: "Expressed sequence tag nucleotide sequence database." [PSI:PI] is_a: MS:1001079 ! database type nucleotide [Term] id: MS:1001180 name: Cleavage agent regular expression def: "Regular expressions for cleavage enzymes." [PSI:PI] relationship: part_of MS:1001044 ! cleavage agent details is_a: MS:1002479 ! regular expression [Term] id: MS:1001184 name: search statistics def: "The details of the actual run of the search." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1001189 name: modification specificity peptide N-term def: "As parameter for search engine: apply the modification only at the N-terminus of a peptide." [PSI:PI] is_a: MS:1001056 ! modification specificity rule [Term] id: MS:1001190 name: modification specificity peptide C-term def: "As parameter for search engine: apply the modification only at the C-terminus of a peptide." [PSI:PI] is_a: MS:1001056 ! modification specificity rule [Term] id: MS:1001191 name: p-value def: "OBSOLETE Quality estimation by p-value." [PSI:PI] comment: This term was made obsolete because now is split into peptide and protein terms. is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001198 ! protein identification confidence metric is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001192 name: Expect value def: "Result of quality estimation: Expect value." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001193 name: confidence score def: "Result of quality estimation: confidence score." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001194 name: quality estimation with decoy database def: "Quality estimation by decoy database." [PSI:PI] is_a: MS:1001060 ! quality estimation method details relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001195 name: decoy DB type reverse def: "Decoy type: Amino acids of protein sequences are used in reverse order." [PSI:PI] is_a: MS:1001450 ! decoy DB details [Term] id: MS:1001196 name: decoy DB type randomized def: "Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass)." [PSI:PI] is_a: MS:1001450 ! decoy DB details [Term] id: MS:1001197 name: DB composition target+decoy def: "Decoy database composition: database contains original (target) and decoy entries." [PSI:PI] is_a: MS:1001450 ! decoy DB details [Term] id: MS:1001198 name: protein identification confidence metric def: "Identification confidence metric for a protein." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic [Term] id: MS:1001199 name: Mascot DAT format def: "Source file for this mzIdentML was in Mascot DAT file format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001200 name: SEQUEST out file format def: "Source file for this mzIdentML was in SEQUEST out file format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001201 name: DB MW filter maximum def: "Maximum value of molecular weight filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters relationship: has_units UO:0000221 ! dalton relationship: has_units UO:0000222 ! kilodalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001202 name: DB MW filter minimum def: "Minimum value of molecular weight filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters relationship: has_units UO:0000221 ! dalton relationship: has_units UO:0000222 ! kilodalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001203 name: DB PI filter maximum def: "Maximum value of isoelectric point filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001204 name: DB PI filter minimum def: "Minimum value of isoelectric point filter." [PSI:PI] is_a: MS:1001512 ! Sequence database filters relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001207 name: Mascot def: "The name of the Mascot search engine." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001208 name: SEQUEST def: "The name of the SEQUEST search engine." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001209 name: Phenyx def: "The name of the Phenyx search engine." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001210 name: mass type settings def: "The type of mass difference value to be considered by the search engine (monoisotopic or average)." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001211 name: parent mass type mono def: "Mass type setting for parent mass was monoisotopic." [PSI:PI] is_a: MS:1001210 ! mass type settings [Term] id: MS:1001212 name: parent mass type average def: "Mass type setting for parent mass was average isotopic." [PSI:PI] is_a: MS:1001210 ! mass type settings [Term] id: MS:1001213 name: search result details def: "OBSOLETE: Scores and global result characteristics." [PSI:PI] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1001214 name: protein-level global FDR def: "Estimation of the global false discovery rate of proteins." [PSI:PI] is_a: MS:1002705 ! protein-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001215 name: SEQUEST:PeptideSp def: "The SEQUEST result 'Sp' in out file (peptide)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001217 name: SEQUEST:PeptideRankSp def: "The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001218 name: SEQUEST:PeptideNumber def: "The SEQUEST result '#' in out file (peptide)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001219 name: SEQUEST:PeptideIdnumber def: "The SEQUEST result 'Id#' in out file (peptide)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1001220 name: frag: y ion def: "Fragmentation information, type of product: y ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001221 name: product ion attribute def: "Fragmentation information like ion types." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1001222 name: frag: b ion - H2O def: "Fragmentation information, type of product: b ion without water." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001223 name: frag: y ion - H2O def: "Fragmentation information, type of product: y ion without water." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001224 name: frag: b ion def: "Fragmentation information, type of product: b ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001225 name: product ion m/z def: "The m/z of the product ion." [PSI:PI] synonym: "fragment ion m/z" EXACT [] is_a: MS:1001221 ! product ion attribute relationship: has_units MS:1000040 ! m/z [Term] id: MS:1001226 name: product ion intensity def: "The intensity of a single product ion." [PSI:PI] synonym: "fragment ion intensity" EXACT [] is_a: MS:1001221 ! product ion attribute relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 [Term] id: MS:1001227 name: product ion m/z error def: "The product ion m/z error." [PSI:PI] is_a: MS:1001221 ! product ion attribute relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million [Term] id: MS:1001228 name: frag: x ion def: "Fragmentation information, type of product: x ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001229 name: frag: a ion def: "Fragmentation information, type of product: a ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001230 name: frag: z ion def: "Fragmentation information, type of product: z ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001231 name: frag: c ion def: "Fragmentation information, type of product: c ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001232 name: frag: b ion - NH3 def: "Ion b-NH3 fragmentation information, type of product: b ion without ammonia." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001233 name: frag: y ion - NH3 def: "Ion y-NH3 fragmentation information, type of product: y ion without ammonia." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001234 name: frag: a ion - H2O def: "Fragmentation information, type of product: a ion without water." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001235 name: frag: a ion - NH3 def: "Ion a-NH3 fragmentation information, type of product: a ion without ammonia." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001236 name: frag: d ion def: "Fragmentation information, type of product: d ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001237 name: frag: v ion def: "Fragmentation information, type of product: v ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001238 name: frag: w ion def: "Fragmentation information, type of product: w ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001239 name: frag: immonium ion def: "Fragmentation information, type of product: immonium ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001240 name: non-identified ion def: "Non-identified ion." [PSI:PI] is_a: MS:1001221 ! product ion attribute [Term] id: MS:1001241 name: co-eluting ion def: "Co-eluting ion." [PSI:PI] is_a: MS:1001221 ! product ion attribute [Term] id: MS:1001242 name: SEQUEST out folder def: "Source file for this mzIdentML was a SEQUEST folder with its out files." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001243 name: SEQUEST summary def: "Source file for this mzIdentML was a SEQUEST summary page (proteins)." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001245 name: PerSeptive PKS format def: "PerSeptive peak list file format." [http://www.matrixscience.com/help/data_file_help.html#PKS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001246 name: SCIEX API III format def: "PE SCIEX peak list file format." [http://www.matrixscience.com/help/data_file_help.html#API] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001247 name: Bruker XML format def: "Bruker data exchange XML format." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001249 name: search input details def: "Details describing the search input." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001250 name: local FDR def: "Result of quality estimation: the local FDR at the current position of a sorted list." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic is_a: MS:1001116 ! single protein identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001251 name: Trypsin def: "Enzyme trypsin." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001176 ! (?<=[KR])(?!P) [Term] id: MS:1001252 name: DB source EBI def: "Database source EBI." [PSI:PI] is_a: MS:1001012 ! database source [Term] id: MS:1001253 name: DB source NCBI def: "Database source NCBI." [PSI:PI] is_a: MS:1001012 ! database source [Term] id: MS:1001254 name: DB source UniProt def: "Database source UniProt." [PSI:PI] is_a: MS:1001012 ! database source [Term] id: MS:1001255 name: fragment mass type average def: "Mass type setting for fragment mass was average isotopic." [PSI:PI] is_a: MS:1001210 ! mass type settings [Term] id: MS:1001256 name: fragment mass type mono def: "Mass type setting for fragment mass was monoisotopic." [PSI:PI] is_a: MS:1001210 ! mass type settings [Term] id: MS:1001257 name: param: v ion def: "Parameter information, type of product: side chain loss v ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001258 name: param: d ion def: "Parameter information, type of product: side chain loss d ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001259 name: param: immonium ion def: "Parameter information, type of product: immonium ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001260 name: param: w ion def: "Parameter information, type of product: side chain loss w ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001261 name: param: x ion def: "Parameter information, type of product: x ion with charge on the C-terminal side." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001262 name: param: y ion def: "Parameter information, type of product: y ion with charge on the C-terminal side." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001263 name: param: z ion def: "Parameter information, type of product: z ion with charge on the C-terminal side." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001266 name: role type def: "Role of a Person or Organization." [PSI:PI] is_a: MS:1000585 ! contact attribute [Term] id: MS:1001267 name: software vendor def: "Software vendor role." [PSI:PI] is_a: MS:1001266 ! role type [Term] id: MS:1001268 name: programmer def: "Programmer role." [PSI:PI] is_a: MS:1001266 ! role type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001269 name: instrument vendor def: "Instrument vendor role." [PSI:PI] is_a: MS:1001266 ! role type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001270 name: lab personnel def: "Lab personnel role." [PSI:PI] is_a: MS:1001266 ! role type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001271 name: researcher def: "Researcher role." [PSI:PI] is_a: MS:1001266 ! role type [Term] id: MS:1001272 name: (?<=R)(?\!P) def: "Regular expression for Arg-C." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001273 name: (?=[BD]) def: "Regular expression for Asp-N." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001274 name: (?=[DE]) def: "Regular expression for Asp-N-ambic." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001275 name: ProteinScape SearchEvent def: "Source data for this mzIdentML was a ProteinScape SearchEvent." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001276 name: ProteinScape Gel def: "Source data for this mzIdentML was a ProteinScape Gel." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001283 name: decoy DB accession regexp def: "Specify the regular expression for decoy accession numbers." [PSI:PI] is_a: MS:1001450 ! decoy DB details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001284 name: decoy DB derived from def: "OBSOLETE The name of the database, the search database was derived from." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_a: MS:1001450 ! decoy DB details is_obsolete: true [Term] id: MS:1001285 name: database IPI_mouse def: "International Protein Index database for Mus musculus sequences." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001286 name: database IPI_rat def: "International Protein Index database for Rattus norvegicus sequences." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001287 name: database IPI_zebrafish def: "International Protein Index database for Danio rerio sequences." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001288 name: database IPI_chicken def: "International Protein Index database for Gallus gallus sequences." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001289 name: database IPI_cow def: "International Protein Index database for Bos taurus sequences." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001290 name: database IPI_arabidopsis def: "International Protein Index database for Arabidopsis thaliana sequences." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1001291 name: decoy DB from nr def: "OBSOLETE Decoy database from a non-redundant GenBank sequence database." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001292 name: decoy DB from IPI_rat def: "OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001293 name: decoy DB from IPI_mouse def: "OBSOLETE Decoy database from a International Protein Index database for Mus musculus." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001294 name: decoy DB from IPI_arabidopsis def: "OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001295 name: decoy DB from EST def: "OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001296 name: decoy DB from IPI_zebrafish def: "OBSOLETE Decoy database from a International Protein Index database for Danio rerio." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001297 name: decoy DB from UniProtKB/Swiss-Prot def: "OBSOLETE Decoy database from a Swiss-Prot protein sequence database." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001298 name: decoy DB from IPI_chicken def: "OBSOLETE Decoy database from a International Protein Index database for Gallus gallus." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001299 name: decoy DB from IPI_cow def: "OBSOLETE Decoy database from a International Protein Index database for Bos taurus." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001300 name: decoy DB from IPI_human def: "OBSOLETE Decoy database from a International Protein Index database for Homo sapiens." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1001301 name: protein rank def: "The rank of the protein in a list sorted by the search engine." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001302 name: search engine specific input parameter def: "Search engine specific input parameters." [PSI:PI] is_a: MS:1002093 ! search engine input parameter [Term] id: MS:1001303 name: Arg-C def: "Endoproteinase Arg-C." [PSI:PI] synonym: "Trypsin/R" EXACT [] synonym: "Clostripain" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001272 ! (?<=R)(?!P) [Term] id: MS:1001304 name: Asp-N def: "Endoproteinase Asp-N." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001273 ! (?=[BD]) [Term] id: MS:1001305 name: Asp-N_ambic def: "Enzyme Asp-N, Ammonium Bicarbonate (AmBic)." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001274 ! (?=[DE]) [Term] id: MS:1001306 name: Chymotrypsin def: "Enzyme chymotrypsin." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001332 ! (?<=[FYWL])(?!P) [Term] id: MS:1001307 name: CNBr def: "Cyanogen bromide." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001333 ! (?<=M) [Term] id: MS:1001308 name: Formic_acid def: "Formic acid." [PubChem_Compound:284] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001334 ! ((?<=D))|((?=D)) [Term] id: MS:1001309 name: Lys-C def: "Endoproteinase Lys-C." [PSI:PI] synonym: "Trypsin/K" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001335 ! (?<=K)(?!P) [Term] id: MS:1001310 name: Lys-C/P def: "Proteinase Lys-C/P." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001336 ! (?<=K) [Term] id: MS:1001311 name: PepsinA def: "PepsinA proteinase." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001337 ! (?<=[FL]) [Term] id: MS:1001312 name: TrypChymo def: "Cleavage agent TrypChymo." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001338 ! (?<=[FYWLKR])(?!P) [Term] id: MS:1001313 name: Trypsin/P def: "Cleavage agent Trypsin/P." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001339 ! (?<=[KR]) [Term] id: MS:1001314 name: V8-DE def: "Cleavage agent V8-DE." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001340 ! (?<=[BDEZ])(?!P) [Term] id: MS:1001315 name: V8-E def: "Cleavage agent V8-E." [PSI:PI] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001341 ! (?<=[EZ])(?!P) [Term] id: MS:1001316 name: Mascot:SigThreshold def: "Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05)." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001317 name: Mascot:MaxProteinHits def: "The number of protein hits to display in the report. If 'Auto', all protein hits that have a protein score exceeding the average peptide identity threshold are reported. Otherwise an integer at least 1." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001318 name: Mascot:ProteinScoringMethod def: "Mascot protein scoring method; either 'Standard' or 'MudPIT'." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001319 name: Mascot:MinMSMSThreshold def: "Mascot peptide match ion score threshold. If between 0 and 1, then peptide matches whose expect value exceeds the thresholds are suppressed; if at least 1, then peptide matches whose ion score is below the threshold are suppressed." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001320 name: Mascot:ShowHomologousProteinsWithSamePeptides def: "If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001321 name: Mascot:ShowHomologousProteinsWithSubsetOfPeptides def: "If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001322 name: Mascot:RequireBoldRed def: "Only used in Peptide Summary and Select Summary reports. If true, a peptide match must be 'bold red' to be included in the report; bold red means the peptide is a top ranking match in a query and appears for the first time (in linear order) in the list of protein hits." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001323 name: Mascot:UseUnigeneClustering def: "If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001324 name: Mascot:IncludeErrorTolerantMatches def: "If true, then the search results are error tolerant and peptide matches from the second pass are included in search results. Otherwise no error tolerant peptide matches are included." [http://www.matrixscience.com/help/error_tolerant_help.html] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001325 name: Mascot:ShowDecoyMatches def: "If true, then the search results are against an automatically generated decoy database and the reported peptide matches and protein hits come from the decoy database. Otherwise peptide matches and protein hits come from the original database." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001326 name: add_others def: "OBSOLETE." [PSI:PI] comment: This former purgatory term was made obsolete. is_obsolete: true [Term] id: MS:1001327 name: Spectronaut def: "Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data." [https://doi.org/10.1074/mcp.M114.044305] is_a: MS:1001456 ! analysis software is_a: MS:1003207 ! library creation software [Term] id: MS:1001328 name: OMSSA:evalue def: "OMSSA E-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001329 name: OMSSA:pvalue def: "OMSSA p-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001330 name: X\!Tandem:expect def: "The X!Tandem expectation value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001331 name: X\!Tandem:hyperscore def: "The X!Tandem hyperscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001332 name: (?<=[FYWL])(?\!P) def: "Regular expression for Chymotrypsin." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001333 name: (?<=M) def: "Regular expression for CNBr." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001334 name: ((?<=D))|((?=D)) def: "Regular expression for formic acid." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001335 name: (?<=K)(?\!P) def: "Regular expression for Lys-C." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001336 name: (?<=K) def: "Regular expression for Lys-C/P." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001337 name: (?<=[FL]) def: "Regular expression for PepsinA." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001338 name: (?<=[FYWLKR])(?\!P) def: "Regular expression for TrypChymo." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001339 name: (?<=[KR]) def: "Regular expression for Trypsin/P." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001340 name: (?<=[BDEZ])(?\!P) def: "Regular expression for V8-DE." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001341 name: (?<=[EZ])(?\!P) def: "Regular expression for V8-E." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001342 name: database sequence details def: "Details about a single database sequence." [PSI:PI] is_a: MS:1001011 ! search database details [Term] id: MS:1001343 name: NA sequence def: "The sequence is a nucleic acid sequence." [PSI:PI] is_a: MS:1001342 ! database sequence details [Term] id: MS:1001344 name: AA sequence def: "The sequence is a amino acid sequence." [PSI:PI] is_a: MS:1001342 ! database sequence details [Term] id: MS:1001345 name: mass table source def: "Children of this term specify the source of the mass table used." [PSI:PI] is_a: MS:1001354 ! mass table options [Term] id: MS:1001346 name: AAIndex mass table def: "The masses used in the mass table are taken from AAIndex." [PSI:PI] is_a: MS:1001345 ! mass table source [Term] id: MS:1001347 name: database file formats def: "The children of this term define file formats of the sequence database used." [PSI:PI] is_a: MS:1001011 ! search database details [Term] id: MS:1001348 name: FASTA format def: "The sequence database was stored in the FASTA format." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1001349 name: ASN.1 def: "The sequence database was stored in the Abstract Syntax Notation 1 format." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1001350 name: NCBI *.p* def: "The sequence database was stored in the NCBI formatdb (*.p*) format." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1001351 name: clustal aln def: "ClustalW ALN (multiple alignment) format." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1001352 name: embl em def: "EMBL entry format." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1001353 name: NBRF PIR def: "The NBRF PIR was used as format." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1001354 name: mass table options def: "Root node for options for the mass table used." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001355 name: peptide descriptions def: "Descriptions of peptides." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute [Term] id: MS:1001356 name: spectrum descriptions def: "Descriptions of the input spectra." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001357 name: spectrum quality descriptions def: "Description of the quality of the input spectrum." [PSI:PI] is_a: MS:1001356 ! spectrum descriptions [Term] id: MS:1001358 name: msmsEval quality def: "This term reports the quality of the spectrum assigned by msmsEval." [PSI:PI] is_a: MS:1001357 ! spectrum quality descriptions relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001359 name: ambiguous residues def: "Children of this term describe ambiguous residues." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001360 name: alternate single letter codes def: "List of standard residue one letter codes which are used to replace a non-standard." [PSI:PI] is_a: MS:1001359 ! ambiguous residues relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001361 name: alternate mass def: "List of masses a non-standard letter code is replaced with." [PSI:PI] is_a: MS:1001359 ! ambiguous residues relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001362 name: number of unmatched peaks def: "The number of unmatched peaks." [PSI:PI] is_a: MS:1002345 ! PSM-level attribute relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001363 name: peptide unique to one protein def: "A peptide matching only one." [PSI:PI] is_a: MS:1001127 ! peptide sharing details [Term] id: MS:1001364 name: peptide sequence-level global FDR def: "Estimation of the global false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1002703 ! peptide sequence-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001365 name: frag: internal yb ion def: "Fragmentation information, type of product: internal yb ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001366 name: frag: internal ya ion def: "Fragmentation information, type of product: internal ya ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001367 name: frag: z+1 ion def: "Fragmentation information, type of product: z+1 ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001368 name: frag: z+2 ion def: "Fragmentation information, type of product: z+2 ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001369 name: text format def: "Simple text file format of \"m/z [intensity]\" values for a PMF (or single MS2) search." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001370 name: Mascot:homology threshold def: "The Mascot result 'homology threshold'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001371 name: Mascot:identity threshold def: "The Mascot result 'identity threshold'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001372 name: SEQUEST:Sequences is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001373 name: SEQUEST:TIC def: "SEQUEST total ion current." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001374 name: SEQUEST:Sum is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001375 name: Phenyx:Instrument Type def: "The instrument type parameter value in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001376 name: Phenyx:Scoring Model def: "The selected scoring model in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001377 name: Phenyx:Default Parent Charge def: "The default parent charge value in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001378 name: Phenyx:Trust Parent Charge def: "The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001379 name: Phenyx:Turbo def: "The turbo mode parameter in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001380 name: Phenyx:Turbo:ErrorTol def: "The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001381 name: Phenyx:Turbo:Coverage def: "The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001382 name: Phenyx:Turbo:Series def: "The list of ion series considered in the turbo mode of Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001383 name: Phenyx:MinPepLength def: "The minimal number of residues for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001384 name: Phenyx:MinPepzscore def: "The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001385 name: Phenyx:MaxPepPvalue def: "The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001386 name: Phenyx:AC Score def: "The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001387 name: Phenyx:Conflict Resolution def: "The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used." [PSI:PI] is_a: MS:1002097 ! Phenyx input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001388 name: Phenyx:AC def: "The primary sequence database identifier of a protein in Phenyx." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001389 name: Phenyx:ID def: "A secondary sequence database identifier of a protein in Phenyx." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001390 name: Phenyx:Score def: "The protein score of a protein match in Phenyx." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001391 name: Phenyx:Peptides1 def: "First number of phenyx result \"#Peptides\"." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001392 name: Phenyx:Peptides2 def: "Second number of phenyx result \"#Peptides\"." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001393 name: Phenyx:Auto def: "The value of the automatic peptide acceptance filter in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001394 name: Phenyx:User def: "The value of the user-defined peptide acceptance filter in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001395 name: Phenyx:Pepzscore def: "The z-score value of a peptide sequence match in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001396 name: Phenyx:PepPvalue def: "The p-value of a peptide sequence match in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001397 name: Phenyx:NumberOfMC def: "The number of missed cleavages of a peptide sequence in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001398 name: Phenyx:Modif def: "The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001399 name: OMSSA csv format def: "Source file for this mzIdentML was in OMSSA csv file format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001400 name: OMSSA xml format def: "Source file for this mzIdentML was in OMSSA xml file format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001401 name: X\!Tandem xml format def: "Source file for this mzIdentML was in X!Tandem xml file format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001405 name: spectrum identification result details def: "This subsection describes terms which can describe details of spectrum identification results." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001406 name: param: internal yb ion def: "Parameter information, type of product: internal yb ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001407 name: param: internal ya ion def: "Parameter information, type of product: internal ya ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001408 name: param: z+1 ion def: "Parameter information, type of product: z+1 ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001409 name: param: z+2 ion def: "Parameter information, type of product: z+2 ion." [PSI:PI] is_a: MS:1002473 ! ion series considered in search [Term] id: MS:1001410 name: translation start codons def: "The translation start codons used to translate the nucleotides to amino acids." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001411 name: search tolerance specification def: "Specification of the search tolerance." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1001412 name: search tolerance plus value is_a: MS:1001411 ! search tolerance specification relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001413 name: search tolerance minus value is_a: MS:1001411 ! search tolerance specification relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001414 name: MGF scans def: "OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000797 relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001415 name: MGF raw scans def: "OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000798 relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001416 name: spectrum title def: "OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details is_obsolete: true replaced_by: MS:1000796 relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001417 name: SpectraST:dot def: "SpectraST dot product of two spectra, measuring spectral similarity." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001418 name: SpectraST:dot_bias def: "SpectraST measure of how much of the dot product is dominated by a few peaks." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001419 name: SpectraST:discriminant score F def: "SpectraST spectrum score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001420 name: SpectraST:delta def: "SpectraST normalised difference between dot product of top hit and runner-up." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001421 name: pepXML format def: "The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001422 name: protXML format def: "The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001423 name: translation table description def: "A URL that describes the translation table used to translate the nucleotides to amino acids." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001424 name: ProteinExtractor:Methodname def: "Name of the used method in the ProteinExtractor algorithm." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001425 name: ProteinExtractor:GenerateNonRedundant def: "Flag indicating if a non redundant scoring should be generated." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001426 name: ProteinExtractor:IncludeIdentified def: "Flag indicating if identified proteins should be included." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001427 name: ProteinExtractor:MaxNumberOfProteins def: "The maximum number of proteins to consider." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001428 name: ProteinExtractor:MaxProteinMass def: "The maximum considered mass for a protein." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001429 name: ProteinExtractor:MinNumberOfPeptides def: "The minimum number of proteins to consider." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001430 name: ProteinExtractor:UseMascot def: "Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001431 name: ProteinExtractor:MascotPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001432 name: ProteinExtractor:MascotUniqueScore def: "In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001433 name: ProteinExtractor:MascotUseIdentityScore is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001434 name: ProteinExtractor:MascotWeighting def: "Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001435 name: ProteinExtractor:UseSequest def: "Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001436 name: ProteinExtractor:SequestPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001437 name: ProteinExtractor:SequestUniqueScore def: "In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001438 name: ProteinExtractor:SequestWeighting def: "Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001439 name: ProteinExtractor:UseProteinSolver def: "Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001440 name: ProteinExtractor:ProteinSolverPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001441 name: ProteinExtractor:ProteinSolverUniqueScore def: "In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001442 name: ProteinExtractor:ProteinSolverWeighting def: "Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001443 name: ProteinExtractor:UsePhenyx def: "Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score." [PSI:PI] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001444 name: ProteinExtractor:PhenyxPeptideScoreThreshold def: "Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001445 name: ProteinExtractor:PhenyxUniqueScore def: "In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001446 name: ProteinExtractor:PhenyxWeighting def: "Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor." [DOI:10.4172/jpb.1000056] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001447 name: prot:FDR threshold def: "False-discovery rate threshold for proteins." [PSI:PI] is_a: MS:1002485 ! protein-level statistical threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001448 name: pep:FDR threshold def: "False-discovery rate threshold for peptides." [PSI:PI] is_a: MS:1002484 ! peptide-level statistical threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001449 name: OMSSA e-value threshold def: "Threshold for OMSSA e-value for quality estimation." [PSI:PI] is_a: MS:1002099 ! OMSSA input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001450 name: decoy DB details def: "Details of decoy generation and database structure." [PSI:PI] is_a: MS:1001011 ! search database details [Term] id: MS:1001451 name: decoy DB generation algorithm def: "Name of algorithm used for decoy generation." [PSI:PI] is_a: MS:1001450 ! decoy DB details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001452 name: decoy DB type shuffle def: "Decoy type: Amino acids of protein sequences are used in a random order." [PSI:PI] is_a: MS:1001450 ! decoy DB details [Term] id: MS:1001453 name: DB composition only decoy def: "Decoy database composition: database contains only decoy entries." [PSI:PI] is_a: MS:1001450 ! decoy DB details [Term] id: MS:1001454 name: quality estimation with implicite decoy sequences def: "Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy)." [PSI:PI] is_a: MS:1001060 ! quality estimation method details [Term] id: MS:1001455 name: acquisition software def: "Acquisition software." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001456 name: analysis software def: "Analysis software." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001457 name: data processing software def: "Data processing software." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001458 name: spectrum generation information def: "Vocabularies describing the spectrum generation information." [PSI:PI] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1001459 name: file format def: "Format of data files." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1001460 name: unknown modification def: "This term should be given if the modification was unknown." [PSI:PI] is_a: MS:1001471 ! peptide modification details [Term] id: MS:1001461 name: greylag def: "Greylag identification software." [http://greylag.org/] is_a: MS:1001456 ! analysis software [Term] id: MS:1001462 name: PEFF format def: "The sequence database was stored in the PEFF (PSI enhanced FastA file) format." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1001463 name: Phenyx XML format def: "Phenyx open XML file format." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001464 name: DTASelect format def: "DTASelect file format." [PMID:12643522, http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001466 name: MS2 format def: "MS2 file format for MS2 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603, http://fields.scripps.edu/sequest/SQTFormat.html] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001467 name: taxonomy: NCBI TaxID def: "This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001468 name: taxonomy: common name def: "This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001469 name: taxonomy: scientific name def: "This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001470 name: taxonomy: Swiss-Prot ID def: "This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible." [PSI:PI] is_a: MS:1001089 ! molecule taxonomy relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001471 name: peptide modification details def: "The children of this term can be used to describe modifications." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001472 name: selected ion monitoring chromatogram def: "Representation of an array of the measurements of a selectively monitored ion versus time." [PSI:MS] synonym: "SIM chromatogram" EXACT [] is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1001473 name: selected reaction monitoring chromatogram def: "Representation of an array of the measurements of a selectively monitored reaction versus time." [PSI:MS] synonym: "SRM chromatogram" EXACT [] is_a: MS:1000810 ! ion current chromatogram [Term] id: MS:1001474 name: consecutive reaction monitoring chromatogram def: "OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time." [PSI:MS] comment: This term was made obsolete because, by design, it can't be properly represented in mzML 1.1. CRM experiments must be represented in a spectrum-centric way. synonym: "CRM chromatogram" EXACT [] is_a: MS:1000810 ! ion current chromatogram is_obsolete: true [Term] id: MS:1001475 name: OMSSA def: "Open Mass Spectrometry Search Algorithm was used to analyze the spectra." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001476 name: X\!Tandem def: "X!Tandem was used to analyze the spectra." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001477 name: SpectraST def: "Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline." [PSI:PI] is_a: MS:1001456 ! analysis software is_a: MS:1003207 ! library creation software [Term] id: MS:1001478 name: Mascot Parser def: "Mascot Parser was used to analyze the spectra." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001479 name: null-terminated ASCII string def: "Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte." [PSI:MS] is_a: MS:1000518 ! binary data type [Term] id: MS:1001480 name: SCIEX TOF/TOF nativeID format def: "Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1001481 name: SCIEX TOF/TOF database def: "Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001482 name: 5800 TOF/TOF def: "SCIEX 5800 TOF-TOF Analyzer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1001483 name: SCIEX TOF/TOF Series Explorer Software def: "SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis." [PSI:MS] is_a: MS:1000690 ! SCIEX software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001484 name: intensity normalization def: "Normalization of data point intensities." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1001485 name: m/z calibration def: "Calibration of data point m/z positions." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1001486 name: data filtering def: "Filtering out part of the data." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1001487 name: ProteinExtractor def: "An algorithm for protein determination/assembly integrated into Bruker's ProteinScape." [PSI:MS] is_a: MS:1000692 ! Bruker software is_a: MS:1001456 ! analysis software [Term] id: MS:1001488 name: Mascot Distiller def: "Mascot Distiller." [PSI:PI] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1001489 name: Mascot Integra def: "Mascot Integra." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001490 name: Percolator def: "Percolator." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1001491 name: percolator:Q value def: "Percolator:Q value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001492 name: percolator:score def: "Percolator:score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001493 name: percolator:PEP def: "Posterior error probability." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001494 name: no threshold def: "In case no threshold was used." [PSI:PI] is_a: MS:1002482 ! statistical threshold [Term] id: MS:1001495 name: ProteinScape:SearchResultId def: "The SearchResultId of this peptide as SearchResult in the ProteinScape database." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001496 name: ProteinScape:SearchEventId def: "The SearchEventId of the SearchEvent in the ProteinScape database." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001497 name: ProteinScape:ProfoundProbability def: "The Profound probability score stored by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001498 name: Profound:z value def: "The Profound z value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001499 name: Profound:Cluster def: "The Profound cluster score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001500 name: Profound:ClusterRank def: "The Profound cluster rank." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001501 name: MSFit:Mowse score def: "The MSFit Mowse score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001502 name: Sonar:Score def: "The Sonar score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001503 name: ProteinScape:PFFSolverExp def: "The ProteinSolver exp value stored by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001504 name: ProteinScape:PFFSolverScore def: "The ProteinSolver score stored by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001505 name: ProteinScape:IntensityCoverage def: "The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001506 name: ProteinScape:SequestMetaScore def: "The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001507 name: ProteinExtractor:Score def: "The score calculated by ProteinExtractor." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001508 name: Agilent MassHunter nativeID format def: "Native format defined by scanId=xsd:nonNegativeInteger." [PSI:PI] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1001509 name: Agilent MassHunter format def: "A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001510 name: TSQ Vantage def: "TSQ Vantage." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001511 name: Sequence database filter types def: "Filter types which are used to filter a sequence database." [PSI:PI] is_a: MS:1001019 ! database filtering [Term] id: MS:1001512 name: Sequence database filters def: "Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search." [PSI:PI] is_a: MS:1001019 ! database filtering [Term] id: MS:1001513 name: DB sequence filter pattern def: "DB sequence filter pattern." [PSI:MS] is_a: MS:1001512 ! Sequence database filters relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001514 name: DB accession filter string def: "DB accession filter string." [PSI:MS] is_a: MS:1001512 ! Sequence database filters relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001515 name: frag: c ion - H2O def: "Fragmentation information, type of product: c ion without water." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001516 name: frag: c ion - NH3 def: "Fragmentation information, type of product: c ion without ammonia." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001517 name: frag: z ion - H2O def: "Fragmentation information, type of product: z ion without water." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001518 name: frag: z ion - NH3 def: "Fragmentation information, type of product: z ion without ammonia." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001519 name: frag: x ion - H2O def: "Fragmentation information, type of product: x ion without water." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001520 name: frag: x ion - NH3 def: "Fragmentation information, type of product: x ion without ammonia." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001521 name: frag: precursor ion - H2O def: "Fragmentation information, type of product: precursor ion without water." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001522 name: frag: precursor ion - NH3 def: "Fragmentation information, type of product: precursor ion without ammonia." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001523 name: frag: precursor ion def: "Fragmentation information, type of product: precursor ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1001524 name: fragment neutral loss def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001525 name: precursor neutral loss def: "This term can describe a neutral loss m/z value that is lost from an ion." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001526 name: spectrum from database integer nativeID format def: "Native format defined by databasekey=xsd:long." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1001527 name: Proteinscape spectra def: "Spectra from Bruker/Protagen Proteinscape database." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001528 name: Mascot query number def: "Native format defined by query=xsd:nonNegativeInteger." [PSI:MS] comment: The spectrum (query) number in a Mascot results file, starting from 1. is_a: MS:1000767 ! native spectrum identifier format is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1001529 name: spectra data details def: "Child-terms contain information to map the results back to spectra." [PSI:MS] is_a: MS:1001249 ! search input details [Term] id: MS:1001530 name: mzML unique identifier def: "Native format defined by mzMLid=xsd:IDREF." [PSI:MS] comment: A unique identifier of a spectrum stored in an mzML file. is_a: MS:1001529 ! spectra data details [Term] id: MS:1001531 name: spectrum from ProteinScape database nativeID format def: "Native format defined by databasekey=xsd:long." [PSI:MS] comment: A unique identifier of a spectrum stored in a ProteinScape database. is_a: MS:1000767 ! native spectrum identifier format is_a: MS:1001529 ! spectra data details [Term] id: MS:1001532 name: spectrum from database string nativeID format def: "Native format defined by databasekey=xsd:string." [PSI:MS] comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier). is_a: MS:1000767 ! native spectrum identifier format is_a: MS:1001529 ! spectra data details [Term] id: MS:1001533 name: Bruker Daltonics esquire series def: "Bruker Daltonics' esquire series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001534 name: Bruker Daltonics flex series def: "Bruker Daltonics' flex series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001535 name: Bruker Daltonics BioTOF series def: "Bruker Daltonics' BioTOF series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001536 name: Bruker Daltonics micrOTOF series def: "Bruker Daltonics' micrOTOF series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001537 name: BioTOF def: "Bruker Daltonics' BioTOF: ESI TOF." [PSI:MS] is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1001538 name: BioTOF III def: "Bruker Daltonics' BioTOF III: ESI TOF." [PSI:MS] is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1001539 name: UltroTOF-Q def: "Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional)." [PSI:MS] is_a: MS:1001535 ! Bruker Daltonics BioTOF series [Term] id: MS:1001540 name: micrOTOF II def: "Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1001541 name: maXis def: "Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI." [PSI:MS] is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1001542 name: amaZon ETD def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR." [PSI:MS] is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] id: MS:1001543 name: microflex LRF def: "Bruker Daltonics' microflex LRF: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001544 name: ultrafleXtreme def: "Bruker Daltonics' ultrafleXtreme: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001545 name: Bruker Daltonics amaZon series def: "Bruker Daltonics' amaZon series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001546 name: amaZon X def: "Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS] is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] id: MS:1001547 name: Bruker Daltonics maXis series def: "Bruker Daltonics' maXis series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001548 name: Bruker Daltonics solarix series def: "Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001549 name: solariX def: "Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR." [PSI:MS] is_a: MS:1001548 ! Bruker Daltonics solarix series [Term] id: MS:1001550 name: microflex II def: "Bruker Daltonics' microflex II: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001553 name: autoflex II TOF/TOF def: "Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001554 name: autoflex III TOF/TOF smartbeam def: "Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001555 name: autoflex def: "Bruker Daltonics' autoflex: MALDI TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1001556 name: Bruker Daltonics apex series def: "Bruker Daltonics' apex series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1001557 name: Shimadzu Corporation software def: "Shimadzu Corporation software." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001558 name: MALDI Solutions def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS] is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software is_a: MS:1001557 ! Shimadzu Corporation software [Term] id: MS:1001559 name: SCIEX TOF/TOF T2D nativeID format def: "Native format defined by file=xsd:IDREF." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1001560 name: SCIEX TOF/TOF T2D format def: "Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001561 name: Scaffold def: "Scaffold analysis software." [http://www.proteomesoftware.com] is_a: MS:1001456 ! analysis software [Term] id: MS:1001562 name: Scaffold nativeID format def: "Scaffold native ID format." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1001563 name: SEQUEST SQT format def: "Source file for this mzIdentML was in SEQUEST SQT format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001564 name: Discoverer MSF format def: "Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001565 name: IdentityE XML format def: "Source file for this mzIdentML was in Waters IdentityE XML format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001566 name: ProteinLynx XML format def: "Source file for this mzIdentML was in Waters ProteinLynx XML format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001567 name: SpectrumMill directories def: "Source file for this mzIdentML was in Agilent SpectrumMill directory format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1001568 name: Scaffold:Peptide Probability def: "Scaffold peptide probability score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001569 name: IdentityE Score def: "Waters IdentityE peptide score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001570 name: ProteinLynx:Log Likelihood def: "ProteinLynx log likelihood score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001571 name: ProteinLynx:Ladder Score def: "Waters ProteinLynx Ladder score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001572 name: SpectrumMill:Score def: "Spectrum mill peptide score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001573 name: SpectrumMill:SPI def: "SpectrumMill SPI score (%)." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001574 name: report only spectra assigned to identified proteins def: "Flag indicating to report only the spectra assigned to identified proteins." [PSI:PI] is_a: MS:1001060 ! quality estimation method details [Term] id: MS:1001575 name: Scaffold: Minimum Peptide Count def: "Minimum number of peptides a protein must have to be accepted." [PSI:PI] is_a: MS:1002106 ! Scaffold input parameter relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1001576 name: Scaffold: Minimum Protein Probability def: "Minimum protein probability a protein must have to be accepted." [PSI:PI] is_a: MS:1002106 ! Scaffold input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001577 name: Scaffold: Minimum Peptide Probability def: "Minimum probability a peptide must have to be accepted for protein scoring." [PSI:PI] is_a: MS:1002106 ! Scaffold input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001578 name: minimum number of enzymatic termini def: "Minimum number of enzymatic termini a peptide must have to be accepted." [PSI:PI] is_a: MS:1002094 ! common search engine input parameter relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001579 name: Scaffold:Protein Probability def: "Scaffold protein probability score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001580 name: SpectrumMill:Discriminant Score def: "Discriminant score from Agilent SpectrumMill software." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001581 name: FAIMS compensation voltage def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] synonym: "FAIMS CV" EXACT [] is_a: MS:1002892 ! ion mobility attribute is_a: MS:1000455 ! ion selection attribute is_a: MS:1003254 ! peak attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001582 name: XCMS def: "Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data." [PSI:MS] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001583 name: MaxQuant def: "MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1001584 name: combined pmf + ms-ms search def: "Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF)." [PSI:MS] is_a: MS:1001080 ! search type [Term] id: MS:1001585 name: MyriMatch def: "Tabb Lab software for directly comparing peptides in a database to tandem mass spectra." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1001586 name: DirecTag def: "Tabb Lab software for generating sequence tags from tandem mass spectra." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1001587 name: TagRecon def: "Tabb Lab software for reconciling sequence tags to a protein database." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1001588 name: Pepitome def: "Tabb Lab software for spectral library searches on tandem mass spectra." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1001589 name: MyriMatch:MVH def: "Using the multivariate hypergeometric distribution and a peak list divided into several intensity classes, this score is the negative natural log probability that the predicted peaks matched to experimental peaks by random chance." [PSI:MS] synonym: "Pepitome:MVH" EXACT [] synonym: "TagRecon:MVH" EXACT [] is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1001590 name: MyriMatch:mzFidelity def: "The negative natural log probability that predicted peaks match to experimental peaks by random chance by scoring the m/z delta of the matches in a multinomial distribution." [PSI:MS] synonym: "Pepitome:mzFidelity" EXACT [] synonym: "TagRecon:mzFidelity" EXACT [] is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1001591 name: anchor protein def: "A representative protein selected from a set of sequence same-set or spectrum same-set proteins." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001592 name: family member protein def: "A protein with significant homology to another protein, but some distinguishing peptide matches." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001593 name: group member with undefined relationship OR ortholog protein def: "TO ENDETAIL: a really generic relationship OR ortholog protein." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship [Term] id: MS:1001594 name: sequence same-set protein def: "A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001595 name: spectrum same-set protein def: "A protein which is indistinguishable or equivalent to another protein, having matches to a set of peptide sequences that cannot be distinguished using the evidence in the mass spectra." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001596 name: sequence sub-set protein def: "A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001597 name: spectrum sub-set protein def: "A protein with a sub-set of the matched spectra for another protein, where the matches cannot be distinguished using the evidence in the mass spectra, and no distinguishing peptide matches." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001598 name: sequence subsumable protein def: "A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001599 name: spectrum subsumable protein def: "A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001600 name: protein inference confidence category def: "Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable)." [PSI:MS] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001601 name: ProteomeDiscoverer:Spectrum Files:Raw File names def: "OBSOLETE Name and location of the .raw file or files." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001602 name: ProteomeDiscoverer:SRF File Selector:SRF File Path def: "OBSOLETE Path and name of the .srf (SEQUEST Result Format) file." [PSI:MS] comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001603 name: ProteomeDiscoverer:Spectrum Selector:Ionization Source def: "OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc)." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'inlet type' (MS:1000007) or 'ionization type' (MS:1000008) terms instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001604 name: ProteomeDiscoverer:Activation Type def: "OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any)." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001605 name: ProteomeDiscoverer:Spectrum Selector:Lower RT Limit def: "Lower retention-time limit." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001606 name: ProteomeDiscoverer:Mass Analyzer def: "OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS)." [PSI:MS] comment: This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001607 name: ProteomeDiscoverer:Max Precursor Mass def: "Maximum mass limit of a singly charged precursor ion." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001608 name: ProteomeDiscoverer:Min Precursor Mass def: "Minimum mass limit of a singly charged precursor ion." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001609 name: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count def: "Minimum number of peaks in a tandem mass spectrum that is allowed to pass the filter and to be subjected to further processing in the workflow." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001610 name: ProteomeDiscoverer:MS Order def: "OBSOLETE Level of the mass spectrum (MS2 ... MS10)." [PSI:MS] comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001611 name: ProteomeDiscoverer:Polarity Mode def: "OBSOLETE Polarity mode (positive or negative)." [PSI:MS] comment: This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001612 name: ProteomeDiscoverer:Spectrum Selector:Precursor Selection def: "Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001613 name: ProteomeDiscoverer:SN Threshold def: "Signal-to-Noise ratio below which peaks are removed." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001614 name: ProteomeDiscoverer:Scan Type def: "OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM))." [PSI:MS] comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579), MSn spectrum (MS:1000580), CRM spectrum (MS:1000581), SIM spectrum (MS:1000582) or SRM spectrum (MS:1000583) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001615 name: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold def: "Used to filter out tandem mass spectra that have a total intensity current(sum of the intensities of all peaks in a spectrum) below the specified value." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001616 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements def: "Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001617 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements def: "Specifies the charge state of the precursor ions, if it is not defined in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001618 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements def: "Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001619 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements def: "Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001620 name: ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements def: "Specifies the polarity of the ions monitored if it is not included in the scan header." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001621 name: ProteomeDiscoverer:Spectrum Selector:Upper RT Limit def: "Upper retention-time limit." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001622 name: ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset def: "Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001623 name: ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass def: "Maximum allowed mass of a neutral loss." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001624 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor def: "Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001625 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks def: "Determines whether neutral loss peaks are removed from ETD and ECD spectra." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001626 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses def: "Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001627 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones def: "Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001628 name: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak def: "Determines whether precursor artifact peaks from the MS2 input spectra are removed." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001629 name: ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch def: "Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001630 name: ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch def: "Determines whether spectra from different MS order scans can be grouped together." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001631 name: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference def: "OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species." [PSI:MS] comment: This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001632 name: ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion def: "Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001633 name: ProteomeDiscoverer:Xtract:Highest Charge def: "Highest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001634 name: ProteomeDiscoverer:Xtract:Highest MZ def: "OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] comment: This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001635 name: ProteomeDiscoverer:Xtract:Lowest Charge def: "Lowest charge state that is allowed for the deconvolution of multiply charged data." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001636 name: ProteomeDiscoverer:Xtract:Lowest MZ def: "OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract." [PSI:MS] comment: This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001637 name: ProteomeDiscoverer:Xtract:Monoisotopic Mass Only def: "Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001638 name: ProteomeDiscoverer:Xtract:Overlapping Remainder def: "Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001639 name: ProteomeDiscoverer:Xtract:Required Fitting Accuracy def: "Accuracy required for a pattern fit to be considered valid." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001640 name: ProteomeDiscoverer:Xtract:Resolution At 400 def: "Resolution at mass 400." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001641 name: ProteomeDiscoverer:Lowest Charge State def: "Minimum charge state below which peptides are filtered out." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001642 name: ProteomeDiscoverer:Highest Charge State def: "Maximum charge above which peptides are filtered out." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001643 name: ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores def: "Determines whether spectra with scores above the threshold score are retained rather than filtered out." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001644 name: ProteomeDiscoverer:Dynamic Modification def: "Determine dynamic post-translational modifications (PTMs)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001645 name: ProteomeDiscoverer:Static Modification def: "Static Modification to all occurrences of a named amino acid." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001646 name: ProteomeDiscoverer:Mascot:Decoy Search def: "OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database." [PSI:MS] comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001647 name: ProteomeDiscoverer:Mascot:Error tolerant Search def: "Determines whether to search error-tolerant." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001648 name: ProteomeDiscoverer:Mascot:Max MGF File Size def: "Maximum size of the .mgf (Mascot Generic Format) file in MByte." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001649 name: ProteomeDiscoverer:Mascot:Mascot Server URL def: "URL (Uniform resource Locator) of the Mascot server." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001650 name: ProteomeDiscoverer:Mascot:Number of attempts to submit the search def: "Number of attempts to submit the Mascot search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001651 name: ProteomeDiscoverer:Mascot:X Static Modification def: "Number of attempts to submit the Mascot search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001652 name: ProteomeDiscoverer:Mascot:User Name def: "OBSOLETE Name of the user submitting the Mascot search." [PSI:MS] comment: This term was made obsolete because it's recommended to use researcher (MS:1001271) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001653 name: ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search def: "Time interval between attempts to submit a search in seconds." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001654 name: ProteomeDiscoverer:Enzyme Name def: "OBSOLETE Specifies the enzyme reagent used for protein digestion." [PSI:MS] comment: This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001655 name: ProteomeDiscoverer:Fragment Mass Tolerance def: "OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu." [PSI:MS] comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001656 name: Mascot:Instrument def: "Type of instrument used to acquire the data in the raw file." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001657 name: ProteomeDiscoverer:Maximum Missed Cleavage Sites def: "Maximum number of missed cleavage sites to consider during the digest." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001658 name: ProteomeDiscoverer:Mascot:Peptide CutOff Score def: "Minimum score in the IonScore column that each peptide must exceed in order to be reported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001659 name: ProteomeDiscoverer:Precursor Mass Tolerance def: "OBSOLETE Mass window for which precursor ions are considered to be the same species." [PSI:MS] comment: This term was made obsolete because it's recommended to use search tolerance minus value (MS:1001413) or search tolerance plus value (MS:1001412) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001660 name: ProteomeDiscoverer:Mascot:Protein CutOff Score def: "Minimum protein score in the IonScore column that each protein must exceed in order to be reported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001661 name: ProteomeDiscoverer:Protein Database def: "OBSOLETE Database to use in the search (configured on the Mascot server)." [PSI:MS] comment: This term was made obsolete because it's recommended to use database name (MS:1001013) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001662 name: ProteomeDiscoverer:Mascot:Protein Relevance Factor def: "Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001663 name: ProteomeDiscoverer:Target FDR Relaxed def: "Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001664 name: ProteomeDiscoverer:Target FDR Strict def: "Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001665 name: ProteomeDiscoverer:Mascot:Taxonomy def: "OBSOLETE Limits searches to entries from a particular species or group of species." [PSI:MS] comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001666 name: ProteomeDiscoverer:Use Average Precursor Mass def: "OBSOLETE Use average mass for the precursor." [PSI:MS] comment: This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001667 name: Mascot:use MudPIT scoring def: "OBSOLETE Determines whether to use MudPIT or normal scoring." [PSI:MS] comment: This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead. is_a: MS:1002095 ! Mascot input parameter is_obsolete: true relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001668 name: ProteomeDiscoverer:Absolute XCorr Threshold def: "Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001669 name: ProteomeDiscoverer:SEQUEST:Calculate Probability Score def: "Determines whether to calculate a probability score for every peptide match." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001670 name: ProteomeDiscoverer:SEQUEST:CTerminal Modification def: "Dynamic C-terminal modification that is used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001671 name: ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage def: "Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001672 name: ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide def: "Maximum number of identical modifications that a single peptide can have." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001673 name: ProteomeDiscoverer:Max Modifications Per Peptide def: "Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001674 name: ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered def: "Maximum number of peptides that are searched and scored per spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001675 name: ProteomeDiscoverer:Maximum Peptides Output def: "Maximum number of peptide matches reported per spectrum." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001676 name: ProteomeDiscoverer:Maximum Protein References Per Peptide def: "Maximum number of proteins that a single identified peptide can be associated with during protein assembly." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001677 name: ProteomeDiscoverer:SEQUEST:NTerminal Modification def: "Dynamic N-terminal modification that is used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001678 name: ProteomeDiscoverer:Peptide CTerminus def: "Static modification for the C terminal of the peptide used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001679 name: ProteomeDiscoverer:Peptide NTerminus def: "Static modification for the N terminal of the peptide used during the search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001680 name: ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor def: "Specifies a factor to apply to the protein score." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001681 name: ProteomeDiscoverer:Protein Relevance Threshold def: "Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001682 name: ProteomeDiscoverer:Search Against Decoy Database def: "OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database." [PSI:MS] comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001683 name: ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses def: "Use average masses for the fragments." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001684 name: ProteomeDiscoverer:Use Neutral Loss a Ions def: "Determines whether a ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001685 name: ProteomeDiscoverer:Use Neutral Loss b Ions def: "Determines whether b ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001686 name: ProteomeDiscoverer:Use Neutral Loss y Ions def: "Determines whether y ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001687 name: ProteomeDiscoverer:Use Neutral Loss z Ions def: "Determines whether z ions with neutral loss are used for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001688 name: ProteomeDiscoverer:SEQUEST:Weight of a Ions def: "Uses a ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001689 name: ProteomeDiscoverer:SEQUEST:Weight of b Ions def: "Uses b ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001690 name: ProteomeDiscoverer:SEQUEST:Weight of c Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001691 name: ProteomeDiscoverer:SEQUEST:Weight of d Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001692 name: ProteomeDiscoverer:SEQUEST:Weight of v Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001693 name: ProteomeDiscoverer:SEQUEST:Weight of w Ions def: "Uses c ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001694 name: ProteomeDiscoverer:SEQUEST:Weight of x Ions def: "Uses x ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001695 name: ProteomeDiscoverer:SEQUEST:Weight of y Ions def: "Uses y ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001696 name: ProteomeDiscoverer:SEQUEST:Weight of z Ions def: "Uses z ions for spectrum matching with this relative factor." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001697 name: ProteomeDiscoverer:ZCore:Protein Score Cutoff def: "Sets a minimum protein score that each protein must exceed in order to be reported." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001698 name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method def: "Specifies which peak to select if more than one peak is found inside the integration window." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001699 name: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance def: "Specifies the mass-to-charge window that enables one to look for the reporter peaks." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001700 name: ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method def: "Quantitation method for isobarically labeled quantitation." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001701 name: ProteomeDiscoverer:Spectrum Exporter:Export Format def: "OBSOLETE Format of the exported spectra (dta, mgf or mzData)." [PSI:MS] comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001702 name: ProteomeDiscoverer:Spectrum Exporter:File name def: "Name of the output file that contains the exported data." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001703 name: ProteomeDiscoverer:Search Modifications Only For Identified Proteins def: "Influences the modifications search." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001704 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1 def: "Standard high confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001705 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2 def: "Standard high confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001706 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3 def: "Standard high confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001707 name: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4 def: "Standard high confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001708 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1 def: "Standard medium confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001709 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2 def: "Standard medium confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001710 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3 def: "Standard medium confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001711 name: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4 def: "Standard medium confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001712 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1 def: "FT high confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001713 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2 def: "FT high confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001714 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3 def: "FT high confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001715 name: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4 def: "FT high confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001716 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1 def: "FT medium confidence XCorr parameter for charge = 1." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001717 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2 def: "FT medium confidence XCorr parameter for charge = 2." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001718 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3 def: "FT medium confidence XCorr parameter for charge = 3." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001719 name: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4 def: "FT medium confidence XCorr parameter for charge >= 4." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001720 name: ProteomeDiscoverer:1. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001721 name: ProteomeDiscoverer:2. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001722 name: ProteomeDiscoverer:3. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001723 name: ProteomeDiscoverer:4. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001724 name: ProteomeDiscoverer:Static Modification for X def: "Static Modification for X." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001725 name: ProteomeDiscoverer:Initial minimal peptide probability def: "Minimal initial peptide probability to contribute to analysis." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001726 name: ProteomeDiscoverer:Minimal peptide probability def: "Minimum adjusted peptide probability contributing to protein probability." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001727 name: ProteomeDiscoverer:Minimal peptide weight def: "Minimum peptide weight contributing to protein probability." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001728 name: ProteomeDiscoverer:Number of input1 spectra def: "Number of spectra from 1+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001729 name: ProteomeDiscoverer:Number of input2 spectra def: "Number of spectra from 2+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001730 name: ProteomeDiscoverer:Number of input3 spectra def: "Number of spectra from 3+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001731 name: ProteomeDiscoverer:Number of input4 spectra def: "Number of spectra from 4+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001732 name: ProteomeDiscoverer:Number of input5 spectra def: "Number of spectra from 5+ precursor ions." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001733 name: ProteomeDiscoverer:Number of predicted correct proteins def: "Total number of predicted correct protein ids (sum of probabilities)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001734 name: ProteomeDiscoverer:Organism def: "OBSOLETE Sample organism (used for annotation purposes)." [PSI:MS] comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001735 name: ProteomeDiscoverer:Reference Database def: "OBSOLETE Full path database name." [PSI:MS] comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001736 name: ProteomeDiscoverer:Residue substitution list def: "Residues considered equivalent when comparing peptides." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001737 name: ProteomeDiscoverer:Source file extension def: "OBSOLETE File type (if not pepXML)." [PSI:MS] comment: This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001738 name: ProteomeDiscoverer:Source Files def: "OBSOLETE Input pepXML files." [PSI:MS] comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001739 name: ProteomeDiscoverer:Source Files old def: "OBSOLETE Input pepXML files (old)." [PSI:MS] comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001740 name: ProteomeDiscoverer:WinCyg reference database def: "Windows full path for database." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001741 name: ProteomeDiscoverer:WinCyg source files def: "Windows pepXML file names." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001742 name: LTQ Orbitrap Velos def: "Finnigan LTQ Orbitrap Velos MS." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001743 name: ProteomeDiscoverer:Mascot:Weight of A Ions def: "Determines if to use A ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001744 name: ProteomeDiscoverer:Mascot:Weight of B Ions def: "Determines if to use B ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001745 name: ProteomeDiscoverer:Mascot:Weight of C Ions def: "Determines if to use C ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001746 name: ProteomeDiscoverer:Mascot:Weight of D Ions def: "Determines if to use D ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001747 name: ProteomeDiscoverer:Mascot:Weight of V Ions def: "Determines if to use V ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001748 name: ProteomeDiscoverer:Mascot:Weight of W Ions def: "Determines if to use W ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001749 name: ProteomeDiscoverer:Mascot:Weight of X Ions def: "Determines if to use X ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001750 name: ProteomeDiscoverer:Mascot:Weight of Y Ions def: "Determines if to use Y ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001751 name: ProteomeDiscoverer:Mascot:Weight of Z Ions def: "Determines if to use z ions for spectrum matching." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001752 name: ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation def: "Determines if to use precursor reevaluation." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001753 name: ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly def: "Signal-to-Noise ratio below which peaks are removed (in FT mode only)." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001754 name: ProteomeDiscoverer:Mascot:Please Do not Touch this def: "Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001755 name: contact phone number def: "Phone number of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001756 name: contact fax number def: "Fax number for the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001757 name: contact toll-free phone number def: "Toll-free phone number of the contact person or organization." [PSI:MS] is_a: MS:1000585 ! contact attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001758 name: Mascot:SigThresholdType def: "Significance threshold type used in Mascot reporting (either 'identity' or 'homology')." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001759 name: Mascot:ProteinGrouping def: "Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering')." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001760 name: Percolator:features def: "List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'." [PSI:MS] is_a: MS:1002107 ! Percolator input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001761 name: ACQUITY UPLC def: "Waters LC-system ACQUITY UPLC." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001762 name: ACQUITY UPLC H-Class def: "Waters LC-system ACQUITY UPLC H-Class." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001763 name: ACQUITY UPLC H-Class Bio def: "Waters LC-system ACQUITY UPLC H-Class Bio." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001764 name: ACQUITY UPLC I-Class def: "Waters LC-system ACQUITY UPLC I-Class." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001765 name: ACQUITY UPLC Systems with 2D Technology def: "Waters LC-system ACQUITY UPLC Systems with 2D Technology." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001766 name: nanoACQUITY UPLC def: "Waters LC-system nanoACQUITY UPLC." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001767 name: nanoACQUITY UPLC System with 1D Technology def: "Waters LC-system nanoACQUITY UPLC System with 1D Technology." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001768 name: nanoACQUITY UPLC with HDX Technology def: "Waters LC-system nanoACQUITY UPLC with HDX Technology." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001769 name: TRIZAIC UPLC nanoTile def: "Waters LC-system TRIZAIC UPLC nanoTile." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001770 name: GCT Premier def: "Waters oa-ToF based GCT Premier." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001771 name: MALDI Synapt G2 HDMS def: "Waters oa-ToF based MALDI Synapt G2 HDMS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001772 name: MALDI Synapt G2 MS def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001773 name: MALDI Synapt G2-S HDMS def: "Waters oa-ToF based MALDI Synapt G2 MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001774 name: MALDI Synapt G2-S MS def: "Waters oa-ToF based MALDI Synapt G2-S MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001775 name: MALDI Synapt HDMS def: "Waters oa-ToF based MALDI Synapt HDMS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001776 name: MALDI Synapt MS def: "Waters oa-ToF based MALDI Synapt MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001777 name: Synapt G2 HDMS def: "Waters oa-ToF based Synapt G2 HDMS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001778 name: Synapt G2 MS def: "Waters oa-ToF based Synapt G2 MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001779 name: Synapt G2-S HDMS def: "Waters oa-ToF based Synapt G2-S HDMS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001780 name: Synapt G2-S MS def: "Waters oa-ToF based Synapt G2-S MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001781 name: Synapt HDMS def: "Waters oa-ToF based Synapt HDMS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001782 name: Synapt MS def: "Waters oa-ToF based Synapt MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001783 name: Xevo G2 Q-Tof def: "Waters oa-ToF based Xevo G2 Q-Tof." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001784 name: Xevo G2 Tof def: "Waters oa-ToF based Xevo G2 Tof." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001785 name: Xevo Q-Tof def: "Waters oa-ToF based Xevo Q-Tof." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001786 name: 3100 def: "Waters quadrupole based 3100." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001787 name: Acquity SQD def: "Waters quadrupole based Acquity SQD." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001788 name: Acquity TQD def: "Waters quadrupole based Acquity TQD." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001789 name: Quattro micro GC def: "Waters (triple) quadrupole based Quattro micro GC." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001790 name: Xevo TQ MS def: "Waters quadrupole based Xevo TQ MS." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001791 name: Xevo TQD def: "Waters quadrupole based Xevo TQD." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001792 name: Xevo TQ-S def: "Waters quadrupole based Xevo TQ-S." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1001793 name: Mascot:PreferredTaxonomy def: "NCBI TaxID taxonomy ID to prefer when two or more proteins match the same set of peptides or when protein entry in database represents multiple sequences." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001795 name: Empower def: "Waters Empower software for liquid chromatography and mass spectrometry acquisition." [PSI:MS] is_a: MS:1000694 ! Waters software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001796 name: UNIFY def: "Waters UNIFY software for liquid chromatography and mass spectrometry acquisition." [PSI:MS] is_a: MS:1000694 ! Waters software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001797 name: travelling wave ion mobility mass spectrometer def: "OBSOLETE An ion mobility mass spectrometry technique based on the superimposition of travelling voltage waves on a radially-confining RF voltage in a gas-filled, stacked-ring ion guide." [PSI:MS] comment: This child of the former purgatory term ion mobility spectrometry was made obsolete. synonym: "TWIMS" EXACT [] is_obsolete: true [Term] id: MS:1001798 name: LECO software def: "LECO software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001799 name: ChromaTOF software def: "Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS] is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software is_a: MS:1001798 ! LECO software [Term] id: MS:1001800 name: LECO instrument model def: "LECO instrument model." [PSI:MS] is_a: MS:1000031 ! instrument model [Term] id: MS:1001801 name: Pegasus HRT def: "LECO high resolution time-of-flight GC mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001802 name: Citius HRT def: "LECO high resolution time-of-flight LC mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001803 name: Pegasus def: "LECO GC time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001804 name: TruTOF def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001805 name: quantification datatype def: "The data type of the value reported in a QuantLayer." [PSI:MS] is_a: MS:1001129 ! quantification information [Term] id: MS:1001806 name: quantification object attribute def: "Attributes describing the details of an object relevant for reporting quantification workflows or values." [PSI:MS] is_a: MS:1001129 ! quantification information [Term] id: MS:1001807 name: study variable attribute def: "Attribute describing a study variable." [PSI:MS] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1001808 name: technical replicate def: "The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'." [PSI:MS] is_a: MS:1001807 ! study variable attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001809 name: biological replicate def: "The study variable is 'biological replicate'. This means, the run was generated from another individual or sample." [PSI:MS] is_a: MS:1001807 ! study variable attribute [Term] id: MS:1001810 name: experimental condition 'case' def: "The experimental condition is 'case' in contrast to 'control'." [PSI:MS] is_a: MS:1001807 ! study variable attribute [Term] id: MS:1001811 name: experimental condition 'control' def: "The experimental condition is 'control' in contrast to 'case'." [PSI:MS] is_a: MS:1001807 ! study variable attribute [Term] id: MS:1001812 name: experimental condition 'disease' def: "The experimental condition is 'disease' in contrast to 'healthy'." [PSI:MS] is_a: MS:1001807 ! study variable attribute [Term] id: MS:1001813 name: experimental condition 'healthy' def: "The experimental condition is 'healthy' in contrast to 'disease'." [PSI:MS] is_a: MS:1001807 ! study variable attribute [Term] id: MS:1001814 name: generic experimental condition def: "The experimental condition is given in the value of this term." [PSI:MS] is_a: MS:1001807 ! study variable attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001815 name: time series, time point X def: "The experimental design followed a time series design. The time point of this run is given in the value of this term." [PSI:MS] is_a: MS:1001807 ! study variable attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001816 name: dilution series, concentration X def: "The experimental design followed a dilution series design. The concentration of this run is given in the value of this term." [PSI:MS] is_a: MS:1001807 ! study variable attribute relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001817 name: raw file attribute def: "Attribute describing a raw file." [PSI:MS] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1001818 name: one sample run def: "The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free)." [PSI:MS] is_a: MS:1001817 ! raw file attribute [Term] id: MS:1001819 name: two sample run def: "The raw file contains the run of two samples (e.g. SILAC, metabolic labelling)." [PSI:MS] is_a: MS:1001817 ! raw file attribute [Term] id: MS:1001820 name: three sample run def: "The raw file contains the run of three samples (e.g. 3-plex SILAC)." [PSI:MS] is_a: MS:1001817 ! raw file attribute [Term] id: MS:1001821 name: four sample run def: "The raw file contains the run of four samples (e.g. 4-plex iTraq)." [PSI:MS] is_a: MS:1001817 ! raw file attribute [Term] id: MS:1001822 name: eight sample run def: "The raw file contains the run of eight samples (e.g. 8-plex iTraq)." [PSI:MS] is_a: MS:1001817 ! raw file attribute [Term] id: MS:1001823 name: raw files group attribute def: "Attribute describing, how raw files build a raw file group." [PSI:MS] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1001824 name: merge of runs of 1D gel bands def: "Attribute describing, how raw files build a raw file group." [PSI:MS] is_a: MS:1001823 ! raw files group attribute [Term] id: MS:1001825 name: feature list attribute def: "Attribute describing a feature list." [PSI:MS] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1001826 name: mass trace reporting: rectangles def: "The mass trace of the features of this feature list specifies rectangles. Each mass trace has the syntax (RT_start,MZ_start,RT_end,MZ_end), i.e. opposite corners are given." [PSI:MS] is_a: MS:1001825 ! feature list attribute [Term] id: MS:1001827 name: mass trace reporting: polygons def: "The mass trace of the features of this feature list specifies polygons. Each mass trace has the syntax (RT_1, MZ_1, RT_2, MZ_2, ... , RT_i, MZ_i, ... , RT_n, MZ_n), where the line (RT_n, MZ_n)->(RT_1, MZ_1) is implicit." [PSI:MS] is_a: MS:1001825 ! feature list attribute [Term] id: MS:1001828 name: feature attribute def: "Attribute describing a feature." [PSI:MS] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1001829 name: SRM transition ID def: "Identifier for an SRM transition in an external document describing additional information about the transition." [PSI:MS] is_a: MS:1001828 ! feature attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001830 name: Progenesis LC-MS def: "Software from Nonlinear Dynamics for LC-MS label-free workflow." [PSI:MS] is_a: MS:1001139 ! quantitation software name [Term] id: MS:1001831 name: SILACAnalyzer def: "Software for SILAC workflow." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1000752 ! TOPP software [Term] id: MS:1001832 name: quantitation software comment or customizations def: "Quantitation software comment or any customizations to the default setup of the software." [PSI:PI] is_a: MS:1001129 ! quantification information relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001833 name: quantitation analysis summary def: "The overall workflow of this quantitation report." [PSI:PI] is_a: MS:1001129 ! quantification information [Term] id: MS:1001834 name: LC-MS label-free quantitation analysis def: "LC-MS label-free workflow (RT m/z map)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1001835 name: SILAC quantitation analysis def: "SILAC workflow (heavy, light, and sometimes medium peak)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1001836 name: spectral counting quantitation analysis def: "Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1001837 name: iTRAQ quantitation analysis def: "Quantification analysis using the SCIEX amine-reactive isobaric tags for relative and absolute quantification (iTRAQ) labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near in the 114-121 m/z range." [PSI:PI, PMID:15385600] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1001838 name: SRM quantitation analysis def: "Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1001839 name: metabolic labeling 14N / 15N quantitation analysis def: "Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens)." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1001840 name: LC-MS feature intensity def: "Maximum peak intensity of the LC-MS feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001841 name: LC-MS feature volume def: "Real (intensity times area) volume of the LC-MS feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001842 name: sequence-level spectral count def: "The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001843 name: MS1 feature maximum intensity def: "Maximum intensity of MS1 feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001844 name: MS1 feature area def: "Area of MS1 feature." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001845 name: peak area def: "OBSOLETE Area of MS1 peak (e.g. SILAC, 15N)." [PSI:PI] comment: This term was made obsolete because it was a duplication of MS:1001844. is_a: MS:1001805 ! quantification datatype is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001846 name: isotopic pattern area def: "Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N)." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001847 name: reporter ion intensity def: "Intensity of MS2 reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001848 name: simple ratio of two values def: "Simple ratio of two values (enumerator and denominator)." [PSI:PI] is_a: MS:1002066 ! ratio calculation method [Term] id: MS:1001849 name: sum of MatchedFeature values def: "OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values." [PSI:PI] comment: This term was made obsolete because the concept MatchedFeature was dropped. is_a: MS:1002735 ! feature-level quantification datatype is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001850 name: normalized peptide value def: "Normalized peptide value." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001851 name: protein value: sum of peptide values def: "Protein quantification value calculated as sum of peptide values." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001852 name: normalized protein value def: "Normalized protein value." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001853 name: max fold change def: "Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis)." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001854 name: ANOVA p-value def: "Global datatype: p-value of ANOVA of group means (e.g. Progenesis)." [PSI:PI] is_a: MS:1002072 ! p-value relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001855 name: t-test p-value def: "P-value of t-Test of two groups." [PSI:PI] is_a: MS:1002072 ! p-value relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001856 name: reporter ion raw value def: "Intensity (or area) of MS2 reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001857 name: reporter ion normalized value def: "Normalized value of MS2 reporter ion (e.g. iTraq)." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001858 name: XIC area def: "Area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001859 name: normalized XIC area def: "Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM)." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001860 name: protein value: mean of peptide ratios def: "Protein quantification value calculated as mean of peptide ratios." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001861 name: quantification data processing def: "Terms used to describe types of quantification data processing." [PSI:MS] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1001862 name: normalization to mean of sum of all proteins def: "Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting)." [PSI:MS] is_a: MS:1001861 ! quantification data processing [Term] id: MS:1001863 name: quantile normalization, proteins def: "Normalization of protein values to approach the same distribution." [PSI:MS] is_a: MS:1001861 ! quantification data processing [Term] id: MS:1001864 name: quantile normalization, peptides def: "Normalization of peptide values to approach the same distribution." [PSI:MS] is_a: MS:1001861 ! quantification data processing [Term] id: MS:1001865 name: Progenesis automatic alignment def: "Automatic RT alignment of Progenesis software." [PSI:MS] is_a: MS:1001861 ! quantification data processing [Term] id: MS:1001866 name: Progenesis manual alignment def: "RT alignment of Progenesis software using automatic and manual vectors." [PSI:MS] is_a: MS:1001861 ! quantification data processing [Term] id: MS:1001867 name: Progenesis normalization def: "Normalization as performed by Progenesis LC-MS." [PSI:MS] is_a: MS:1001861 ! quantification data processing [Term] id: MS:1001868 name: distinct peptide-level q-value def: "Estimation of the q-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs, possibly with different mass modifications, mapping to the same sequence have been collapsed to one entry)." [PSI:PI] is_a: MS:1002484 ! peptide-level statistical threshold relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001869 name: protein-level q-value def: "Estimation of the q-value for proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001870 name: peptide sequence-level p-value def: "Estimation of the p-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001871 name: protein-level p-value def: "Estimation of the p-value for proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001872 name: peptide sequence-level e-value def: "Estimation of the e-value for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001873 name: protein-level e-value def: "Estimation of the e-value for proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002306 ! value greater than zero relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001874 name: FDRScore def: "OBSOLETE A smoothing of the distribution of q-values calculated for PSMs from individual search engines, such that ordering of result quality is maintained and all FDRScore values are guaranteed to have a value > 0." [PMID:19253293] comment: This term was made obsolete because it was split into the more specific terms for PSM-level FDRScore (1002355), distinct peptide-level FDRScore (MS:1002360), protein-level FDRScore (MS:1002365) and protein group-level FDRScore (MS:1002374). is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001875 name: modification motif def: "The regular expression describing the sequence motif for a modification." [PSI:PI] is_a: MS:1001056 ! modification specificity rule relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001876 name: modification probability def: "The a priori probability of a modification." [PSI:PI] is_a: MS:1001056 ! modification specificity rule [Term] id: MS:1001877 name: ChromaTOF HRT software def: "Software for acquisition, processing and analysis of data for LECO instruments." [PSI:MS] is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software is_a: MS:1001798 ! LECO software [Term] id: MS:1001878 name: MALDI Solutions Microbial Identification def: "Shimadzu Biotech software for data acquisition, processing, and analysis." [PSI:MS] is_a: MS:1001558 ! MALDI Solutions [Term] id: MS:1001879 name: offset voltage def: "The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001880 name: in-source collision-induced dissociation def: "The dissociation of an ion as a result of collisional excitation during ion transfer from an atmospheric pressure ion source and the mass spectrometer vacuum." [PSI:MS] is_a: MS:1000044 ! dissociation method [Term] id: MS:1001881 name: mz5 format def: "mz5 file format, modelled after mzML." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1001882 name: transition validation attribute def: "Attributes of the quality of a transition that affect its selection as appropriate." [PSI:MS] relationship: part_of MS:1000908 ! transition [Term] id: MS:1001883 name: coefficient of variation def: "Variation of a set of signal measurements calculated as the standard deviation relative to the mean." [PSI:MS] is_a: MS:1001882 ! transition validation attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001884 name: signal-to-noise ratio def: "Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal." [PSI:MS] is_a: MS:1001882 ! transition validation attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001885 name: command-line parameters def: "Parameters string passed to a command-line interface software application, omitting the executable name." [PSI:MS] is_a: MS:1000630 ! data processing parameter is_a: MS:1003201 ! library provenance attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001886 name: SQID def: "Software for data analysis of peptides and proteins." [PSI:MS] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001887 name: SQID:score def: "The SQID result 'Score'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1001888 name: SQID:deltaScore def: "The SQID result 'deltaScore'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic [Term] id: MS:1001889 name: SQID:protein score def: "The SQID result 'protein score'." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins [Term] id: MS:1001890 name: Progenesis:protein normalised abundance def: "The data type normalised abundance for proteins produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001891 name: Progenesis:peptide normalised abundance def: "The data type normalised abundance for peptides produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001892 name: Progenesis:protein raw abundance def: "The data type raw abundance for proteins produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001893 name: Progenesis:peptide raw abundance def: "The data type raw abundance for peptide produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001894 name: Progenesis:confidence score def: "The data type confidence score produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001895 name: Progenesis:peptide count def: "The data type peptide count produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001896 name: Progenesis:feature intensity def: "The data type feature intensity produced by Progenesis LC-MS." [PSI:MS] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001897 name: MaxQuant:peptide counts (unique) def: "The data type peptide counts (unique) produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001898 name: MaxQuant:peptide counts (all) def: "The data type peptide counts (all) produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001899 name: MaxQuant:peptide counts (razor+unique) def: "The data type peptide counts (razor+unique) produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001900 name: MaxQuant:sequence length def: "The data type sequence length produced by MaxQuant." [PSI:MS] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001901 name: MaxQuant:PEP def: "The data type PEP (posterior error probability) produced by MaxQuant." [PSI:MS] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001902 name: MaxQuant:LFQ intensity def: "The data type LFQ intensity produced by MaxQuant." [PSI:MS] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001903 name: MaxQuant:feature intensity def: "The data type feature intensity produced by MaxQuant." [PSI:MS] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001904 name: MaxQuant:MS/MS count def: "The data type MS2 count produced by MaxQuant." [PSI:MS] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1001905 name: emPAI value def: "The emPAI value of protein abundance, produced from the emPAI algorithm." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001906 name: APEX value def: "The APEX value of protein abundance, produced from the APEX software." [PSI:MS] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001907 name: retention time window width def: "The full width of a retention time window for a chromatographic peak." [PSI:MS] is_a: MS:1000915 ! retention time window attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001908 name: ISQ def: "Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001909 name: Velos Plus def: "Thermo Scientific second generation Velos." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001910 name: LTQ Orbitrap Elite def: "Thermo Scientific LTQ Orbitrap Elite, often just referred to as the Orbitrap Elite." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001911 name: Q Exactive def: "Thermo Scientific Q Exactive." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1001912 name: PinPoint def: "Thermo Scientific PinPoint SRM analysis software." [PSI:MS] is_a: MS:1000693 ! Thermo Finnigan software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001913 name: S-lens voltage def: "Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001914 name: pymzML def: "Python module to interface mzML Data." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1001915 name: leukocyte elastase def: "Enzyme leukocyte elastase (EC 3.4.21.37)." [BRENDA:3.4.21.37] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001957 ! (?<=[ALIV])(?!P) [Term] id: MS:1001916 name: proline endopeptidase def: "Enzyme proline endopeptidase (EC 3.4.21.26)." [BRENDA:3.4.21.26] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001958 ! (?<=[HKR]P)(?!P) [Term] id: MS:1001917 name: glutamyl endopeptidase def: "Enzyme glutamyl endopeptidase (EC 3.4.21.19)." [BRENDA:3.4.21.19] synonym: "staphylococcal protease" EXACT [] synonym: "Glu-C" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001959 ! (?<=[^E]E) [Term] id: MS:1001918 name: 2-iodobenzoate def: "Chemical iodobenzoate. Cleaves after W." [PubChem_Compound:4739928] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001960 ! (?<=W) [Term] id: MS:1001919 name: ProteomeXchange accession number def: "Main identifier of a ProteomeXchange dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001921 name: ProteomeXchange accession number version number def: "Version number of a ProteomeXchange accession number." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001922 name: Digital Object Identifier (DOI) def: "DOI unique identifier of a publication." [PSI:PI, http://dx.doi.org] synonym: "doi" EXACT [] is_a: MS:1000878 ! external reference identifier relationship: has_regexp MS:1002480 ! (10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+) relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001923 name: external reference keyword def: "Free text attribute that can enrich the information about an entity." [PSI:PI] is_a: MS:1002840 ! external reference data relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001924 name: journal article keyword def: "Keyword present in a scientific publication." [PSI:PI] is_a: MS:1001923 ! external reference keyword relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001925 name: submitter keyword def: "Keyword assigned by the data submitter." [PSI:PI] is_a: MS:1001923 ! external reference keyword relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001926 name: curator keyword def: "Keyword assigned by a data curator." [PSI:PI] is_a: MS:1001923 ! external reference keyword relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001927 name: Tranche file hash def: "Hash assigned by the Tranche resource to an individual file." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001928 name: Tranche project hash def: "Hash assigned by the Tranche resource to a whole project." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001929 name: PRIDE experiment URI def: "URI that allows the access to one experiment in the PRIDE database." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001930 name: PRIDE project URI def: "URI that allows the access to one project in the PRIDE database." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1001931 name: source interface def: "The source interface." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001932 name: source interface model def: "The source interface model." [PSI:MS] relationship: part_of MS:1001931 ! source interface relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001933 name: source sprayer def: "The source sprayer." [PSI:MS] relationship: part_of MS:1000458 ! source relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001934 name: source sprayer type def: "The source sprayer type." [PSI:MS] relationship: part_of MS:1001933 ! source sprayer [Term] id: MS:1001935 name: source sprayer manufacturer def: "The source sprayer manufacturer." [PSI:MS] relationship: part_of MS:1001933 ! source sprayer relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001936 name: source sprayer model def: "The source sprayer model." [PSI:MS] relationship: part_of MS:1001933 ! source sprayer relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001937 name: sample plate def: "Plate where the sample solution is spotted in a MALDI or similar instrument." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001938 name: sample plate type def: "The sample plate type." [PSI:MS] relationship: part_of MS:1001937 ! sample plate [Term] id: MS:1001939 name: stainless steel plate def: "Stainless steel plate." [PSI:MS] is_a: MS:1001938 ! sample plate type [Term] id: MS:1001940 name: coated glass plate def: "Coated glass plate." [PSI:MS] is_a: MS:1001938 ! sample plate type [Term] id: MS:1001941 name: electrospray supply type def: "Whether the sprayer is fed or is loaded with sample once." [PSI:MS] relationship: part_of MS:1000458 ! source [Term] id: MS:1001942 name: static supply electrospray def: "The sprayer is loaded with sample once." [PSI:MS] is_a: MS:1001941 ! electrospray supply type [Term] id: MS:1001943 name: fed supply electrospray def: "The sprayer is continuously fed with sample." [PSI:MS] is_a: MS:1001941 ! electrospray supply type [Term] id: MS:1001944 name: Collision cell exit potential def: "Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000218 ! volt synonym: "CXP" EXACT [] relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001945 name: Pegasus 4D def: "LECO nominal mass resolution time-of-flight GCxGC mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1001946 name: PEAKS Studio def: "PEAKS Studio software for data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001947 name: PEAKS Online def: "PEAKS Online software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001948 name: PEAKS Node def: "PEAKS Node software for high throughput data analysis." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1001949 name: BSI software def: "Bioinformatics Solutions Inc. Software for data processing and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1001950 name: PEAKS:peptideScore def: "The PEAKS peptide '-10lgP Score'." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001951 name: PEAKS:proteinScore def: "The PEAKS protein '-10lgP Score'." [PSI:MS] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001952 name: ZCore:probScore def: "The ZCore probability score." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001953 name: source interface manufacturer def: "The source interface manufacturer." [PSI:MS] relationship: part_of MS:1001931 ! source interface relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001954 name: acquisition parameter def: "Parameters used in the mass spectrometry acquisition." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001955 name: no cleavage def: "No cleavage." [PSI:MS] is_a: MS:1001045 ! cleavage agent name [Term] id: MS:1001956 name: unspecific cleavage def: "Unspecific cleavage." [PSI:MS] is_a: MS:1001045 ! cleavage agent name [Term] id: MS:1001957 name: (?<=[ALIV])(?!P) def: "Regular expression for leukocyte elastase." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001958 name: (?<=[HKR]P)(?!P) def: "Regular expression for proline endopeptidase." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001959 name: (?<=[^E]E) def: "Regular expression for glutamyl endopeptidase." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001960 name: (?<=W) def: "Regular expression for 2-iodobenzoate." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1001961 name: peptide spectrum match scoring algorithm def: "Algorithm used to score the match between a spectrum and a peptide ion." [PSI:MS] relationship: part_of MS:1001458 ! spectrum generation information relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001962 name: Mascot:C13 counts def: "C13 peaks to use in peak detection." [PSI:MS] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1001963 name: ProteinExtractor:Weighting def: "Weighting factor for protein list compilation by ProteinExtractor." [PSI:MS] is_a: MS:1002098 ! ProteinExtractor input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001964 name: ProteinScape:second round Mascot def: "Flag indicating a second round search with Mascot." [PSI:MS] is_a: MS:1002100 ! ProteinScape input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001965 name: ProteinScape:second round Phenyx def: "Flag indicating a second round search with Phenyx." [PSI:MS] is_a: MS:1002100 ! ProteinScape input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1001966 name: product ion mobility def: "The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry." [PSI:MS] is_a: MS:1001221 ! product ion attribute [Term] id: MS:1001967 name: product ion drift time def: "OBSOLETE The ion drift time of an MS2 product ion." [PSI:MS] is_a: MS:1002222 ! SRM transition attribute relationship: has_units UO:0000028 ! millisecond comment: This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476). is_obsolete: true relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1001968 name: PTM localization PSM-level statistic def: "Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level." [PSI:MS] is_a: MS:1002689 ! PTM localization single result statistic [Term] id: MS:1001969 name: phosphoRS score def: "phosphoRS score for PTM site location at the PSM-level." [DOI:10.1021/pr200611n, PMID:22073976] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001970 name: phosphoRS sequence probability def: "Probability that the respective isoform is correct." [DOI:10.1021/pr200611n, PMID:22073976] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001971 name: phosphoRS site probability def: "Estimate of the probability that the respective site is truly phosphorylated." [DOI:10.1021/pr200611n, PMID:22073976] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001972 name: PTM scoring algorithm version def: "Version of the post-translational modification scoring algorithm." [PSI:MS] is_a: MS:1001471 ! peptide modification details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001973 name: DeBunker def: "DeBunker software." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1001974 name: DeBunker:score def: "Score specific to DeBunker." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001975 name: delta m/z def: "The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value." [PSI:MS] synonym: "m/z difference" EXACT [] is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001976 name: delta M def: "The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value." [PSI:MS] synonym: "mass difference" EXACT [] is_a: MS:1001405 ! spectrum identification result details relationship: has_units UO:0000166 ! parts per notation unit relationship: has_units UO:0000169 ! parts per million relationship: has_units UO:0000187 ! percent relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1001977 name: MSQuant def: "MSQuant software." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1001978 name: MSQuant:PTM-score def: "The PTM score from MSQuant software." [DOI:10.1021/pr900721e, PMID:19888749] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001979 name: MaxQuant:PTM Score def: "The PTM score from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001980 name: MaxQuant:Phospho (STY) Probabilities def: "The Phospho (STY) Probabilities from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001981 name: MaxQuant:Phospho (STY) Score Diffs def: "The Phospho (STY) Score Diffs from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001982 name: MaxQuant:P-site localization probability def: "The P-site localization probability value from MaxQuant software." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001983 name: MaxQuant:PTM Delta Score def: "The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest)." [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001984 name: Ascore software def: "Ascore software." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1001985 name: Ascore def: "A-score for PTM site location at the PSM-level." [DOI:10.1038/nbt1240, PMID:16964243] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001986 name: H-Score def: "H-Score for peptide phosphorylation site location." [DOI:10.1021/pr1006813, PMID:20836569] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1001987 name: vacuum drying MALDI sample preparation def: "Vacuum-drying MALDI sample preparation crystallization method." [PSI:MS] is_a: MS:1000833 ! matrix application type [Term] id: MS:1001988 name: crushed crystal MALDI sample preparation def: "Crushed-crystal MALDI sample preparation method." [PSI:MS] is_a: MS:1000833 ! matrix application type [Term] id: MS:1001989 name: fast evaporation MALDI sample preparation def: "Fast-evaporation MALDI sample preparation method." [DOI:10.1021/ac00091a044] is_a: MS:1000833 ! matrix application type [Term] id: MS:1001990 name: overlayer MALDI sample preparation def: "Overlayer method combining features of the crushed-crystal method and the fast-evaporation method." [PSI:MS] is_a: MS:1000833 ! matrix application type [Term] id: MS:1001991 name: sandwich MALDI sample preparation def: "Sandwich MALDI sample preparation method." [DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4] is_a: MS:1000833 ! matrix application type [Term] id: MS:1001992 name: spin coating MALDI sample preparation def: "Spin coating MALDI sample preparation method." [DOI:10.1021/cc0500710, PMID:16283807] is_a: MS:1000833 ! matrix application type [Term] id: MS:1001993 name: quick and dirty MALDI sample preparation def: "Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling." [PSI:MS] is_a: MS:1000833 ! matrix application type [Term] id: MS:1001994 name: top hat baseline reduction def: "Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'." [PSI:MS] is_a: MS:1000593 ! baseline reduction [Term] id: MS:1001995 name: convex hull baseline reduction def: "Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures." [PSI:MS] is_a: MS:1000593 ! baseline reduction [Term] id: MS:1001996 name: median baseline reduction def: "The spectrum that will be baseline subtracted is divided into a number of segments." [PSI:MS] is_a: MS:1000593 ! baseline reduction [Term] id: MS:1001997 name: wavelet transformation smoothing def: "The random noise is removed by using the undecimated wavelet transform." [DOI:10.1093/bioinformatics/btl355, PMID:16820428] is_a: MS:1000592 ! smoothing [Term] id: MS:1001998 name: sophisticated numerical annotation procedure def: "It searches for known patterns in the measured spectrum." [DOI:10.1021/ac951158i, PMID:21619291] synonym: "SNAP" EXACT [] is_a: MS:1000801 ! area peak picking [Term] id: MS:1001999 name: area normalization def: "Normalization of areas below the curves." [PSI:MS] is_a: MS:1001484 ! intensity normalization [Term] id: MS:1002000 name: LIFT def: "A Bruker's proprietary technique where molecular ions are initially accelerated at lower energy, then collide with inert gas in a collision cell that is then 'lifted' to high potential. The use of inert gas is optional, as it could lift also fragments provided by LID." [DOI:10.1007/s00216-003-2057-0 , PMID:12830354] is_a: MS:1000044 ! dissociation method [Term] id: MS:1002001 name: MS1 label-based raw feature quantitation def: "MS1 label-based raw feature quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002002 name: MS1 label-based peptide level quantitation def: "MS1 label-based peptide level quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002003 name: MS1 label-based protein level quantitation def: "MS1 label-based protein level quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002004 name: MS1 label-based proteingroup level quantitation def: "MS1 label-based proteingroup level quantitation." [PSI:PI] is_a: MS:1002018 ! MS1 label-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002005 name: iRT retention time normalization standard def: "A de facto standard providing the retention times at which a specific set of 10 reference peptides exit the reference chromatographic column. The kit may be obtain from Biognosys." [DOI:10.1002/pmic.201100463, http://www.biognosys.ch/products/rt-kit.html] is_a: MS:1000901 ! retention time normalization standard [Term] id: MS:1002006 name: SRM transition type def: "The type of the transitions, e.g. target or decoy." [PSI:MS] synonym: "MRM transition type" EXACT [] relationship: part_of MS:1000908 ! transition [Term] id: MS:1002007 name: target SRM transition def: "A transition used to target a specific compound that may be in the sample." [PSI:MS] synonym: "target MRM transition" EXACT [] is_a: MS:1002006 ! SRM transition type [Term] id: MS:1002008 name: decoy SRM transition def: "A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows." [PSI:MS] synonym: "decoy MRM transition" EXACT [] is_a: MS:1002006 ! SRM transition type [Term] id: MS:1002009 name: isobaric label quantitation analysis def: "Quantitation analysis using an isobaric labelling workflow." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1002010 name: TMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher amine-reactive tandem mass tag (TMT) labelling workflow, wherein 2-10 reporter ions are measured in MS2 spectra in the 126-131 m/z." [PSI:PI, PMID:12713048] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002011 name: desorption electrospray ionization def: "Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure." [DOI:10.1126/science.1104404, PMID:15486296] synonym: "DESI" EXACT [] is_a: MS:1000240 ! atmospheric pressure ionization [Term] id: MS:1002012 name: Mascot:PTM site assignment confidence def: "Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score)." [http://www.matrixscience.com/help/pt_mods_help.html#SITE] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_units UO:0000187 ! percent relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002013 name: collision energy ramp start def: "Collision energy at the start of the collision energy ramp." [PSI:PI] is_a: MS:1000045 ! collision energy relationship: has_units UO:0000266 ! electronvolt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002014 name: collision energy ramp end def: "Collision energy at the end of the collision energy ramp." [PSI:PI] is_a: MS:1000045 ! collision energy relationship: has_units UO:0000266 ! electronvolt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002015 name: spectral count peptide level quantitation def: "Spectral count peptide level quantitation." [PSI:PI] is_a: MS:1001836 ! spectral counting quantitation analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002016 name: spectral count protein level quantitation def: "Spectral count protein level quantitation." [PSI:PI] is_a: MS:1001836 ! spectral counting quantitation analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002017 name: spectral count proteingroup level quantitation def: "Spectral count proteingroup level quantitation." [PSI:PI] is_a: MS:1001836 ! spectral counting quantitation analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002018 name: MS1 label-based analysis def: "MS1 label-based analysis." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1002019 name: label-free raw feature quantitation def: "Label-free raw feature quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002020 name: label-free peptide level quantitation def: "Label-free peptide level quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002021 name: label-free protein level quantitation def: "Label-free protein level quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002022 name: label-free proteingroup level quantitation def: "Label-free proteingroup level quantitation." [PSI:PI] is_a: MS:1001834 ! LC-MS label-free quantitation analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002023 name: MS2 tag-based analysis def: "MS2 tag-based analysis." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1002024 name: MS2 tag-based feature level quantitation def: "MS2 tag-based feature level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002025 name: MS2 tag-based peptide level quantitation def: "MS2 tag-based peptide level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002026 name: MS2 tag-based protein level quantitation def: "MS2 tag-based protein level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002027 name: MS2 tag-based proteingroup level quantitation def: "MS2 tag-based proteingroup level quantitation." [PSI:PI] is_a: MS:1002023 ! MS2 tag-based analysis relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002028 name: nucleic acid base modification def: "Nucleic acid base modification (substitution, insertion or deletion)." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002029 name: original nucleic acid sequence def: "Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002030 name: modified nucleic acid sequence def: "Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002031 name: PASSEL transition group browser URI def: "URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002032 name: PeptideAtlas dataset URI def: "URI that allows access to a PeptideAtlas dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002033 name: contact role def: "Role of the contact person." [PSI:PI] is_a: MS:1000585 ! contact attribute [Term] id: MS:1002034 name: first author def: "The first of a set of authors associated with a publication or release. There may be more than one first author in cases where several authors share primary attribution." [PSI:MS] is_a: MS:1002033 ! contact role [Term] id: MS:1002035 name: senior author def: "The last of a set of authors associated with a publication or release. There may be more than one senior author in cases where several authors share senior attribution." [PSI:MS] is_a: MS:1002033 ! contact role [Term] id: MS:1002036 name: co-author def: "One of a set of authors associated with a publication or release." [PSI:MS] is_a: MS:1002033 ! contact role [Term] id: MS:1002037 name: dataset submitter def: "A person who submits a dataset to a repository." [PSI:MS] is_a: MS:1002033 ! contact role [Term] id: MS:1002038 name: label free sample def: "A sample that has not been labelled or modified. This is often referred to as \"light\" to distinguish from \"heavy\"." [PSI:PI] synonym: "light sample" EXACT [] is_a: MS:1000548 ! sample attribute [Term] id: MS:1002039 name: inlet attribute def: "Inlet properties that are associated with a value." [PSI:MS] is_a: MS:1000547 ! object attribute relationship: part_of MS:1000458 ! source [Term] id: MS:1002040 name: inlet temperature def: "The temperature of the inlet of a mass spectrometer." [PSI:MS] is_a: MS:1000482 ! source attribute is_a: MS:1002039 ! inlet attribute relationship: has_units UO:0000012 ! kelvin relationship: has_units UO:0000027 ! degree Celsius relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002041 name: source temperature def: "The temperature of the source of a mass spectrometer." [PSI:MS] is_a: MS:1000482 ! source attribute relationship: has_units UO:0000012 ! kelvin relationship: has_units UO:0000027 ! degree Celsius relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002042 name: modulation time def: "The duration of a complete cycle of modulation in a comprehensive two-dimensional separation system, equals the length of a second dimension chromatogram, i.e., the time between two successive injections into the second column." [http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429] is_a: MS:1000857 ! run attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002043 name: ProteinProspector def: "ProteinProspector software for data acquisition and analysis." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002044 name: ProteinProspector:score def: "The ProteinProspector result 'Score'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002045 name: ProteinProspector:expectation value def: "The ProteinProspector result 'Expectation value'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002046 name: native source path def: "The original source path used for directory-based sources." [PSI:MS] is_a: MS:1001458 ! spectrum generation information relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002047 name: MS-GF def: "MS-GF software used to re-score the peptide-spectrum matches." [DOI:10.1074/mcp.M110.003731, PMID:20829449] is_a: MS:1001456 ! analysis software [Term] id: MS:1002048 name: MS-GF+ synonym: "MS-GFDB" EXACT [] def: "MS-GF+ software used to analyze the spectra." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002049 name: MS-GF:RawScore def: "MS-GF raw score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002050 name: MS-GF:DeNovoScore def: "MS-GF de novo score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002051 name: MS-GF:Energy def: "MS-GF energy score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002052 name: MS-GF:SpecEValue def: "MS-GF spectral E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002053 name: MS-GF:EValue def: "MS-GF E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002054 name: MS-GF:QValue def: "MS-GF Q-value." [PSI:PI] is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002055 name: MS-GF:PepQValue def: "MS-GF peptide-level Q-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002056 name: MS-GF:PEP def: "MS-GF posterior error probability." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002057 name: modification specificity protein N-term def: "As parameter for search engine: apply the modification only at the N-terminus of a protein." [PSI:PI] is_a: MS:1001056 ! modification specificity rule [Term] id: MS:1002058 name: modification specificity protein C-term def: "As parameter for search engine: apply the modification only at the C-terminus of a protein." [PSI:PI] is_a: MS:1001056 ! modification specificity rule [Term] id: MS:1002059 name: Microsoft Excel def: "Microsoft Excel (can be used for spectral counting)." [PSI:PI] is_a: MS:1001139 ! quantitation software name [Term] id: MS:1002060 name: database UniProtKB/TrEMBL def: "The name of the UniProtKB/TrEMBL database." [PSI:PI] is_a: MS:1002126 ! database UniProtKB [Term] id: MS:1002061 name: decoy DB from UniProtKB/TrEMBL def: "OBSOLETE Decoy database from a TrEMBL protein sequence database." [PSI:PI] comment: This term was made obsolete, because a combination of database name, DB composition , decoy DB type , decoy DB generation algorithm, decoy DB accession regexp and decoy DB details suffices. is_obsolete: true [Term] id: MS:1002062 name: metabolic labelling: natural N (mainly 14N) def: "Metabolic labelling: natural N (mainly 14N)." [PSI:PI] is_a: MS:1001055 ! modification parameters [Term] id: MS:1002063 name: FindPairs def: "Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite." [http://www.medizinisches-proteom-center.de/software] is_a: MS:1001139 ! quantitation software name [Term] id: MS:1002064 name: peptide consensus RT def: "Peptide consensus retention time." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002065 name: peptide consensus m/z def: "Peptide consensus mass/charge ratio." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002066 name: ratio calculation method def: "Method used to calculate the ratio." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002067 name: protein value: median of peptide ratios def: "Protein quantification value calculated as median of peptide ratios." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002068 name: metabolic labelling: heavy N (mainly 15N) def: "Metabolic labelling: heavy N (mainly 15N)." [PSI:PI] is_a: MS:1001055 ! modification parameters [Term] id: MS:1002069 name: metabolic labelling purity def: "Metabolic labelling: Description of labelling purity. Usually the purity of feeding material (e.g. 95%), or the inclusion rate derived from isotopic peak pattern shape." [PSI:PI] is_a: MS:1001055 ! modification parameters relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002070 name: t-test def: "Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed." [PSI:PI] is_a: MS:1001861 ! quantification data processing relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002071 name: ANOVA-test def: "Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed." [PSI:PI] is_a: MS:1001861 ! quantification data processing relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002072 name: p-value def: "P-value as result of one of the processing steps described. Specify in the description, which processing step it was." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002073 name: mzIdentML format def: "The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'." [PSI:PI, http://www.psidev.info/mzidentml] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1002074 name: quantification file format def: "File format containing quantification results." [PSI:PI] is_a: MS:1001459 ! file format [Term] id: MS:1002075 name: mzQuantML format def: "The mzQuantML format for quantification data from the PSI. File extension '.mzq'." [PSI:PI, http://www.psidev.info/mzquantml] is_a: MS:1002074 ! quantification file format [Term] id: MS:1002076 name: PAnalyzer def: "PAnalyzer software for getting protein evidence categories." [http://code.google.com/p/ehu-bio/wiki/PAnalyzer] is_a: MS:1001456 ! analysis software [Term] id: MS:1002077 name: impact def: "Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002078 name: ProteomeDiscoverer:1. Static Modification def: "OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002079 name: ProteomeDiscoverer:2. Static Modification def: "OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002080 name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before def: "Precursor clipping range before." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002081 name: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After def: "Precursor clipping range after." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002082 name: first column elution time def: "The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002083 name: second column elution time def: "The time of elution from the second chromatographic column in the chromatographic separation step, relative to the start of the chromatography on the second column." [PSI:MS] is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000010 ! second relationship: has_units UO:0000031 ! minute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002084 name: multidimensional chromatography modulation description def: "Multidimensional chromatography modulation description." [PSI:MS] is_a: MS:1000857 ! run attribute [Term] id: MS:1002085 name: two-dimensional gas chromatography with fixed modulation time def: "Two-dimensional gas chromatography where a single modulation time is used throughout the acquisition." [PSI:MS] is_a: MS:1002084 ! multidimensional chromatography modulation description [Term] id: MS:1002086 name: two-dimensional gas chromatography with discrete modulation time steps def: "Two-dimensional gas chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS] is_a: MS:1002084 ! multidimensional chromatography modulation description [Term] id: MS:1002087 name: two-dimensional liquid chromatography with fixed modulation time def: "Two-dimensional liquid chromatography where a single modulation time is used throughout the acquisition." [PSI:MS] is_a: MS:1002084 ! multidimensional chromatography modulation description [Term] id: MS:1002088 name: two-dimensional liquid chromatography with discrete modulation time steps def: "Two-dimensional liquid chromatography where the acquisition is divided into steps, each with a different modulation time." [PSI:MS] is_a: MS:1002084 ! multidimensional chromatography modulation description [Term] id: MS:1002089 name: ProteomeDiscoverer:Peptide Without Protein XCorr Threshold def: "XCorr threshold for storing peptides that do not belong to a protein." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002090 name: Calculate Probability Scores def: "Flag indicating that a probability score for the assessment that a reported peptide match is a random occurrence is calculated." [PSI:MS] is_a: MS:1002094 ! common search engine input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002091 name: ProteomeDiscoverer:Maximum Delta Cn def: "Delta Cn threshold for filtering out PSM's." [PSI:MS] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002092 name: Percolator:Validation based on def: "Algorithm (e.g. q-value or PEP) used for calculation of the validation score using Percolator." [PSI:MS] is_a: MS:1002107 ! Percolator input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002093 name: search engine input parameter def: "Search engine input parameter." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1002094 name: common search engine input parameter def: "Search engine input parameter that is shared by more than one search engine." [PSI:PI] is_a: MS:1002093 ! search engine input parameter [Term] id: MS:1002095 name: Mascot input parameter def: "Search engine input parameters specific to Mascot." [PSI:PI, source:http://www.matrixscience.com/help/search_field_help.html] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002096 name: SEQUEST input parameter def: "Search engine input parameters specific to SEQUEST." [PSI:PI, source:http://fields.scripps.edu/sequest/parameters.html] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002097 name: Phenyx input parameter def: "Search engine input parameters specific to Phenyx." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002098 name: ProteinExtractor input parameter def: "Search engine input parameters specific to ProteinExtractor." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002099 name: OMSSA input parameter def: "Search engine input parameters specific to OMSSA." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002100 name: ProteinScape input parameter def: "Search engine input parameters specific to ProteinScape." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002101 name: ProteomeDiscoverer input parameter def: "Search engine input parameters specific to ProteomeDiscoverer." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002103 name: software input parameter def: "Software input parameters." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1002104 name: common software input parameter def: "Software input parameter that is shared by more than one software." [PSI:PI] is_a: MS:1002103 ! software input parameter [Term] id: MS:1002105 name: software specific input parameter def: "Software specific input parameter." [PSI:PI] is_a: MS:1002103 ! software input parameter [Term] id: MS:1002106 name: Scaffold input parameter def: "Search engine input parameters specific to Scaffold." [PSI:PI] is_a: MS:1002105 ! software specific input parameter [Term] id: MS:1002107 name: Percolator input parameter def: "Search engine input parameters specific to Percolator." [PSI:PI] is_a: MS:1002105 ! software specific input parameter [Term] id: MS:1002108 name: higher score better def: "Indicates that a higher score is better." [PSI:PI] relationship: part_of MS:1001153 ! search engine specific score [Term] id: MS:1002109 name: lower score better def: "Indicates that a lower score is better." [PSI:PI] relationship: part_of MS:1001153 ! search engine specific score [Term] id: MS:1002110 name: assay attribute def: "Attribute describing an assay." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002111 name: assay label attribute def: "Attribute describing an assay label." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002112 name: protein group list attribute def: "Attribute describing a protein group list." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002113 name: protein group attribute def: "Attribute describing a protein group." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002114 name: protein list attribute def: "Attribute describing a protein list." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002115 name: peptide consensus list attribute def: "Attribute describing a peptide consensus list." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002116 name: peptide consensus attribute def: "Attribute describing a peptide consensus." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002117 name: small molecule list attribute def: "Attribute describing a small molecule list." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002118 name: small molecule attribute def: "Attribute describing a small molecule." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002119 name: small molecule modification attribute def: "Attribute describing a small molecule modification." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002120 name: experiment name def: "The name for identifying an experiment." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002121 name: spectral count feature def: "Dummy decribing a spectral count feature." [PSI:PI] is_a: MS:1001828 ! feature attribute [Term] id: MS:1002122 name: counts reporting def: "FeatureList of spectral counts." [PSI:PI] is_a: MS:1001825 ! feature list attribute [Term] id: MS:1002123 name: x-Tracker def: "X-Tracker generic tool for quantitative proteomics." [https://bessantlab.org/software/x-tracker/] is_a: MS:1001139 ! quantitation software name [Term] id: MS:1002124 name: ProteoSuite def: "ProteoSuite software for the analysis of quantitative proteomics data." [DOI:10.1089/omi.2012.0022, PMID:22804616, http://www.proteosuite.org/] is_a: MS:1001139 ! quantitation software name [Term] id: MS:1002125 name: combined FDRScore def: "OBSOLETE FDRScore values specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] comment: This term was made obsolete because it was split into the more specific terms for PSM-level combined FDRScore (MS:1002356), distinct peptide-level combined FDRScore (MS:1002361), protein-level combined FDRScore (MS:1002366) and protein group-level combined FDRScore (MS:1002375). is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score is_obsolete: true relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002126 name: database UniProtKB def: "The name of the UniProtKB knowledgebase." [PSI:PI] is_a: MS:1001013 ! database name [Term] id: MS:1002127 name: identification file attribute def: "Attribute describing an identification file." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002128 name: method file format def: "Attribute describing a method file format." [PSI:PI] is_a: MS:1001459 ! file format [Term] id: MS:1002129 name: ITRAQAnalyzer def: "Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment." [http://www-bs2.informatik.uni-tuebingen.de/services/OpenMS/OpenMS-release/html/TOPP__ITRAQAnalyzer.html] is_a: MS:1001139 ! quantitation software name is_a: MS:1000752 ! TOPP software [Term] id: MS:1002130 name: identification file format def: "Attribute describing an identification file format." [PSI:PI] is_a: MS:1001459 ! file format [Term] id: MS:1002131 name: TOPP noise filter def: "Noise filter component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002132 name: TOPP NoiseFilterGaussian def: "Removes noise from profile spectra by using a gaussian smoothing." [PSI:PI] is_a: MS:1002131 ! TOPP noise filter [Term] id: MS:1002133 name: TOPP NoiseFilterSGolay def: "Removes noise from profile spectra by using a Savitzky-Golay smoothing." [PSI:PI] is_a: MS:1002131 ! TOPP noise filter [Term] id: MS:1002134 name: TOPP peak picker def: "Peak picker component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002135 name: TOPP PeakPickerHiRes def: "Finds mass spectrometric peaks in high-resoluted profile mass spectra." [PSI:PI] is_a: MS:1002134 ! TOPP peak picker [Term] id: MS:1002136 name: TOPP PeakPickerWavelet def: "Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra." [PSI:PI] is_a: MS:1002134 ! TOPP peak picker [Term] id: MS:1002137 name: TOPP spectra filter def: "Spectra filter component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002138 name: TOPP SpectraFilterBernNorm def: "Applies a Bern et al normalization to peak spectra." [PMID:15262780, DOI:10.1093/bioinformatics/bth947] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002139 name: TOPP SpectraFilterMarkerMower def: "Applies a filter to peak spectra for marked peaks." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002140 name: TOPP SpectraFilterNLargest def: "Retains the n largest peaks of a peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002141 name: TOPP SpectraFilterNormalizer def: "Applies a TIC/maximal intensity normalization to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002142 name: TOPP SpectraFilterParentPeakMower def: "Filters putative unfragmented precursor ions from tandem spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002143 name: TOPP SpectraFilterScaler def: "Applies a filter to peak spectra after intensity scaling according to rank." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002144 name: TOPP SpectraFilterSqrtMower def: "Applies a filter to peak spectra after intensity scaling to the square root." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002145 name: TOPP SpectraFilterThresholdMower def: "Applies a filter of peaks below a given threshold to peak spectra." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002146 name: TOPP SpectraFilterWindowMower def: "Applies a filter of the largest peaks in a sliding window over a peak spectrum." [PSI:PI] is_a: MS:1002137 ! TOPP spectra filter [Term] id: MS:1002147 name: TOPP map aligner def: "Map aligner component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002148 name: TOPP MapAlignerIdentification def: "Corrects retention time distortions between maps based on common peptide identifications." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002149 name: TOPP MapAlignerPoseClustering def: "Corrects retention time distortions between maps using a pose clustering approach." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002150 name: TOPP MapAlignerSpectrum def: "Corrects retention time distortions between maps by spectrum alignment." [PSI:PI] is_a: MS:1002147 ! TOPP map aligner [Term] id: MS:1002151 name: numerator data type attribute def: "Attribute describing the data type of the numerator of a ratio." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002152 name: denominator data type attribute def: "Attribute describing the data type of the denominator of a ratio." [PSI:PI] is_a: MS:1001806 ! quantification object attribute [Term] id: MS:1002153 name: protein level PSM counts def: "The number of spectra identified for this protein in spectral counting." [PSI:PI] is_a: MS:1002738 ! protein-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002154 name: TOPP DTAExtractor def: "Extracts spectra of an MS run file to several files in DTA format." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002155 name: TOPP IDMerger def: "Merges several protein/peptide identification files into one file." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002156 name: TOPP IDFileConverter def: "Converts identification engine file formats." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002157 name: TOPP SpectraMerger def: "Merges spectra from an LC/MS map, either by precursor or by RT blocks." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002158 name: TOPP MzTabExporter def: "Exports various XML formats to an mzTab file." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002159 name: TOPP MassTraceExtractor def: "Annotates mass traces in centroided LC/MS maps." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002160 name: TOPP PrecursorMassCorrector def: "Correct the precursor entries of tandem MS scans." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002161 name: TOPP HighResPrecursorMassCorrector def: "Performs precursor mz correction on centroided high resolution data." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002162 name: TOPP AdditiveSeries def: "Computes an additive series to quantify a peptide in a set of samples." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002163 name: TOPP Decharger def: "Decharges and merges different feature charge variants of the same chemical entity." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002164 name: TOPP EICExtractor def: "Quantifies signals at given positions in (raw or picked) LC/MS maps." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002165 name: TOPP feature finder def: "Feature finder component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002166 name: TOPP FeatureFinderCentroided def: "Detects two-dimensional features in centroided LC-MS data." [PSI:PI] is_a: MS:1002165 ! TOPP feature finder [Term] id: MS:1002167 name: TOPP FeatureFinderRaw def: "Detects two-dimensional features in uncentroided LC-MS data." [PSI:PI] is_a: MS:1002165 ! TOPP feature finder [Term] id: MS:1002168 name: TOPP FeatureFinderIsotopeWavelet def: "Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm." [PSI:PI] is_a: MS:1002165 ! TOPP feature finder [Term] id: MS:1002169 name: TOPP FeatureFinderMetabo def: "Detects two-dimensional features in centroided LC-MS data of metabolites." [PSI:PI] is_a: MS:1002165 ! TOPP feature finder [Term] id: MS:1002170 name: TOPP FeatureFinderMRM def: "Quantifies features LC-MS/MS MRM data." [PSI:PI] is_a: MS:1002165 ! TOPP feature finder [Term] id: MS:1002171 name: TOPP ProteinQuantifier def: "Computes protein abundances from annotated feature/consensus maps." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002172 name: TOPP ConsensusMapNormalizer def: "Normalizes maps of one consensus XML file (after linking)." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002173 name: TOPP MapRTTransformer def: "Applies retention time transformations to maps." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002174 name: TOPP feature linker def: "Feature linker component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002175 name: TOPP FeatureLinkerLabeled def: "Groups corresponding isotope-labeled features in a feature map." [PSI:PI] is_a: MS:1002174 ! TOPP feature linker [Term] id: MS:1002176 name: TOPP FeatureLinkerUnlabeled def: "Groups corresponding features from multiple maps." [PSI:PI] is_a: MS:1002174 ! TOPP feature linker [Term] id: MS:1002177 name: TOPP FeatureLinkerUnlabeledQT def: "Groups corresponding features from multiple maps using a quality threshold clustering approach." [PSI:PI] is_a: MS:1002174 ! TOPP feature linker [Term] id: MS:1002178 name: TOPP CompNovo def: "Performs a peptide/protein identification with the CompNovo engine." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002179 name: TOPP CompNovoCID def: "Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002180 name: TOPP software adaptor def: "Software adaptor to an external program in the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002181 name: TOPP InspectAdapter def: "Identifies MS2 spectra using the external program Inspect." [PSI:PI] is_a: MS:1002180 ! TOPP software adaptor [Term] id: MS:1002182 name: TOPP MascotAdapter def: "Identifies MS2 spectra using the external program Mascot." [PSI:PI] is_a: MS:1002180 ! TOPP software adaptor [Term] id: MS:1002183 name: TOPP MascotAdapterOnline def: "Identifies MS2 spectra using the online version of the external program Mascot." [PSI:PI] is_a: MS:1002180 ! TOPP software adaptor [Term] id: MS:1002184 name: TOPP OMSSAAdapter def: "Identifies MS2 spectra using the external program OMSSA." [PSI:PI] is_a: MS:1002180 ! TOPP software adaptor [Term] id: MS:1002185 name: TOPP PepNovoAdapter def: "Identifies MS2 spectra using the external program PepNovo." [PSI:PI] is_a: MS:1002180 ! TOPP software adaptor [Term] id: MS:1002186 name: TOPP XTandemAdapter def: "Identifies MS2 spectra using the external program XTandem." [PSI:PI] is_a: MS:1002180 ! TOPP software adaptor [Term] id: MS:1002187 name: TOPP SpecLibSearcher def: "Identifies peptide MS2 spectra by spectral matching with a searchable spectral library." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002188 name: TOPP ConsensusID def: "Computes a consensus identification from peptide identifications of several identification engines." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002189 name: TOPP IDConflictResolver def: "Resolves ambiguous annotations of features with peptide identifications." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002190 name: TOPP IDFilter def: "Filters results from protein or peptide identification engines based on different criteria." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002191 name: TOPP IDMapper def: "Assigns protein/peptide identifications to feature or consensus features." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002192 name: TOPP IDPosteriorErrorProbability def: "Estimates posterior error probabilities using a mixture model." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002193 name: TOPP IDRTCalibration def: "Calibrate Retention times of peptide hits to standards." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002194 name: TOPP PeptideIndexer def: "Refreshes the protein references for all peptide hits." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002195 name: TOPP PrecursorIonSelector def: "A tool for precursor ion selection based on identification results." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002196 name: TOPP MRMMapper def: "MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002197 name: TOPP OpenSwath component def: "OpenSwath component of the TOPP software." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002198 name: TOPP OpenSwathAnalyzer def: "Picks peaks and finds features in an SRM experiment." [PSI:PI] is_a: MS:1002197 ! TOPP OpenSwath component [Term] id: MS:1002199 name: TOPP OpenSwathChromatogramExtractor def: "Extract chromatograms (XIC) from a MS2 map file." [PSI:PI] is_a: MS:1002197 ! TOPP OpenSwath component [Term] id: MS:1002200 name: TOPP OpenSwathDecoyGenerator def: "Generates decoys according to different models for a specific TraML." [PSI:PI] is_a: MS:1002197 ! TOPP OpenSwath component [Term] id: MS:1002201 name: TOPP OpenSwathFeatureXMLToTSV def: "Converts a featureXML to a mProphet tsv (tab separated values)." [PSI:PI] is_a: MS:1002197 ! TOPP OpenSwath component [Term] id: MS:1002202 name: TOPP OpenSwathRTNormalizer def: "Generates a transformation file for retention time space into normalized space." [PSI:PI] is_a: MS:1002197 ! TOPP OpenSwath component [Term] id: MS:1002203 name: TOPP ProteinInference def: "Infer proteins from a list of (high-confidence) peptides." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002204 name: TOPP FalseDiscoveryRate def: "Estimates the false discovery rate on peptide and protein level using decoy searches." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002205 name: ProteoWizard msconvert def: "Converts, filters, and processes mass spectrometry data in variety of formats." [PSI:MS] is_a: MS:1000615 ! ProteoWizard software [Term] id: MS:1002206 name: ProteoWizard idconvert def: "Converts, filters, and processes identifications from shotgun proteomics experiments." [PSI:MS] is_a: MS:1000615 ! ProteoWizard software [Term] id: MS:1002207 name: ProteoWizard chainsaw def: "Filters and processes protein sequence databases." [PSI:MS] is_a: MS:1000615 ! ProteoWizard software [Term] id: MS:1002208 name: ProteoWizard msaccess def: "Filters, processes, and displays mass spectrometry data in a variety of ways." [PSI:MS] is_a: MS:1000615 ! ProteoWizard software [Term] id: MS:1002209 name: ProteoWizard SeeMS def: "An interactive GUI application to view and filter mass spectrometry data in a variety of formats." [PSI:MS] is_a: MS:1000615 ! ProteoWizard software [Term] id: MS:1002210 name: IsobariQ def: "A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data." [PMID:21067241, DOI:10.1021/pr1009977, http://folk.uio.no/magnusar/isobariq] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1002211 name: Variance stabilizing normalization def: "The model incorporates data calibration (normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation." [PMID:16646781] is_a: MS:1001861 ! quantification data processing [Term] id: MS:1002212 name: IPTL quantitation analysis def: "Quantification analysis using a labelling strategy where both peptide termini are labelled so that the peptides from different labelling schema are isobaric." [PSI:PI, PMID:19655813] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002213 name: PAnalyzer:conclusive protein def: "A protein identified by at least one unique (distinct, discrete) peptide (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002214 name: PAnalyzer:indistinguishable protein def: "A member of a group of proteins sharing all peptides that are exclusive to the group (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002215 name: PAnalyzer:non-conclusive protein def: "A protein sharing all its matched peptides with either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002216 name: PAnalyzer:ambiguous group member def: "A protein sharing at least one peptide not matched to either conclusive or indistinguishable proteins (peptides are considered different only if they can be distinguished by evidence in mass spectrum)." [PSI:PI] is_a: MS:1001600 ! protein inference confidence category relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002217 name: decoy peptide def: "A putative identified peptide issued from a decoy sequence database." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002218 name: percent collision energy ramp start def: "Collision energy at the start of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] is_a: MS:1000138 ! normalized collision energy relationship: has_units UO:0000187 ! percent relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002219 name: percent collision energy ramp end def: "Collision energy at the end of the collision energy ramp in percent, normalized to the mass of the ion." [PSI:PI] is_a: MS:1000138 ! normalized collision energy relationship: has_units UO:0000187 ! percent relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002220 name: MRMaid def: "A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI's PRIDE database." [PSI:PI] is_a: MS:1000871 ! SRM software [Term] id: MS:1002221 name: MRMaid:peptide score def: "Score in MRMaid to indicate the expected performance of the peptide in SRM." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute is_a: MS:1002363 ! search engine specific score for proteins [Term] id: MS:1002222 name: SRM transition attribute def: "Attribute associated with a SRM transition." [PSI:MS] is_a: MS:1000455 ! ion selection attribute relationship: part_of MS:1000908 ! transition [Term] id: MS:1002223 name: precursor ion detection probability def: "Probability of detecting precursor when parent protein is present." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002224 name: product ion detection probability def: "Probability of detecting product ion when precursor ion is present." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002225 name: average product ion intensity def: "Average value of product ion intensity in a collection of identified spectra." [PSI:PI] is_a: MS:1001226 ! product ion intensity relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 [Term] id: MS:1002226 name: product ion intensity standard deviation def: "Standard deviation of product ion intensity in a collection of identified spectra." [PSI:PI] is_a: MS:1001226 ! product ion intensity relationship: has_units MS:1000131 ! number of detector counts relationship: has_units MS:1000132 ! percent of base peak relationship: has_units MS:1000814 ! counts per second relationship: has_units MS:1000905 ! percent of base peak times 100 [Term] id: MS:1002227 name: number of product ion observations def: "The number of times the specific product ion has been observed in a series of SRM experiments." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002228 name: number of precursor ion observations def: "The number of times the specific precursor ion has been observed in a series of SRM experiments." [PSI:PI] is_a: MS:1002222 ! SRM transition attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002229 name: ProteomeDiscoverer:Mascot:Significance Middle def: "Calculated relaxed significance when performing a decoy search for high-confidence peptides." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002230 name: ProteomeDiscoverer:Mascot:Significance High def: "Calculated relaxed significance when performing a decoy search for medium-confidence peptides." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002231 name: regular expressions for a GUID def: "([A-Fa-f0-9]\{8\}-([A-Fa-f0-9]\{4\}-)\{3\}[A-Fa-f0-9]\{12\})." [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1002232 name: ProteomeDiscoverer:Default FDR calculator def: "The default FDR calculator as globally unique identifier (GUID)." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_regexp MS:1002231 ! regular expressions for a GUID [Term] id: MS:1002233 name: ProteomeDiscoverer:SEQUEST:Low resolution spectra contained def: "Flag indicating if low-resolution spectra are taken into consideration." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002234 name: selected precursor m/z def: "Mass-to-charge ratio of a precursor ion selected for fragmentation." [PSI:PI] synonym: "selected ion m/z" RELATED [] is_a: MS:1000455 ! ion selection attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002235 name: ProteoGrouper:PDH score def: "A score assigned to a single protein accession (modelled as ProteinDetectionHypothesis in mzIdentML), based on summed peptide level scores." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002236 name: ProteoGrouper:PAG score def: "A score assigned to a protein group (modelled as ProteinAmbiguityGroup in mzIdentML), based on all summed peptide level scores that have been assigned to the group as unique or razor peptides." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002237 name: mzidLib def: "A library of Java routines for manipulating mzIdentML files." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002238 name: mzidLib:Omssa2Mzid def: "A converter for OMSSA OMX to mzIdentML." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002239 name: mzidLib:Tandem2Mzid def: "A converter for Tandem XML to mzIdentML." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002240 name: mzidLib:Csv2Mzid def: "A converter for CSV files (following OMSSA CSV style) to mzIdentML." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002241 name: mzidLib:ProteoGrouper def: "A generic and parameterizable protein inference algorithm for mzIdentML files." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002242 name: mzidLib:Thresholder def: "A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002243 name: mzidLib:Perform emPAI on mzid def: "A routine for adding emPAI quantitative values to an mzIdentML file." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002244 name: mzidLib:FalseDiscoveryRate def: "A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002245 name: mzidLib:Mzidentml2Csv def: "A tool for converting mzIdentML files to CSV format." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002246 name: mzidLib:CombineSearchEngines def: "A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file." [PMID:19253293] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002247 name: mzidLib:InsertMetaDataFromFasta def: "A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files." [PSI:PI] is_a: MS:1002237 ! mzidLib [Term] id: MS:1002248 name: SEQUEST:spscore def: "The SEQUEST result 'SpScore'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002249 name: SEQUEST:sprank def: "The SEQUEST result 'SpRank'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002250 name: SEQUEST:deltacnstar def: "The SEQUEST result 'DeltaCnStar'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002251 name: Comet def: "Comet open-source sequence search engine developed at the University of Washington." [PMID:23148064] is_a: MS:1001456 ! analysis software [Term] id: MS:1002252 name: Comet:xcorr def: "The Comet result 'XCorr'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002253 name: Comet:deltacn def: "The Comet result 'DeltaCn'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002254 name: Comet:deltacnstar def: "The Comet result 'DeltaCnStar'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002255 name: Comet:spscore def: "The Comet result 'SpScore'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002256 name: Comet:sprank def: "The Comet result 'SpRank'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002257 name: Comet:expectation value def: "The Comet result 'Expectation value'." [PSI:PI] is_a: MS:1001153 ! search engine specific score relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002258 name: Comet:matched ions def: "The Comet result 'Matched Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002259 name: Comet:total ions def: "The Comet result 'Total Ions'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002260 name: PSM:FDR threshold def: "False-discovery rate threshold for peptide-spectrum matches." [PSI:PI] is_a: MS:1002483 ! PSM-level statistical threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002261 name: Byonic def: "Byonic search engine from Protein Metrics." [PMID:23255153] is_a: MS:1001456 ! analysis software [Term] id: MS:1002262 name: Byonic:Score def: "The Byonic score is the primary indicator of PSM correctness. The Byonic score reflects the absolute quality of the peptide-spectrum match, not the relative quality compared to other candidate peptides. Byonic scores range from 0 to about 1000, with 300 a good score, 400 a very good score, and PSMs with scores over 500 almost sure to be correct." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002263 name: Byonic:Delta Score def: "The drop in Byonic score from the top-scoring peptide to the next peptide with distinct sequence. In this computation, the same peptide with different modifications is not considered distinct." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002264 name: Byonic:DeltaMod Score def: "The drop in Byonic score from the top-scoring peptide to the next peptide different in any way, including placement of modifications. DeltaMod gives an indication of whether modifications are confidently localized; DeltaMod over 10.0 means that there is high likelihood that all modification placements are correct." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002265 name: Byonic:PEP def: "Byonic posterior error probability." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002266 name: Byonic:Peptide LogProb def: "The log p-value of the PSM. This is the log of the probability that the PSM with such a score and delta would arise by chance in a search of this size (the size of the protein database, as expanded by the modification rules). A log p-value of -3.0 should happen by chance on only one of a thousand spectra. Caveat: it is very hard to compute a p-value that works for all searches and all spectra, so read Byonic p-values with a certain amount of skepticism." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002267 name: Byonic:Protein LogProb def: "The log p-value of the protein." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002268 name: Byonic:Best LogProb def: "Best (most negative) log p-value of an individual PSM." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002269 name: Byonic:Best Score def: "Best (largest) Byonic score of a PSM." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002270 name: chromatography separation def: "A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure." [PSI:MS] is_a: MS:1000857 ! run attribute [Term] id: MS:1002271 name: liquid chromatography separation def: "Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid." [PSI:MS] is_a: MS:1002270 ! chromatography separation [Term] id: MS:1002272 name: gas chromatography separation def: "Gas chromatography (GC) is a separation technique in which the mobile phase is a gas." [PSI:MS] is_a: MS:1002270 ! chromatography separation [Term] id: MS:1002273 name: detector potential def: "Detector potential difference in volts." [PSI:MS] is_a: MS:1000481 ! detector attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002274 name: SQ Detector 2 def: "Waters quadrupole based SQ Detector 2." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002275 name: Xevo G2-S Tof def: "Waters oa-ToF based Xevo G2-S Tof." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002276 name: Xevo G2-S QTof def: "Waters oa-ToF based Xevo G2-S QTof." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002277 name: AutoSpec Premier def: "Waters AutoSpec Premier magnetic sector instrument." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002278 name: Pegasus III def: "LECO nominal mass resolution time-of-flight GC mass spectrometer." [PSI:MS] is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1002279 name: maXis 4G def: "Bruker Daltonics' maXis 4G: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1002280 name: compact def: "Bruker Daltonics' compact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002281 name: SRM feature level quantitation def: "Selected Reaction Monitoring feature level quantitation." [PSI:PI] is_a: MS:1001838 ! SRM quantitation analysis [Term] id: MS:1002282 name: SRM peptide level quantitation def: "Selected Reaction Monitoring peptide level quantitation." [PSI:PI] is_a: MS:1001838 ! SRM quantitation analysis [Term] id: MS:1002283 name: SRM protein level quantitation def: "Selected Reaction Monitoring protein level quantitation." [PSI:PI] is_a: MS:1001838 ! SRM quantitation analysis [Term] id: MS:1002284 name: SRM proteingroup level quantitation def: "Selected Reaction Monitoring proteingroup level quantitation." [PSI:PI] is_a: MS:1001838 ! SRM quantitation analysis [Term] id: MS:1002285 name: Trans-Proteomic Pipeline def: "A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology." [PSI:PI] synonym: "TPP" EXACT [] is_a: MS:1001456 ! analysis software [Term] id: MS:1002286 name: Trans-Proteomic Pipeline software def: "A software program that is a component of the Trans-Proteomic Pipeline." [PSI:PI] is_a: MS:1001456 ! analysis software relationship: part_of MS:1002285 ! Trans-Proteomic Pipeline [Term] id: MS:1002287 name: PeptideProphet def: "A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format." [PMID:12403597, PMID:23176103] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002288 name: iProphet def: "A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format." [PMID:21876204] synonym: "InterProphet" EXACT [] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002289 name: ProteinProphet def: "A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format." [PMID:14632076] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002290 name: XPRESS def: "A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002291 name: Libra def: "A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc." [PSI:PI] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002292 name: PTMProphet def: "A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites." [PSI:PI] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002293 name: Bruker Daltonics SCION series def: "Bruker Daltonics' SCION series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1002294 name: Bruker Daltonics EVOQ series def: "Bruker Daltonics' EVOQ series." [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1002295 name: SCION SQ def: "Bruker Daltonics' SCION SQ: GC-single quadrupole." [PSI:MS] is_a: MS:1002293 ! Bruker Daltonics SCION series [Term] id: MS:1002296 name: SCION TQ def: "Bruker Daltonics' SCION TQ: GC-triple quadrupole." [PSI:MS] is_a: MS:1002293 ! Bruker Daltonics SCION series [Term] id: MS:1002297 name: EVOQ Elite def: "Bruker Daltonics' EVOQ Elite: LC-triple quadrupole." [PSI:MS] is_a: MS:1002294 ! Bruker Daltonics EVOQ series [Term] id: MS:1002298 name: EVOQ Qube def: "Bruker Daltonics' EVOQ Qube: LC-triple quadrupole." [PSI:MS] is_a: MS:1002294 ! Bruker Daltonics EVOQ series [Term] id: MS:1002299 name: micrOTOF-Q III def: "Bruker Daltonics' micrOTOF-Q III: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002300 name: amaZon Speed ETD def: "Bruker Daltonics' amaZon Speed ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR, GC-APCI, CaptiveSpray." [PSI:MS] is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] id: MS:1002301 name: amaZon Speed def: "Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray." [PSI:MS] is_a: MS:1001545 ! Bruker Daltonics amaZon series [Term] id: MS:1002302 name: Bruker Container format def: "Bruker Container raw file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002303 name: Bruker Container nativeID format def: "Native identifier (UUID)." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002304 name: domain range def: "Domain range of a numerical value." [PSI:PI] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1002305 name: value between 0 and 1 inclusive def: "Value range for probabilities." [PSI:PI] is_a: MS:1002304 ! domain range [Term] id: MS:1002306 name: value greater than zero def: "Positive value range." [PSI:PI] is_a: MS:1002304 ! domain range [Term] id: MS:1002307 name: fragmentation ion type def: "Type of fragment ion based on where the backbone breaks, such as a y ion or a c ion." [PSI:PI] is_a: MS:1001221 ! product ion attribute [Term] id: MS:1002308 name: fluorescence detector def: "A detector using a fluorescent signal after excitation with light." [PSI:MS] is_a: MS:1000026 ! detector type [Term] id: MS:1002309 name: Byonic: Peptide AbsLogProb def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the PSM." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002310 name: Byonic: Protein AbsLogProb def: "The absolute value of the log-base10 of the Byonic posterior error probability (PEP) of the protein." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002311 name: Byonic: Peptide AbsLogProb2D def: "The absolute value of the log-base10 Byonic two-dimensional posterior error probability (PEP) of the PSM. The two-dimensional PEP takes into account protein ranking information as well as PSM information." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002312 name: MS-Numpress linear prediction compression def: "Compression using MS-Numpress linear prediction compression." [https://github.com/ms-numpress/ms-numpress] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1002313 name: MS-Numpress positive integer compression def: "Compression using MS-Numpress positive integer compression." [https://github.com/ms-numpress/ms-numpress] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1002314 name: MS-Numpress short logged float compression def: "Compression using MS-Numpress short logged float compression." [https://github.com/ms-numpress/ms-numpress] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1002315 name: consensus result def: "Indicates a consensus result from several search engine runs." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1002316 name: ProteomeDiscoverer:Amanda:high confidence threshold def: "Strict confidence probability score." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002317 name: ProteomeDiscoverer:Amanda:middle confidence threshold def: "Relaxed confidence probability score." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002318 name: ProteomeDiscoverer:automatic workload def: "Flag indicating automatic estimation of the workload level." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002319 name: Amanda:AmandaScore def: "The Amanda score of the scoring function for a PSM." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002320 name: ProteomeDiscoverer:max differential modifications def: "Maximum dynamic modifications per PSM." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002321 name: ProteomeDiscoverer:max equal modifications def: "Maximum equal modifications per PSM." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002322 name: ProteomeDiscoverer:min peptide length def: "Minimum peptide length." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002323 name: ProteomeDiscoverer:max peptide length def: "Maximum peptide length." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002324 name: ProteomeDiscoverer:max number neutral loss def: "Maximum number of same neutral losses." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002325 name: ProteomeDiscoverer:max number neutral loss modifications def: "Max number of same neutral losses of modifications." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002326 name: ProteomeDiscoverer:use flanking ions def: "Flag for usage of flanking ions." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002327 name: ProteomeDiscoverer:max number of same modifs def: "The maximum number of possible equal modifications per PSM." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002328 name: ProteomeDiscoverer:perform deisotoping def: "Defines whether a simple deisotoping shall be performed." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002329 name: ProteomeDiscoverer:ion settings def: "Specifies the fragment ions and neutral losses that are calculated." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002330 name: ProteomeDiscoverer:3. Static Modification def: "OBSOLETE ProteomeDiscoverer's 3rd static post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002331 name: ProteomeDiscoverer:5. Dynamic Modification def: "OBSOLETE ProteomeDiscoverer's 5th dynamic post-translational modification (PTM) input parameter." [PSI:PI] comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead. is_a: MS:1002101 ! ProteomeDiscoverer input parameter is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002332 name: lab head def: "The scientist responsible for personnel, grants, and instrumentation in a functional laboratory group." [PSI:PI] is_a: MS:1002033 ! contact role [Term] id: MS:1002333 name: conversion software def: "Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process." [PSI:PI] is_a: MS:1001457 ! data processing software [Term] id: MS:1002334 name: ProCon def: "Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML." [PSI:PI, http://www.medizinisches-proteom-center.de/procon] is_a: MS:1002333 ! conversion software [Term] id: MS:1002335 name: PRIDE Converter2 def: "Java software designed to convert one of several proteomics identification results formats into PRIDE XML." [PMID:22949509] is_a: MS:1002333 ! conversion software [Term] id: MS:1002336 name: Amanda def: "Amanda scoring system for PSM identification." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002337 name: Andromeda def: "Andromeda is a peptide search engine." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002338 name: Andromeda:score def: "The probability based score of the Andromeda search engine." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002339 name: site:global FDR def: "Estimation of global false discovery rate of peptides with a post-translational modification." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002340 name: ProteomeXchange project tag def: "Tag that can be added to a ProteomeXchange dataset, to enable the grouping of datasets. One tag can be used for indicating that a given dataset is part of a bigger project, like e.g. the Human Proteome Project." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002341 name: second-pass peptide identification def: "A putative identified peptide found in a second-pass search of protein sequences selected from a first-pass search." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002342 name: MZmine def: "A framework for differential analysis of mass spectrometry data." [PMID:16403790, PMID:20650010] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002343 name: ion stability type def: "OBSOLETE Stability type of the ion." [PSI:PI] comment: This child of the former purgatory term ion was made obsolete. is_obsolete: true [Term] id: MS:1002344 name: Maltcms def: "Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers." [PSI:PI, http://maltcms.sf.net] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002345 name: PSM-level attribute def: "Attribute of a single peptide-spectrum match." [PSI:PI] is_a: MS:1002694 ! single identification result attribute relationship: part_of MS:1003301 ! peptide-spectrum match [Term] id: MS:1002346 name: protein group-level identification attribute def: "Protein group level information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002347 name: PSM-level identification statistic def: "Identification confidence metric for a peptide spectrum match." [PSI:PI] is_a: MS:1002345 ! PSM-level attribute [Term] id: MS:1002348 name: protein group-level identification statistic def: "Identification confidence metric for a protein group." [PSI:PI] is_a: MS:1002346 ! protein group-level identification attribute [Term] id: MS:1002349 name: value greater than zero but less than or equal to one def: "Positive value range less than or equal to 1." [PSI:PI] is_a: MS:1002304 ! domain range [Term] id: MS:1002350 name: PSM-level global FDR def: "Estimation of the global false discovery rate of peptide spectrum matches." [PSI:PI] is_a: MS:1002701 ! PSM-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002351 name: PSM-level local FDR def: "Estimation of the local false discovery rate of peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002352 name: PSM-level p-value def: "Estimation of the p-value for peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002353 name: PSM-level e-value def: "Estimation of the e-value for peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002354 name: PSM-level q-value def: "Estimation of the q-value for peptide spectrum matches." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002355 name: PSM-level FDRScore def: "mzidLibrary FDRScore for peptide spectrum matches." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002356 name: PSM-level combined FDRScore def: "mzidLibrary Combined FDRScore for peptide spectrum matches specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to 1 relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002357 name: PSM-level probability def: "Probability that the reported peptide ion is truly responsible for some or all of the components of the specified mass spectrum." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002358 name: search engine specific peptide sequence-level identification statistic def: "Search engine specific distinct peptide score." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic [Term] id: MS:1002359 name: peptide sequence-level local FDR def: "Estimation of the local false discovery rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002360 name: distinct peptide-level FDRScore def: "MzidLibrary FDRScore for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002361 name: distinct peptide-level combined FDRScore def: "Combined FDRScore for peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry) specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given peptide, used for integrating results from these distinct pools." [PSI:PI] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002362 name: peptide sequence-level probability def: "Probability that the reported distinct peptide sequence (irrespective of mass modifications) has been correctly identified via the referenced PSMs." [PSI:PI] is_a: MS:1001092 ! peptide sequence-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002363 name: search engine specific score for proteins def: "Search engine specific protein scores." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic [Term] id: MS:1002364 name: protein-level local FDR def: "Estimation of the local false discovery rate of proteins." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002365 name: FDRScore for proteins def: "MzidLibrary FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002366 name: combined FDRScore for proteins def: "MzidLibrary Combined FDRScore for proteins." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002367 name: probability for proteins def: "Probability that a specific protein sequence has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002368 name: search engine specific score for protein groups def: "Search engine specific protein group scores." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic [Term] id: MS:1002369 name: protein group-level global FDR def: "Estimation of the global false discovery rate of protein groups." [PSI:PI] is_a: MS:1002706 ! protein group-level result list statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002370 name: protein group-level local FDR def: "Estimation of the local false discovery rate of protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002371 name: protein group-level p-value def: "Estimation of the p-value for protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002372 name: protein group-level e-value def: "Estimation of the e-value for protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002306 ! value greater than zero relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002373 name: protein group-level q-value def: "Estimation of the q-value for protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002374 name: protein group-level FDRScore def: "mzidLibrary FDRScore for protein groups." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002375 name: protein group-level combined FDRScore def: "mzidLibrary Combined FDRScore for proteins specifically obtained for distinct combinations of single, pairs or triplets of search engines making a given PSM, used for integrating results from these distinct pools." [PMID:19253293] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_domain MS:1002349 ! value greater than zero but less than or equal to one relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002376 name: protein group-level probability def: "Probability that at least one of the members of a group of protein sequences has been correctly identified from the PSM and distinct peptide evidence, and based on the available protein sequences presented to the analysis software." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002377 name: ProteomeDiscoverer:Relaxed Score Threshold def: "Specifies the threshold value for relaxed scoring." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002378 name: ProteomeDiscoverer:Strict Score Threshold def: "Specifies the threshold value for strict scoring." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002379 name: ProteomeDiscoverer:Peptide Without Protein Cut Off Score def: "Cut off score for storing peptides that do not belong to a protein." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002380 name: false localization rate def: "Estimation of the false localization rate for modification site assignment." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002381 name: MALDI Solutions LC-MALDI def: "Software for automated LC-MALDI analysis and reporting." [PSI:PI] is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software is_a: MS:1001557 ! Shimadzu Corporation software [Term] id: MS:1002382 name: Shimadzu MALDI-7090 def: "Shimadzu MALDI-7090: MALDI-TOF-TOF." [PSI:PI] is_a: MS:1000602 ! Shimadzu MALDI-TOF instrument model [Term] id: MS:1002383 name: SCiLS software def: "SCiLS software for data acquisition and analysis." [PSI:MS] is_a: MS:1000531 ! software [Term] id: MS:1002384 name: SCiLS Lab def: "SCiLS Lab software." [PSI:MS] is_a: MS:1002383 ! SCiLS software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002385 name: SCiLS Lab format def: "SCiLS Lab file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002386 name: preprocessing software def: "Preprocessing software." [PSI:PI] is_a: MS:1001457 ! data processing software [Term] id: MS:1002387 name: PIA def: "PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis." [PSI:PI, http://www.medizinisches-proteom-center.de/pia] is_a: MS:1002414 ! postprocessing software is_a: MS:1001456 ! analysis software [Term] id: MS:1002388 name: PIA XML format def: "A compilation of search engine results in the PIA XML format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1002389 name: PIA workflow parameter def: "A parameter set for a single PIA analysis." [PSI:PI] is_a: MS:1002105 ! software specific input parameter is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002390 name: PIA:FDRScore calculated def: "Indicates whether the FDR score was calculated for the input file." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002391 name: PIA:Combined FDRScore calculated def: "Indicates whether the combined FDR score was calculated for the PIA compilation." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002392 name: PIA:PSM sets created def: "Indicates whether PSM sets were created." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002393 name: PIA:used top identifications for FDR def: "The number of top identifications per spectrum used for the FDR calculation, 0 means all." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1002394 name: PIA:protein score def: "The score given to a protein by any protein inference." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002395 name: PIA:protein inference def: "The used algorithm for the protein inference using PIA." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002396 name: PIA:protein inference filter def: "A filter used by PIA for the protein inference." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002397 name: PIA:protein inference scoring def: "The used scoring method for the protein inference using PIA." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002398 name: PIA:protein inference used score def: "The used base score for the protein inference using PIA." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002399 name: PIA:protein inference used PSMs def: "The method to determine the PSMs used for scoring by the protein inference." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002400 name: PIA:filter def: "A filter used for the report generation." [PSI:PI] is_a: MS:1002389 ! PIA workflow parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002401 name: leading protein def: "At least one protein within each group should be annotated as a leading protein to indicate it has the strongest evidence, or approximately equal evidence as other group members." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship [Term] id: MS:1002402 name: non-leading protein def: "Zero to many proteins within each group should be annotated as non-leading to indicate that other proteins have stronger evidence." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship [Term] id: MS:1002403 name: group representative def: "An arbitrary and optional flag applied to exactly one protein per group to indicate it can serve as the representative of the group, amongst leading proteins, in effect serving as a tiebreaker for approaches that require exactly one group representative." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship [Term] id: MS:1002404 name: count of identified proteins def: "The number of proteins that have been identified, which must match the number of groups that pass the threshold in the file." [PSI:PI] is_a: MS:1002704 ! protein-level result list attribute is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002405 name: protein group-level result list attribute def: "Details describing a protein cluster." [PSI:PI] is_a: MS:1002699 ! result list attribute [Term] id: MS:1002406 name: count of identified clusters def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [DOI:10.1002/pmic.201400080, PMID:25092112] is_a: MS:1002405 ! protein group-level result list attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002407 name: cluster identifier def: "An identifier applied to protein groups to indicate that they are linked by shared peptides." [PSI:PI] is_a: MS:1002698 ! protein cluster identification attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002408 name: number of distinct protein sequences def: "The number of protein clusters that have been identified, which must match the number of clusters that pass the threshold in the file." [PSI:PI] is_a: MS:1002405 ! protein group-level result list attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002409 name: marginally distinguished protein def: "Assigned to a non-leading protein that has some independent evidence to support its presence relative to the leading protein(s), e.g. the protein may have a unique peptide but not sufficient to be promoted as a leading protein of another group." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship [Term] id: MS:1002410 name: Anubis def: "Anubis software for selected reaction monitoring data." [PSI:PI, http://quantitativeproteomics.org/anubis] is_a: MS:1000871 ! SRM software is_a: MS:1001139 ! quantitation software name [Term] id: MS:1002411 name: TraML format def: "The TraML format for transitions in SRM from the PSI. File extension '.TraML'." [PSI:PI, http://www.psidev.info/traml] is_a: MS:1002128 ! method file format [Term] id: MS:1002412 name: total XIC area def: "Summed area of all the extracted ion chromatogram for the peptide (e.g. of all the transitions in SRM)." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002413 name: product background def: "The background area for the quantified transition." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002414 name: postprocessing software def: "Postprocessing software." [PSI:PI] is_a: MS:1001457 ! data processing software [Term] id: MS:1002415 name: protein group passes threshold def: "A Boolean attribute to determine whether the protein group has passed the threshold indicated in the file." [PSI:PI] is_a: MS:1002346 ! protein group-level identification attribute relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002416 name: Orbitrap Fusion def: "Thermo Scientific Orbitrap Fusion." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002417 name: Orbitrap Fusion ETD def: "Thermo Scientific Orbitrap Fusion with ETD." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002418 name: TSQ Quantiva def: "Thermo Scientific TSQ Quantiva MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002419 name: TSQ Endura def: "Thermo Scientific TSQ Endura MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002420 name: PASSEL experiment URI def: "URI that allows access to a PASSEL experiment." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002421 name: Paragon input parameter def: "Search engine input parameters specific to Paragon." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002422 name: Paragon: sample type def: "The Paragon method setting indicating the type of sample at the high level, generally meaning the type of quantitation labelling or lack thereof. 'Identification' is indicated for samples without any labels for quantitation." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002423 name: Paragon: cysteine alkylation def: "The Paragon method setting indicating the actual cysteine alkylation agent; 'None' is indicated if there was no cysteine alkylation." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002424 name: Paragon: instrument setting def: "The Paragon method setting (translating to a large number of lower level settings) indicating the instrument used or a category of instrument." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002425 name: Paragon: search effort def: "The Paragon method setting that controls the two major modes of search effort of the Paragon algorithm: the Rapid mode uses a conventional database search, while the Thorough mode uses a hybrid search, starting with the same approach as the Rapid mode but then follows it with a separate tag-based approach enabling a more extensive search." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002426 name: Paragon: ID focus def: "A Paragon method setting that allows the inclusion of large sets of features such as biological modification or substitutions." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002427 name: Paragon: FDR analysis def: "The Paragon method setting that controls whether FDR analysis is conducted." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002428 name: Paragon: quantitation def: "The Paragon method setting that controls whether quantitation analysis is conducted." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002429 name: Paragon: background correction def: "The Paragon method setting that controls whether the 'Background Correction' analysis is conducted; this processing estimates a correction to the attenuation in extremity ratios that can occur in isobaric quantatitation workflows on complex samples." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002430 name: Paragon: bias correction def: "The Paragon method setting that controls whether 'Bias Correction' is invoked in quantitation analysis; this correction is a normalization to set the central tendency of protein ratios to unity." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002431 name: Paragon: channel to use as denominator in ratios def: "The Paragon method setting that controls which label channel is used as the denominator in calculating relative expression ratios." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002432 name: search engine specific input metadata def: "Search engine specific metadata that are not user-controlled settings." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1002433 name: Paragon: modified data dictionary or parameter translation def: "This metric detects if any changes have been made to the originally installed key control files for the software; if no changes have been made, then the software version and settings are sufficient to enable exact reproduction; if changes have been made, then the modified ParameterTranslation- and ProteinPilot DataDictionary-XML files much also be provided in order to exactly reproduce a result." [PSI:PI] is_a: MS:1002432 ! search engine specific input metadata relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002434 name: number of spectra searched def: "Number of spectra in a search." [PSI:PI] is_a: MS:1001249 ! search input details relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002435 name: data processing start time def: "The time that a data processing action was started." [PSI:MS] is_a: MS:1000630 ! data processing parameter relationship: has_value_type xsd:dateTime ! The allowed value-type for this CV term [Term] id: MS:1002436 name: Paragon: digestion def: "The Paragon method setting indicating the actual digestion agent - unlike other search tools, this setting does not include options that control partial specificity like 'semitrypsin'; if trypsin is used, trypsin is set, and partially conforming peptides are found in the Thorough mode of search; 'None' should be indicated only if there was really no digestion done." [PSI:PI] is_a: MS:1001249 ! search input details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002437 name: number of decoy sequences def: "The number of decoy sequences, if the concatenated target-decoy approach is used." [PSI:PI] is_a: MS:1001011 ! search database details relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1002438 name: spectrum identification list result details def: "Information about the list of PSMs (SpectrumIdentificationList)." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1002439 name: final PSM list def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is the final set of identifications to be interpreted by consuming software. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum must not be referenced from more than one SpectrumIdentificationResult." [PSI:PI] is_a: MS:1002438 ! spectrum identification list result details [Term] id: MS:1002440 name: intermediate PSM list def: "A flag on a list of PSMs (SpectrumIdentificationList) to indicate that this is not the final set of identifications to be interpreted by consuming software. This term should be used when results are provided from multiple search engines for the results from each search engine before they are combined to give consensus identifications. Amongst the set of SpectrumIdentificationList(s) that are flagged with the term, each spectrum may be referenced from more than one SpectrumIdentificationResult." [PSI:PI] is_a: MS:1002438 ! spectrum identification list result details [Term] id: MS:1002441 name: Andi-MS format def: "AIA Analytical Data Interchange file format for mass spectrometry data." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002442 name: chromatograph file format def: "The format of the chromatography file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format." [PSI:PI] is_a: MS:1001459 ! file format [Term] id: MS:1002443 name: Andi-CHROM format def: "AIA Analytical Data Interchange file format for chromatography data." [PSI:PI] is_a: MS:1002442 ! chromatograph file format [Term] id: MS:1002444 name: 6420 Triple Quadrupole LC/MS def: "The 6420 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002445 name: 6460 Triple Quadrupole LC/MS def: "The 6460 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds Agilent Jet Stream (AJS) technology to increase sensitivity." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002446 name: 6490 Triple Quadrupole LC/MS def: "The 6490 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer. It is similar to the 6420 but adds the Agilent iFunnel technology to increase sensitivity." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002447 name: Paragon:special factor def: "The Paragon method setting indicating a list of one or more 'special factors', which generally capture secondary effects (relative to other settings) as a set of probabilities of modification features that override the assumed levels. For example the 'gel-based ID' special factor causes an increase probability of oxidation on several resides because of the air exposure impact on a gel, in addition to other effects." [PSI:PI] is_a: MS:1002421 ! Paragon input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002448 name: PEAKS:inChorusPeptideScore def: "The PEAKS inChorus peptide score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002449 name: PEAKS:inChorusProteinScore def: "The PEAKS inChorus protein score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002450 name: param: b ion-H3PO4 DEPRECATED def: "Ion b-H3PO4: b ion with lost phosphoric acid." [PSI:PI] is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1002451 name: param: y ion-H3PO4 DEPRECATED def: "Ion y-H3PO4: y ion with lost phosphoric acid." [PSI:PI] is_a: MS:1001066 ! ions series considered in search [Term] id: MS:1002452 name: Maui def: "The Maltcms Graphical User Interface." [PSI:PI, http://maltcms.sf.net] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002453 name: No fixed modifications searched def: "No fixed modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI] is_a: MS:1002094 ! common search engine input parameter [Term] id: MS:1002454 name: No variable modifications searched def: "No variable modifications are included as a parameter for the search, and therefore they are not reported." [PSI:PI] is_a: MS:1002094 ! common search engine input parameter [Term] id: MS:1002455 name: H2O neutral loss def: "OBSOLETE Neutral loss of water." [PSI:PI] comment: This term was obsoleted because it should be replaced by MS:1000336 with value H2O. is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search is_obsolete: true [Term] id: MS:1002456 name: NH3 neutral loss def: "OBSOLETE Neutral loss of ammonia." [PSI:PI] comment: This term was obsoleted because it should be replaced by MS:1000336 with value NH3. is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search is_obsolete: true [Term] id: MS:1002457 name: H3PO4 neutral loss def: "OBSOLETE Neutral loss of phosphoric acid." [PSI:PI] comment: This term was obsoleted because it should be replaced by MS:1000336 with value H3PO4. is_a: MS:1000336 ! neutral loss is_a: MS:1002473 ! ion series considered in search is_obsolete: true [Term] id: MS:1002458 name: PeptideShaker def: "PeptideShaker is a software for the interpretation of proteomics identification results." [PSI:PI, http://peptide-shaker.googlecode.com] is_a: MS:1001456 ! analysis software [Term] id: MS:1002459 name: MS Amanda csv format def: "MS Amanda csv output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1002460 name: protein group-level global FNR def: "Estimation of the global false negative rate of protein groups." [PSI:PI] is_a: MS:1002706 ! protein group-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002461 name: protein group-level confidence def: "Estimation of the global confidence of protein groups." [PSI:PI] is_a: MS:1002348 ! protein group-level identification statistic [Term] id: MS:1002462 name: peptide sequence-level global FNR def: "Estimation of the global false negative rate for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1002703 ! peptide sequence-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002463 name: peptide sequence-level global confidence def: "Estimation of the global confidence for distinct peptides once redundant identifications of the same peptide have been removed (id est multiple PSMs have been collapsed to one entry)." [PSI:PI] is_a: MS:1002703 ! peptide sequence-level result list statistic [Term] id: MS:1002464 name: PSM-level global FNR def: "Estimation of the global false negative rate of peptide spectrum matches." [PSI:PI] is_a: MS:1002701 ! PSM-level result list statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive [Term] id: MS:1002465 name: PSM-level global confidence def: "Estimation of the global confidence of peptide spectrum matches." [PSI:PI] is_a: MS:1002701 ! PSM-level result list statistic [Term] id: MS:1002466 name: PeptideShaker PSM score def: "The probability based PeptideShaker PSM score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002467 name: PeptideShaker PSM confidence def: "The probability based PeptideShaker PSM confidence." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002468 name: PeptideShaker peptide score def: "The probability based PeptideShaker peptide score." [PSI:PI] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002469 name: PeptideShaker peptide confidence def: "The probability based PeptideShaker peptide confidence." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002470 name: PeptideShaker protein group score def: "The probability based PeptideShaker protein group score." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002471 name: PeptideShaker protein group confidence def: "The probability based PeptideShaker protein group confidence." [PSI:PI] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002472 name: trap-type collision-induced dissociation def: "A collision-induced dissociation process that occurs in a trap-type collision cell." [PSI:PI] is_a: MS:1000133 ! collision-induced dissociation [Term] id: MS:1002473 name: ion series considered in search def: "The description of the ion fragment series (including charges and neutral losses) that are considered by the search engine." [PSI:PI] is_a: MS:1001249 ! search input details [Term] id: MS:1002474 name: ProteoAnnotator:non-canonical gene model score def: "The sum of peptide-level scores for peptides mapped only to non-canonical gene models within the group." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002475 name: ProteoAnnotator:count alternative peptides def: "The count of the number of peptide sequences mapped to non-canonical gene models only within the group." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002476 name: ion mobility drift time def: "Drift time of an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This time might refer to the central value of a bin into which all ions within a narrow range of drift time have been aggregated." [PSI:MS] is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute is_a: MS:1003254 ! peak attribute relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002477 name: mean ion mobility drift time array def: "Array of population mean ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002478 name: mean charge array def: "Array of mean charge values where the mean charge is calculated as a weighted mean of the charges of individual peaks that are aggregated into a processed spectrum." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" is_a: MS:1000513 ! binary data array [Term] id: MS:1002479 name: regular expression def: "Regular expression." [PSI:PI] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1002480 name: regular expression for a digital object identifier (DOI) def: "(10[.][0-9]\{4,\}(?:[.][0-9]+)*/(?:(?![\"&\'<>])[^ \t\\r\n\\v\\f])+)." [PSI:PI, http://dx.doi.org/] is_a: MS:1002479 ! regular expression [Term] id: MS:1002481 name: higher energy beam-type collision-induced dissociation def: "A collision-induced dissociation process wherein the projectile ion has the translational energy higher than approximately 1000 eV." [PSI:MS] is_a: MS:1000422 ! beam-type collision-induced dissociation [Term] id: MS:1002482 name: statistical threshold def: "Estimated statistical threshold." [PSI:MS] is_a: MS:1001060 ! quality estimation method details [Term] id: MS:1002483 name: PSM-level statistical threshold def: "Estimated statistical threshold at PSM-level." [PSI:MS] is_a: MS:1002573 ! spectrum identification statistical threshold [Term] id: MS:1002484 name: peptide-level statistical threshold def: "Estimated statistical threshold at peptide-level." [PSI:MS] is_a: MS:1002573 ! spectrum identification statistical threshold [Term] id: MS:1002485 name: protein-level statistical threshold def: "Estimated statistical threshold at protein-level." [PSI:MS] is_a: MS:1002572 ! protein detection statistical threshold [Term] id: MS:1002486 name: protein group-level statistical threshold def: "Estimated statistical threshold at protein group-level." [PSI:PI] is_a: MS:1002572 ! protein detection statistical threshold [Term] id: MS:1002487 name: MassIVE dataset identifier def: "Dataset identifier issued by the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002488 name: MassIVE dataset URI def: "URI that allows the access to one dataset in the MassIVE repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002489 name: special processing def: "Details describing a special processing." [PSI:PI] is_a: MS:1001080 ! search type relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1002490 name: peptide-level scoring def: "Peptide-level scoring performed." [PSI:PI] is_a: MS:1002489 ! special processing [Term] id: MS:1002491 name: modification localization scoring def: "Modification localization scoring performed." [PSI:PI] is_a: MS:1002489 ! special processing [Term] id: MS:1002492 name: consensus scoring def: "Consensus multiple search engine approach performed." [PSI:PI] is_a: MS:1002489 ! special processing [Term] id: MS:1002493 name: sample pre-fractionation def: "Sample pre-fractionation performed." [PSI:PI] is_a: MS:1002489 ! special processing [Term] id: MS:1002494 name: crosslinking search def: "Crosslinking search performed." [PSI:PI] synonym: "cross-linking search" EXACT [] is_a: MS:1002489 ! special processing [Term] id: MS:1002495 name: no special processing def: "No special processing performed." [PSI:PI] is_a: MS:1002489 ! special processing [Term] id: MS:1002496 name: group PSMs by sequence def: "Group PSMs by distinct peptide sequence ignoring modifications." [PSI:PI] is_a: MS:1002658 ! identification parameter [Term] id: MS:1002497 name: group PSMs by sequence with modifications def: "Group PSMs by distinct peptide sequence with taking modifications into account." [PSI:PI] is_a: MS:1002658 ! identification parameter [Term] id: MS:1002498 name: group PSMs by sequence with modifications and charge def: "Group PSMs by distinct peptide sequence with taking modifications and charge into account." [PSI:PI] is_a: MS:1002658 ! identification parameter [Term] id: MS:1002499 name: peptide level score def: "OBSOLETE Peptide level score." [PSI:PI] comment: This term was obsoleted because it was never intended to go in the CV. is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic is_obsolete: true [Term] id: MS:1002500 name: peptide passes threshold def: "A Boolean attribute to determine whether the peptide has passed the threshold indicated in the file." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002501 name: no PSM threshold def: "Indicating that no PSM threshold was used." [PSI:PI] is_a: MS:1002701 ! PSM-level result list statistic [Term] id: MS:1002502 name: no peptide-level threshold def: "Indicating that no peptide-level threshold was used." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute [Term] id: MS:1002503 name: PSM is used for peptide-level scoring def: "Flags a PSM that it is used for peptide-level scoring." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute [Term] id: MS:1002504 name: modification index def: "The order of modifications to be referenced elsewhere in the document." [PSI:PI] is_a: MS:1001055 ! modification parameters relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002505 name: regular expression for modification localization scoring def: "(?[0-9]+):(?[01][.][0-9]+(?:[Ee][+\-]?[0-9]+)?):(?[0-9]+(?:[|][0-9]+)*):(?true|false)" [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1002506 name: modification position score def: "Modification position score." [PSI:PI] is_a: MS:1001055 ! modification parameters [Term] id: MS:1002507 name: modification rescoring:false localization rate def: "Mod position score: false localization rate." [PSI:PI] is_a: MS:1002506 ! modification position score relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002508 name: crosslinking attribute def: "Crosslinking attribute." [PSI:PI] synonym: "cross-linking attribute" EXACT [] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002509 name: crosslink donor def: "The crosslinking donor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] synonym: "cross-link donor" EXACT [] is_a: MS:1002508 ! crosslinking attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002510 name: crosslink acceptor def: "Crosslinking acceptor, assigned according to the following rules: the export software SHOULD use the following rules to choose the crosslink donor as the: longer peptide, then higher peptide neutral mass, then alphabetical order." [PSI:PI] synonym: "cross-link acceptor" EXACT [] is_a: MS:1002508 ! crosslinking attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002511 name: crosslink spectrum identification item def: "Crosslinked spectrum identification item." [PSI:PI] synonym: "cross-link spectrum identification item" EXACT [] is_a: MS:1002508 ! crosslinking attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002512 name: crosslinking score def: "Crosslinking scoring value." [PSI:PI] synonym: "cross-linking score" EXACT [] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002513 name: molecules per cell def: "The absolute abundance of protein in a cell." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002514 name: absolute quantitation analysis def: "Absolute quantitation analysis." [PSI:PI] is_a: MS:1001833 ! quantitation analysis summary [Term] id: MS:1002515 name: internal peptide reference used def: "States whether an internal peptide reference is used or not in absolute quantitation analysis." [PSI:PI] is_a: MS:1001832 ! quantitation software comment or customizations relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002516 name: internal protein reference used def: "States whether an internal protein reference is used or not in absolute quantitation analysis." [PSI:PI] is_a: MS:1001832 ! quantitation software comment or customizations relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002517 name: internal reference abundance def: "The absolute abundance of the spiked in reference peptide or protein used for absolute quantitation analysis." [PSI:PI] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002518 name: Progenesis:protein group normalised abundance def: "The data type normalised abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] is_a: MS:1002739 ! protein group-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002519 name: Progenesis:protein group raw abundance def: "The data type raw abundance for protein groups produced by Progenesis LC-MS." [PSI:PI] is_a: MS:1002739 ! protein group-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002520 name: peptide group ID def: "Peptide group identifier for peptide-level stats." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002521 name: mass spectrometry imaging def: "A technique in which mass spectra are acquired in a spatially resolved manner. This is typically achieved by scanning a laser or primary ion beam over a sample and acquiring a mass spectrum at each position." [PSI:PI] is_a: MS:1000857 ! run attribute [Term] id: MS:1002522 name: ProteomeDiscoverer:1. Static Terminal Modification def: "Determine 1st static terminal post-translational modifications (PTMs)." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002523 name: Q Exactive HF def: "Thermo Scientific Q Exactive." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002524 name: PepFinder def: "Thermo Scientific PepFinder BioPharma analysis software." [PSI:PI] is_a: MS:1001457 ! data processing software [Term] id: MS:1002525 name: TSQ 8000 Evo def: "Thermo Scientific TSQ 8000 Evo MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002526 name: Exactive Plus def: "Thermo Scientific Exactive Plus MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002527 name: instrument specific scan attribute def: "Instrument specific scan properties that are associated with a value." [PSI:PI] is_a: MS:1000503 ! scan attribute [Term] id: MS:1002528 name: synchronous prefilter selection def: "Synchronous prefilter selection." [PSI:PI] synonym: "SPS" EXACT [] is_a: MS:1002527 ! instrument specific scan attribute [Term] id: MS:1002529 name: resolution array def: "A data array of resolution values." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array [Term] id: MS:1002530 name: baseline array def: "A data array of signal baseline values (the signal in the absence of analytes)." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array [Term] id: MS:1002531 name: UIMF format def: "SQLite-based file format created at Pacific Northwest National Lab. It stores an intermediate analysis of ion-mobility mass spectrometry data." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002532 name: UIMF nativeID format def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger frameType=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1002533 name: TripleTOF 6600 def: "SCIEX TripleTOF 6600, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002534 name: ProLuCID:xcorr def: "The ProLuCID result 'XCorr'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002535 name: ProLuCID:deltacn def: "The ProLuCID result 'DeltaCn'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002536 name: D-Score def: "D-Score for PTM site location at the PSM-level." [PMID:23307401] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002537 name: MD-Score def: "MD-Score for PTM site location at the PSM-level." [PMID:21057138] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002538 name: PTM localization confidence metric def: "Localization confidence metric for a post translational modification (PTM)." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002539 name: PeptideShaker PTM confidence type def: "PeptideShaker quality criteria for the confidence of PTM localizations." [PSI:PI] is_a: MS:1002538 ! PTM localization confidence metric relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002540 name: PeptideShaker PSM confidence type def: "PeptideShaker quality criteria for the confidence of PSM's." [PSI:PI] is_a: MS:1002347 ! PSM-level identification statistic relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002541 name: PeptideShaker peptide confidence type def: "PeptideShaker quality criteria for the confidence of peptide identifications." [PSI:PI] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002542 name: PeptideShaker protein confidence type def: "PeptideShaker quality criteria for the confidence of protein identifications." [PSI:PI] is_a: MS:1001116 ! single protein identification statistic relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002543 name: xiFDR def: "Target/Decoy based FDR estimation for crosslinking peptide-identifications." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002544 name: xi def: "Search engine for crosslinked peptides." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002545 name: xi:score def: "The xi result 'Score'." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002546 name: Skyline mzQuantML converter def: "A software package to convert Skyline report to mzQuantML." [PSI:PI, http://code.google.com/p/srm-mzquantml-convertor/] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1002547 name: normalized spectral abundance factor def: "A normalized spectral abundance factor (NSAF)." [DOI:10.1021/pr060161n, PMID:16944946] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002548 name: distributed normalized spectral abundance factor def: "A distributed normalized spectral abundance factor (dNSAF)." [DOI:10.1021/ac9023999, PMID:20166708] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002549 name: PTM localization distinct peptide-level statistic def: "Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence." [PSI:PI] is_a: MS:1002689 ! PTM localization single result statistic [Term] id: MS:1002550 name: peptide:phosphoRS score def: "phosphoRS score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002551 name: peptide:Ascore def: "A-score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002552 name: peptide:H-Score def: "H-Score for peptide phosphorylation site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002553 name: peptide:D-Score def: "D-Score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002554 name: peptide:MD-Score def: "MD-Score for PTM site location at the peptide-level." [PSI:PI] is_a: MS:1002549 ! PTM localization distinct peptide-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002555 name: PTM localization score threshold def: "Threshold for PTM site location score." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1002556 name: Ascore threshold def: "Threshold for Ascore PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002557 name: D-Score threshold def: "Threshold for D-score PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002558 name: MD-Score threshold def: "Threshold for MD-score PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002559 name: H-Score threshold def: "Threshold for H-score PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002560 name: DeBunker:score threshold def: "Threshold for DeBunker PTM site location score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002561 name: Mascot:PTM site assignment confidence threshold def: "Threshold for Mascot PTM site assignment confidence." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002562 name: MSQuant:PTM-score threshold def: "Threshold for MSQuant:PTM-score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002563 name: MaxQuant:PTM Score threshold def: "Threshold for MaxQuant:PTM Score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002564 name: MaxQuant:P-site localization probability threshold def: "Threshold for MaxQuant:P-site localization probability." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002565 name: MaxQuant:PTM Delta Score threshold def: "Threshold for MaxQuant:PTM Delta Score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002566 name: MaxQuant:Phospho (STY) Probabilities threshold def: "Threshold for MaxQuant:Phospho (STY) Probabilities." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002567 name: phosphoRS score threshold def: "Threshold for phosphoRS score." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002568 name: phosphoRS site probability threshold def: "Threshold for phosphoRS site probability." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002569 name: ProteomeDiscoverer:Number of Spectra Processed At Once def: "Number of spectra processed at once in a ProteomeDiscoverer search." [PSI:PI] is_a: MS:1002101 ! ProteomeDiscoverer input parameter relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002570 name: sequence multiply subsumable protein def: "A protein for which the matched peptide sequences are the same, or a subset of, the matched peptide sequences for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002571 name: spectrum multiply subsumable protein def: "A protein for which the matched spectra are the same, or a subset of, the matched spectra for two or more other proteins combined. These other proteins need not all be in the same group." [PSI:PI] is_a: MS:1001101 ! protein group or subset relationship relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002572 name: protein detection statistical threshold def: "Estimated statistical threshold used for protein detection." [PSI:MS] is_a: MS:1002482 ! statistical threshold [Term] id: MS:1002573 name: spectrum identification statistical threshold def: "Estimated statistical threshold used for spectrum identification." [PSI:MS] is_a: MS:1002482 ! statistical threshold [Term] id: MS:1002574 name: ASAPRatio def: "A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc." [PSI:PI] is_a: MS:1002286 ! Trans-Proteomic Pipeline software [Term] id: MS:1002575 name: Tide def: "Tide open-source sequence search program developed at the University of Washington." [PMID:21761931] is_a: MS:1001456 ! analysis software [Term] id: MS:1002576 name: Andromeda result format def: "Andromeda result file output format." [PSI:PI] is_a: MS:1001040 ! intermediate analysis format [Term] id: MS:1002577 name: 2000 QTRAP def: "SCIEX 2000 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002578 name: 2500 QTRAP def: "SCIEX 2500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002579 name: 3500 QTRAP def: "SCIEX 3500 QTRAP." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002580 name: QTRAP 4500 def: "SCIEX QTRAP 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002581 name: QTRAP 6500 def: "SCIEX QTRAP 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002582 name: QTRAP 6500+ def: "SCIEX QTRAP 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002583 name: TripleTOF 4600 def: "SCIEX TripleTOF 4600 time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002584 name: TripleTOF 5600+ def: "SCIEX TripleTOF 5600+ time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002585 name: API 100 def: "Applied Biosystems/MDS SCIEX API 100 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002586 name: API 100LC def: "Applied Biosystems/MDS SCIEX API 100LC MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002587 name: API 165 def: "Applied Biosystems/MDS SCIEX API 165 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002588 name: API 300 def: "Applied Biosystems/MDS SCIEX API 300 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002589 name: API 350 def: "Applied Biosystems/MDS SCIEX API 350 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002590 name: API 365 def: "Applied Biosystems/MDS SCIEX API 365 MS." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002591 name: Triple Quad 3500 def: "SCIEX Triple Quad 3500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002592 name: Triple Quad 4500 def: "SCIEX Triple Quad 4500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002593 name: Triple Quad 5500 def: "SCIEX Triple Quad 5500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002594 name: Triple Quad 6500 def: "SCIEX Triple Quad 6500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002595 name: Triple Quad 6500+ def: "SCIEX Triple Quad 6500+." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002596 name: ProLuCID def: "The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute." [PMID:26171723] is_a: MS:1001456 ! analysis software [Term] id: MS:1002597 name: MS1 format def: "MS1 file format for MS1 spectral data." [PMID:15317041, DOI:10.1002/rcm.1603] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002598 name: DTASelect def: "Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches." [PMID:12643522, http://fields.scripps.edu/DTASelect/] is_a: MS:1001456 ! analysis software [Term] id: MS:1002599 name: splash key def: "Spectral Hash key, an unique identifier for spectra." [PMID:27824832] is_a: MS:1001405 ! spectrum identification result details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002600 name: PRIDE XML def: "Internal data and submission format of the PRIDE database." [http://ftp.pride.ebi.ac.uk/pride/resources/schema/pride/pride.xsd] is_a: MS:1002130 ! identification file format is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1002601 name: mzTab def: "Tabular result format for proteomics and metabolomics experiments." [PMID:24980485, http://www.psidev.info/mztab/] is_a: MS:1000914 ! tab delimited text format [Term] id: MS:1002602 name: sample label def: "Reagent used in labeled quantification methods." [PSI:PI] is_a: MS:1002111 ! assay label attribute is_a: MS:1000548 ! sample attribute [Term] id: MS:1002603 name: ICAT reagent def: "Isotope coded affinity tag reagent." [PSI:PI] is_a: MS:1002602 ! sample label [Term] id: MS:1002604 name: ICAT heavy reagent def: "The name of the sample labelled with the heavy ICAT label." [PSI:PI] is_a: MS:1002603 ! ICAT reagent [Term] id: MS:1002605 name: ICAT light reagent def: "The name of the sample labelled with the light ICAT label." [PSI:PI] is_a: MS:1002603 ! ICAT reagent [Term] id: MS:1002606 name: ICPL reagent def: "Isotope coded protein labeling reagent." [PSI:PI] is_a: MS:1002602 ! sample label [Term] id: MS:1002607 name: ICPL reagent 0 def: "The name of the sample labelled with the ICPL reagent 0." [PSI:PI] is_a: MS:1002606 ! ICPL reagent [Term] id: MS:1002608 name: ICPL reagent 4 def: "The name of the sample labelled with the ICPL reagent 4." [PSI:PI] is_a: MS:1002606 ! ICPL reagent [Term] id: MS:1002609 name: ICPL reagent 6 def: "The name of the sample labelled with the ICPL reagent 6." [PSI:PI] is_a: MS:1002606 ! ICPL reagent [Term] id: MS:1002610 name: ICPL reagent 10 def: "The name of the sample labelled with the ICPL reagent 10." [PSI:PI] is_a: MS:1002606 ! ICPL reagent [Term] id: MS:1002611 name: SILAC reagent def: "Stable isotope labeling with amino acids in cell culture reagent." [PSI:PI] is_a: MS:1002602 ! sample label [Term] id: MS:1002612 name: SILAC heavy reagent def: "The name of the sample labelled with the heavy SILAC label." [PSI:PI] is_a: MS:1002611 ! SILAC reagent [Term] id: MS:1002613 name: SILAC medium reagent def: "The name of the sample labelled with the medium SILAC label." [PSI:PI] is_a: MS:1002611 ! SILAC reagent [Term] id: MS:1002614 name: SILAC light reagent def: "The name of the sample labelled with the light SILAC label." [PSI:PI] is_a: MS:1002611 ! SILAC reagent [Term] id: MS:1002615 name: TMT reagent def: "Tandem mass tag reagent used in TMT, glycoTMT, iodoTMT, aminoxyTMT or hydrazideTMT isobaric labeling." [PSI:PI] is_a: MS:1002602 ! sample label [Term] id: MS:1002616 name: TMT reagent 126 def: "The name of the sample labelled with the TMT reagent 126." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002617 name: TMT reagent 127 def: "The name of the sample labelled with the TMT reagent 127." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002618 name: TMT reagent 128 def: "The name of the sample labelled with the TMT reagent 128." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002619 name: TMT reagent 129 def: "The name of the sample labelled with the TMT reagent 129." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002620 name: TMT reagent 130 def: "The name of the sample labelled with the TMT reagent 130." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002621 name: TMT reagent 131 def: "The name of the sample labelled with the TMT reagent 131." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002622 name: iTRAQ reagent def: "Isobaric tag for relative and absolute quantitation (iTRAQ or iTRAQH) reagent." [PSI:PI] is_a: MS:1002602 ! sample label [Term] id: MS:1002623 name: iTRAQ reagent 113 def: "The name of the sample labelled with the iTRAQ reagent 113." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002624 name: iTRAQ reagent 114 def: "The name of the sample labelled with the iTRAQ reagent 114." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002625 name: iTRAQ reagent 115 def: "The name of the sample labelled with the iTRAQ reagent 115." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002626 name: iTRAQ reagent 116 def: "The name of the sample labelled with the iTRAQ reagent 116." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002627 name: iTRAQ reagent 117 def: "The name of the sample labelled with the iTRAQ reagent 117." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002628 name: iTRAQ reagent 118 def: "The name of the sample labelled with the iTRAQ reagent 118." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002629 name: iTRAQ reagent 119 def: "The name of the sample labelled with the iTRAQ reagent 119." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002630 name: iTRAQ reagent 121 def: "The name of the sample labelled with the iTRAQ reagent 121." [PSI:PI] is_a: MS:1002622 ! iTRAQ reagent [Term] id: MS:1002631 name: electron-transfer/higher-energy collision dissociation def: "Dissociation process combining electron-transfer dissociation and higher-energy collision dissociation. It combines ETD (reaction time) followed by HCD (activation energy)." [PSI:PI] synonym: "EThcD" EXACT [] is_a: MS:1003181 ! combined dissociation method [Term] id: MS:1002632 name: jPOST dataset identifier def: "Dataset identifier issued by the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002633 name: jPOST dataset URI def: "URI that allows the access to one dataset in the jPOST repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002634 name: Q Exactive Plus def: "Thermo Scientific Q Exactive Plus." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002635 name: proteogenomics search def: "Proteogenomics search performed." [PSI:PI] is_a: MS:1002489 ! special processing [Term] id: MS:1002636 name: proteogenomics attribute def: "Proteogenomics attribute." [PSI:PI] is_a: MS:1001105 ! peptide sequence-level identification attribute [Term] id: MS:1002637 name: chromosome name def: "The name or number of the chromosome to which a given peptide has been mapped." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002638 name: chromosome strand def: "The strand (+ or -) to which the peptide has been mapped." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002639 name: peptide start on chromosome def: "OBSOLETE The overall start position on the chromosome to which a peptide has been mapped i.e. the position of the first base of the first codon, using a zero-based counting system." [PSI:PI] comment: This term was obsoleted because it contains redundant info contained in term MS:1002643 - peptide start positions on chromosome. is_a: MS:1002636 ! proteogenomics attribute is_obsolete: true relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002640 name: peptide end on chromosome def: "The overall end position on the chromosome to which a peptide has been mapped i.e. the position of the third base of the last codon, using a zero-based counting system." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002641 name: peptide exon count def: "The number of exons to which the peptide has been mapped." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002642 name: peptide exon nucleotide sizes def: "A comma separated list of the number of DNA bases within each exon to which a peptide has been mapped. Assuming standard operation of a search engine, the peptide exon sizes should sum to exactly three times the peptide length." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002643 name: peptide start positions on chromosome def: "A comma separated list of start positions within exons to which the peptide has been mapped, relative to peptide-chromosome start, assuming a zero-based counting system. The first value MUST match the value in peptide start on chromosome." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002644 name: genome reference version def: "The reference genome and versioning string as used for mapping. All coordinates are within this frame of reference." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002645 name: MSDK def: "Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data." [PSI:PI, http://msdk.github.io/] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002646 name: native spectrum identifier format, combined spectra def: "Describes how the native spectrum identifiers that have been combined prior to searching or interpretation are formated." [PSI:PI] synonym: "nativeID format, combined spectra" EXACT [] relationship: part_of MS:1000577 ! source data file [Term] id: MS:1002647 name: Thermo nativeID format, combined spectra def: "Thermo comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002648 name: Waters nativeID format, combined spectra def: "Waters comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002649 name: WIFF nativeID format, combined spectra def: "WIFF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002650 name: Bruker/Agilent YEP nativeID format, combined spectra def: "Bruker/Agilent comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002651 name: Bruker BAF nativeID format, combined spectra def: "Bruker BAF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002652 name: Bruker FID nativeID format, combined spectra def: "Bruker FID comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: The nativeID must be the same as the source file ID. is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002653 name: multiple peak list nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion of peak list files with multiple spectra, i.e. MGF, PKL, merged DTA files. Index is the spectrum number in the file, starting from 0. is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002654 name: single peak list nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: The nativeID must be the same as the source file ID. Used for conversion of peak list files with one spectrum per file, typically folder of PKL or DTAs, each sourceFileRef is different. is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002655 name: scan number only nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived. is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002656 name: spectrum identifier nativeID format, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: Used for conversion from mzData. The spectrum id attribute is referenced. is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002657 name: mzML unique identifier, combined spectra def: "Comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] comment: A unique identifier of a spectrum stored in an mzML file. is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002658 name: identification parameter def: "Identification parameter for the search engine run." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1002659 name: UniProtKB text sequence format def: "Text-based format used by UniProtKB for sequence entries." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1002660 name: UniProtKB XML sequence format def: "XML-based format used by UniProtKB for sequence entries." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1002661 name: Morpheus def: "Morpheus search engine." [PMID:23323968] is_a: MS:1001456 ! analysis software [Term] id: MS:1002662 name: Morpheus:Morpheus score def: "Morpheus score for PSMs." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002663 name: Morpheus:summed Morpheus score def: "Summed Morpheus score for protein groups." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002664 name: interaction score derived from crosslinking def: "Parent term for interaction scores derived from crosslinking." [PSI:PI] synonym: "interaction score derived from cross-linking" EXACT [] is_a: MS:1002675 ! crosslinking result details relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002665 name: regular expression for interaction scores derived from crosslinking def: "((?[0-9]+)[.](?[a|b]):(?[0-9]+|null):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?):(?true|false))|(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+)?)" [PSI:PI] synonym: "regular expression for interaction scores derived from cross-linking" EXACT [] is_a: MS:1002479 ! regular expression [Term] id: MS:1002666 name: impact II def: "Bruker Daltonics' impact II." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002667 name: impact HD def: "Bruker Daltonics' impact HD." [PSI:MS] is_a: MS:1001536 ! Bruker Daltonics micrOTOF series [Term] id: MS:1002668 name: frag: iTRAQ 4plex reporter ion def: "Standard reporter ion for iTRAQ 4Plex. The value slot holds the integer mass of the iTRAQ 4Plex reporter ion, e.g. 114." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002669 name: frag: iTRAQ 8plex reporter ion def: "Standard reporter ion for iTRAQ 8Plex. The value slot holds the integer mass of the iTRAQ 8Plex reporter ion, e.g. 113." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002670 name: frag: TMT reporter ion def: "Standard reporter ion for TMT. The value slot holds the integer mass of the TMT reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127N." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002671 name: frag: TMT ETD reporter ion def: "Standard reporter ion for TMT with ETD fragmentation. The value slot holds the integer mass of the TMT ETD reporter ion and can be suffixed with either N or C, indicating whether the mass difference is encoded at a Nitrogen or Carbon atom, e.g. 127C." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002672 name: no modification threshold def: "No statistical threshold for accepting or rejecting that a modification position." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold [Term] id: MS:1002673 name: OpenXQuest def: "Cross-Linking MS search engine." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1002674 name: X500R QTOF def: "SCIEX X500R QTOF, a quadrupole - quadrupole - time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1002675 name: crosslinking result details def: "This subsection describes terms which can describe details of crosslinking results." [PSI:PI] synonym: "cross-linking result details" EXACT [] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1002676 name: protein-pair-level global FDR def: "Estimation of the global false discovery rate of proteins-pairs in crosslinking experiments." [PSI:PI] is_a: MS:1002664 ! interaction score derived from crosslinking relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002677 name: residue-pair-level global FDR def: "Estimation of the global false discovery rate of residue-pairs in crosslinking experiments." [PSI:PI] is_a: MS:1002664 ! interaction score derived from crosslinking relationship: has_domain MS:1003277 ! value between -1 and 1 inclusive relationship: has_regexp MS:1002665 ! regular expression for interaction scores derived from crosslinking relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002678 name: supplemental beam-type collision-induced dissociation def: "A supplemental collision-induced dissociation process that occurs in a beam-type collision cell in addition to another primary type of dissociation." [PSI:MS] is_a: MS:1000422 ! beam-type collision-induced dissociation [Term] id: MS:1002679 name: supplemental collision-induced dissociation def: "The dissociation of an ion after supplemental collisional excitation." [PSI:MS] is_a: MS:1000133 ! collision-induced dissociation [Term] id: MS:1002680 name: supplemental collision energy def: "Energy for an ion experiencing supplemental collision with a stationary gas particle resulting in dissociation of the ion." [PSI:MS] is_a: MS:1000510 ! precursor activation attribute relationship: has_units UO:0000266 ! electronvolt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002681 name: OpenXQuest:combined score def: "OpenXQuest's combined score for a crosslink spectrum match." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002682 name: OpenXQuest:xcorr xlink def: "OpenXQuest's cross-correlation of crosslinked ions subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002683 name: OpenXQuest:xcorr common def: "OpenXQuest's cross-correlation of unlinked ions subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002684 name: OpenXQuest:match-odds def: "OpenXQuest's match-odds subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002685 name: OpenXQuest:intsum def: "OpenXQuest's sum of matched peak intensity subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002306 ! value greater than zero relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002686 name: OpenXQuest:wTIC def: "OpenXQuest's weighted percent of total ion current subscore." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002687 name: analysis attribute def: "Attribute of an item in the result of mass spectrometry proteomics data analysis." [PSI:PI] is_a: MS:1001405 ! spectrum identification result details [Term] id: MS:1002688 name: PTM localization attribute def: "Statistic derived from a post-translational modification localization analysis." [PSI:PI] is_a: MS:1002687 ! analysis attribute [Term] id: MS:1002689 name: PTM localization single result statistic def: "Statistic for a single item derived from a post-translational modification localization analysis." [PSI:PI] is_a: MS:1002688 ! PTM localization attribute [Term] id: MS:1002690 name: PTM localization result list statistic def: "Statistic for all items derived from a post-translational modification localization analysis." [PSI:PI] is_a: MS:1002688 ! PTM localization attribute [Term] id: MS:1002691 name: global FLR def: "Global false localization rate for all localizations in a dataset." [PSI:PI] is_a: MS:1002690 ! PTM localization result list statistic [Term] id: MS:1002692 name: local FLR at threshold def: "Local false localization rate for the bottom item in list of localizations sorted from most to least confident." [PSI:PI] is_a: MS:1002690 ! PTM localization result list statistic [Term] id: MS:1002693 name: identification attribute def: "Attribute of an identification item in the result of mass spectrometry proteomics data analysis." [PSI:PI] is_a: MS:1002687 ! analysis attribute [Term] id: MS:1002694 name: single identification result attribute def: "Attribute of a single identification item (as opposed to a list) in the result of mass spectrometry proteomics data analysis." [PSI:PI] is_a: MS:1002693 ! identification attribute [Term] id: MS:1002695 name: frag: isobaric label ion def: "Fragment ion corresponding to an isobaric label artifact." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002697 name: secondary isotope peak def: "Fragment ion is an isotopic peak other than that monoisotopic peak. This is used in conjuction with another ion type, such as frag: y ion." [PSI:PI] is_a: MS:1002307 ! fragmentation ion type [Term] id: MS:1002698 name: protein cluster identification attribute def: "An attribute of the protein cluster concept as used in mzIdentML." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002699 name: result list attribute def: "General property of an entire result list." [PSI:PI] is_a: MS:1002693 ! identification attribute [Term] id: MS:1002700 name: PSM-level result list attribute def: "General property of the list of all PSMs." [PSI:PI] is_a: MS:1002699 ! result list attribute [Term] id: MS:1002701 name: PSM-level result list statistic def: "Statistic pertaining to the full list of all PSMs." [PSI:PI] is_a: MS:1002700 ! PSM-level result list attribute [Term] id: MS:1002702 name: peptide sequence-level result list attribute def: "General property of all peptide sequences in the list." [PSI:PI] is_a: MS:1002699 ! result list attribute [Term] id: MS:1002703 name: peptide sequence-level result list statistic def: "Statistic pertaining to all peptide sequences in the list." [PSI:PI] is_a: MS:1002702 ! peptide sequence-level result list attribute [Term] id: MS:1002704 name: protein-level result list attribute def: "Attribute of an entire protein list." [PSI:PI] is_a: MS:1002699 ! result list attribute [Term] id: MS:1002705 name: protein-level result list statistic def: "A statistical metric of an entire protein list." [PSI:PI] is_a: MS:1002704 ! protein-level result list attribute [Term] id: MS:1002706 name: protein group-level result list statistic def: "Attrbiute of an entire list of protein groups." [PSI:PI] is_a: MS:1002405 ! protein group-level result list attribute [Term] id: MS:1002707 name: (?=[KR]) def: "Regular expression for LysargiNase." [PSI:PI] is_a: MS:1001180 ! Cleavage agent regular expression [Term] id: MS:1002708 name: LysargiNase def: "Metalloproteinase found in Methanosarcina acetivorans that cleaves on the N-terminal side of lysine and arginine residues." [PMID:25419962] synonym: "Tryp-N" EXACT [] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1002707 ! (?=[KR]) [Term] id: MS:1002709 name: compound data type def: "A data type representing more than a single value." [] [Term] id: MS:1002710 name: list of type def: "A data type defining a list of values of a single type." [] is_a: MS:1002709 ! compound data type [Term] id: MS:1002711 name: list of strings def: "A list of xsd:string." [] is_a: MS:1002710 ! list of type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002712 name: list of integers def: "A list of xsd:integer." [] is_a: MS:1002710 ! list of type relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002713 name: list of floats def: "A list of xsd:float." [] is_a: MS:1002710 ! list of type relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002714 name: FLASHDeconv def: "Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics." [DOI:10.1016/j.cels.2020.01.003] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002719 name: Pegasus BT def: "LECO bench-top GC time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1001800 ! LECO instrument model [Term] id: MS:1002720 name: MSPathFinder def: "PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002721 name: MSPathFinder:SpecEValue def: "MSPathFinder spectral E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002722 name: MSPathFinder:EValue def: "MSPathFinder E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002723 name: MSPathFinder:QValue def: "MSPathFinder Q-value." [PSI:PI] is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002724 name: MSPathFinder:PepQValue def: "MSPathFinder peptide-level Q-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002725 name: MSPathFinder:RawScore def: "MSPathFinder raw score." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002726 name: SYNAPT G2-Si def: "Waters Corporation SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002727 name: MALDI SYNAPT G2-Si def: "Waters Corporation MALDI SYNAPT G2-Si orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002728 name: Vion IMS QTof def: "Waters Corporation Vion IMS QTof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002729 name: Xevo G2-XS Tof def: "Waters Corporation Xevo G2 XS Tof orthogonal acceleration time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002730 name: Xevo TQ-XS def: "Waters Corporation Xevo TQ-XS triple quadrupole mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002731 name: Xevo TQ-S micro def: "Waters Corporation Xevo TQ-S micro triple quadrupole mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1002732 name: Orbitrap Fusion Lumos def: "Thermo Scientific Orbitrap Fusion Lumos mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002733 name: peptide-level spectral count def: "The number of MS2 spectra identified for a peptide sequence specified by the amino acid one-letter codes plus optional PTMs in spectral counting." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002734 name: peptide ion-level spectral count def: "The number of MS2 spectra identified for a molecular ion defined by the peptide sequence represented by the amino acid one-letter codes, plus optional PTMs plus optional charged aducts plus the charge state, in spectral counting." [PSI:PI] is_a: MS:1002737 ! peptide-level quantification datatype relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1002735 name: feature-level quantification datatype def: "The data type of the value reported in a QuantLayer for a feature." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002736 name: PSM-level quantification datatype def: "The data type of the value reported in a QuantLayer for a PSM." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002737 name: peptide-level quantification datatype def: "The data type of the value reported in a QuantLayer for a peptide." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002738 name: protein-level quantification datatype def: "The data type of the value reported in a QuantLayer for a protein." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002739 name: protein group-level quantification datatype def: "The data type of the value reported in a QuantLayer for a protein group." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002740 name: unmapped peptide def: "Within the context of a proteogenomics approach, a peptide sequence that has not been mapped to a genomic location." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute [Term] id: MS:1002741 name: unmapped protein def: "Within the context of a proteogenomics approach, a protein sequence that has not been mapped to a genomic location." [PSI:PI] is_a: MS:1002636 ! proteogenomics attribute [Term] id: MS:1002742 name: noise array def: "A data array of noise values." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array [Term] id: MS:1002743 name: sampled noise m/z array def: "A data array of parallel, independent m/z values for a sampling of noise across a spectrum (typically much smaller than MS:1000514, the m/z array)." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units MS:1000040 ! m/z [Term] id: MS:1002744 name: sampled noise intensity array def: "A data array of intensity values for the amplitude of noise variation superposed on the baseline (MS:1002745) across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units MS:1000131 ! number of detector counts [Term] id: MS:1002745 name: sampled noise baseline array def: "A data array of baseline intensity values (the intensity in the absence of analytes) for a sampling of noise across a spectrum (for use with MS:1002743, sampled noise m/z array)." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array [Term] id: MS:1002746 name: MS-Numpress linear prediction compression followed by zlib compression def: "Compression using MS-Numpress linear prediction compression and zlib." [https://github.com/ms-numpress/ms-numpress] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1002747 name: MS-Numpress positive integer compression followed by zlib compression def: "Compression using MS-Numpress positive integer compression and zlib." [https://github.com/ms-numpress/ms-numpress] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1002748 name: MS-Numpress short logged float compression followed by zlib compression def: "Compression using MS-Numpress short logged float compression and zlib." [https://github.com/ms-numpress/ms-numpress] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1002749 name: Mascot:IntegratedSpectralLibrarySearch def: "Means that Mascot has integrated the search results of database and spectral library search into a single data set." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002750 name: NIST MSPepSearch def: "Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002751 name: NIST MSP format def: "MSP text format defined by the NIST." [PSI:PI] is_a: MS:1001347 ! database file formats [Term] id: MS:1002752 name: database type spectral library def: "Database containing spectra." [PSI:PI] is_a: MS:1001073 ! database type amino acid [Term] id: MS:1002753 name: value between 0 and 1000 inclusive def: "Value range for scores." [PSI:PI] is_a: MS:1002304 ! domain range [Term] id: MS:1002754 name: MSPepSearch:score def: "MSPepSearch score (0 for entirely dissimilar and 1000 for identical observed spectrum and library spectrum." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002753 ! value between 0 and 1000 inclusive [Term] id: MS:1002755 name: combined ms-ms + spectral library search def: "A combined MS2 (with fragment ions) and spectral library search." [PSI:PI] is_a: MS:1001080 ! search type [Term] id: MS:1002756 name: iodoTMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher sulfhydryl-reactive iodo tandem mass tag (iodoTMT) labelling workflow." [PSI:PI, PMID:24926564] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002757 name: glyco-TMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive glyco-tandem mass tag (glyco-TMT) labelling workflow." [PSI:PI, PMID:22455665] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002758 name: aminoxyTMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive aminoxy tandem mass tag (aminoxyTMT) labelling workflow." [PSI:PI, PMID:25337643] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002759 name: hydrazideTMT quantitation analysis def: "Quantitation analysis using the Thermo Fisher carbonyl-reactive hydrazide tandem mass tag (hydrazide-TMT) labelling workflow." [PSI:PI, PMID:25337643] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002760 name: iTRAQH quantitation analysis def: "Quantification analysis using the carbonyl-reactive isobaric tags for relative and absolute quantification hydrazide (iTRAQH) labelling workflow." [PSI:PI, PMID:22926130] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002761 name: DiART quantitation analysis def: "Quantification analysis using the amine-reactive deuterium isobaric amine reactive tag (DiART) labelling workflow." [PSI:PI, PMID:20715779] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002762 name: DiLeu quantitation analysis def: "Quantification analysis using the amine-reactive dimethyl leucine (DiLeu) tag labelling workflow." [PSI:PI, PMID:20715779] is_a: MS:1002009 ! isobaric label quantitation analysis [Term] id: MS:1002763 name: TMT reagent 127N def: "The name of the sample labelled with the TMT reagent 127N." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002764 name: TMT reagent 127C def: "The name of the sample labelled with the TMT reagent 127C." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002765 name: TMT reagent 128N def: "The name of the sample labelled with the TMT reagent 128N." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002766 name: TMT reagent 128C def: "The name of the sample labelled with the TMT reagent 128C." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002767 name: TMT reagent 129N def: "The name of the sample labelled with the TMT reagent 129N." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002768 name: TMT reagent 129C def: "The name of the sample labelled with the TMT reagent 129C." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002769 name: TMT reagent 130N def: "The name of the sample labelled with the TMT reagent 130N." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002770 name: TMT reagent 130C def: "The name of the sample labelled with the TMT reagent 130C." [PSI:PI] is_a: MS:1002615 ! TMT reagent [Term] id: MS:1002771 name: DiART reagent def: "Deuterium isobaric amine reactive tag labeling reagent." [PSI:PI] is_a: MS:1002602 ! sample label [Term] id: MS:1002772 name: DiART reagent 114 def: "The name of the sample labelled with the DiART reagent 114." [PSI:PI] is_a: MS:1002771 ! DiART reagent [Term] id: MS:1002773 name: DiART reagent 115 def: "The name of the sample labelled with the DiART reagent 115." [PSI:PI] is_a: MS:1002771 ! DiART reagent [Term] id: MS:1002774 name: DiART reagent 116 def: "The name of the sample labelled with the DiART reagent 116." [PSI:PI] is_a: MS:1002771 ! DiART reagent [Term] id: MS:1002775 name: DiART reagent 117 def: "The name of the sample labelled with the DiART reagent 117." [PSI:PI] is_a: MS:1002771 ! DiART reagent [Term] id: MS:1002776 name: DiART reagent 118 def: "The name of the sample labelled with the DiART reagent 118." [PSI:PI] is_a: MS:1002771 ! DiART reagent [Term] id: MS:1002777 name: DiART reagent 119 def: "The name of the sample labelled with the DiART reagent 119." [PSI:PI] is_a: MS:1002771 ! DiART reagent [Term] id: MS:1002778 name: DiLeu reagent def: "Dimethyl leucine labeling reagent." [PSI:PI] is_a: MS:1002602 ! sample label [Term] id: MS:1002779 name: DiLeu reagent 115 def: "The name of the sample labelled with the DiLeu reagent 115." [PSI:PI] is_a: MS:1002778 ! DiLeu reagent [Term] id: MS:1002780 name: DiLeu reagent 116 def: "The name of the sample labelled with the DiLeu reagent 116." [PSI:PI] is_a: MS:1002778 ! DiLeu reagent [Term] id: MS:1002781 name: DiLeu reagent 117 def: "The name of the sample labelled with the DiLeu reagent 117." [PSI:PI] is_a: MS:1002778 ! DiLeu reagent [Term] id: MS:1002782 name: DiLeu reagent 118 def: "The name of the sample labelled with the DiLeu reagent 118." [PSI:PI] is_a: MS:1002778 ! DiLeu reagent [Term] id: MS:1002783 name: 6550 iFunnel Q-TOF LC/MS def: "The 6550 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002784 name: 6550A iFunnel Q-TOF LC/MS def: "The 6550A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002785 name: 6520B Q-TOF LC/MS def: "The 6520B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002786 name: 6530A Q-TOF LC/MS def: "The 6530A Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002787 name: 6530B Q-TOF LC/MS def: "The 6530B Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002788 name: 6538 Q-TOF LC/MS def: "The 6538 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002789 name: 6540 Q-TOF LC/MS def: "The 6540 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002790 name: 6542 Q-TOF LC/MS def: "The 6542 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002791 name: 6545 Q-TOF LC/MS def: "The 6545 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002792 name: 6560 Q-TOF LC/MS def: "The 6560 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002793 name: 6570 Q-TOF LC/MS def: "The 6570 Quadrupole Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002794 name: 6120B Quadrupole LC/MS def: "The 6120B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002795 name: 6150 Quadrupole LC/MS def: "The 6150 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a single quadrupole mass spectrometer from the 6100 Series of Agilent mass spectrometers." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002796 name: 6224 Time-of-Flight LC/MS def: "The 6224 Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002797 name: 6230A Time-of-Flight LC/MS def: "The 6230A Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002798 name: 6230B Time-of-Flight LC/MS def: "The 6230B Time-of-Flight LC/MS is a Agilent liquid chromatography instrument combined with a Agilent time of flight mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002799 name: 6430 Triple Quadrupole LC/MS def: "The 6430 Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002800 name: 6495A Triple Quadrupole LC/MS def: "The 6495A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002801 name: 6495B Triple Quadrupole LC/MS def: "The 6495B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002802 name: 7000A Triple Quadrupole GC/MS def: "The 7000A Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002803 name: 7000B Triple Quadrupole GC/MS def: "The 7000B Quadrupole GC/MS system is a Agilent gas chromatography instrument combined with a Agilent triple quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002804 name: 7800 Quadrupole ICP-MS def: "The 7800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002805 name: 8800 Triple Quadrupole ICP-MS def: "The 8800 Quadrupole ICP-MS system is a Agilent inductively couple plasma instrument combined with a Agilent quadrupole mass spectrometer." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1002806 name: ion def: "Molecular entity having a net positive or negative electric charge." [PSI:MS] is_a: MS:1000881 ! molecular entity [Term] id: MS:1002807 name: positive mode adduct ion def: "Adduct ion with positive ionization." [PSI:MS] is_a: MS:1000353 ! adduct ion [Term] id: MS:1002808 name: negative mode adduct ion def: "Adduct ion with negative ionization." [PSI:MS] is_a: MS:1000353 ! adduct ion [Term] id: MS:1002809 name: adduct ion attribute def: "Nonphysical characteristic attributed to an adduct ion." [PSI:MS] relationship: part_of MS:1000353 ! adduct ion [Term] id: MS:1002810 name: adduct ion X m/z def: "Theoretical m/z of the X component in the adduct (addition product) M+X or M-X. This term was formerly called 'adduct ion mass', but it is not really a mass. It corresponds to the column mislabelled as 'mass' at https://fiehnlab.ucdavis.edu/staff/kind/Metabolomics/MS-Adduct-Calculator." [PSI:MS] is_a: MS:1003056 ! adduct ion property relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000040 ! m/z [Term] id: MS:1002811 name: adduct ion isotope def: "Isotope of the matrix molecule M of an adduct formation." [PSI:MS] is_a: MS:1003056 ! adduct ion property relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002812 name: Regular expression for adduct ion formula def: "(\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-])." [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1002813 name: adduct ion formula def: "Adduct formation formula of the form M+X or M-X, as constrained by the provided regular expression." [PSI:MS] is_a: MS:1002809 ! adduct ion attribute relationship: has_regexp MS:1002812 ! (\[[:digit:]{0,1}M([+][:digit:]{0,1}(H|K|(Na)|(Li)|(Cl)|(Br)|(NH3)|(NH4)|(CH3OH)|(IsoProp)|(DMSO)|(FA)|(Hac)|(TFA)|(NaCOOH)|(HCOOH)|(CF3COOH)|(ACN))){0,}([-][:digit:]{0,1}(H|(H2O)|(CH2)|(CH4)|(NH3)|(CO)|(CO2)|(COCH2)|(HCOOH)|(C2H4)|(C4H8)|(C3H2O3)|(C5H8O4)|(C6H10O4)|(C6H10O5)|(C6H8O6))){0,}\][:digit:]{0,1}[+-]) relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002814 name: volt-second per square centimeter def: "An electrical mobility unit that equals the speed [cm/s] an ion reaches when pulled through a gas by a Voltage[V] over a certain distance [cm]." [PSI:PI] synonym: "Vs/cm^2" EXACT [] is_a: UO:0000000 ! unit [Term] id: MS:1002815 name: inverse reduced ion mobility def: "Ion mobility measurement for an ion or spectrum of ions as measured in an ion mobility mass spectrometer. This might refer to the central value of a bin into which all ions within a narrow range of mobilities have been aggregated." [PSI:MS] is_a: MS:1000455 ! ion selection attribute is_a: MS:1002892 ! ion mobility attribute is_a: MS:1003254 ! peak attribute relationship: has_units MS:1002814 ! volt-second per square centimeter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002816 name: mean ion mobility array def: "Array of population mean ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002817 name: Bruker TDF format def: "Bruker TDF raw file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002818 name: Bruker TDF nativeID format def: "Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1002819 name: Bruker TDF nativeID format, combined spectra def: "Bruker TDF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002820 name: M+H ion def: "Adduct formed by protonation of a matrix molecule M, i.e. the addition of a matrix molecule M plus a proton." [PSI:MS] property_value: ionMass: "M + 1.007276" xsd:string is_a: MS:1002807 ! positive mode adduct ion [Term] id: MS:1002821 name: M-H ion def: "Adduct formed by deprotonation of a matrix molecule M, i.e. the removal of a proton from a matrix molecule M." [PSI:MS] property_value: ionMass: "M - 1.007276" xsd:string is_a: MS:1002808 ! negative mode adduct ion [Term] id: MS:1002822 name: OpenMS file format def: "File format developed by the OpenMS team." [PMID:27575624] is_a: MS:1001459 ! file format [Term] id: MS:1002823 name: idXML def: "OpenMS intermediate identification format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format [Term] id: MS:1002824 name: featureXML def: "OpenMS feature file format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format [Term] id: MS:1002825 name: consensusXML def: "OpenMS consensus map format." [PSI:PI] is_a: MS:1002822 ! OpenMS file format [Term] id: MS:1002826 name: MetaMorpheus def: "MetaMorpheus search engine." [https://github.com/smith-chem-wisc/MetaMorpheus] is_a: MS:1001456 ! analysis software [Term] id: MS:1002827 name: MetaMorpheus:score def: "MetaMorpheus score for PSMs." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002828 name: MetaMorpheus:protein score def: "MetaMorpheus score for protein groups." [PSI:PI] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002829 name: XCMS:into def: "Feature intensity produced by XCMS findPeaks() from integrated peak intensity." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002830 name: XCMS:intf def: "Feature intensity produced by XCMS findPeaks() from baseline corrected integrated peak intensity." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002831 name: XCMS:maxo def: "Feature intensity produced by XCMS findPeaks() from maximum peak intensity." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002832 name: XCMS:area def: "Feature intensity produced by XCMS findPeaks() from feature area that is not normalized by the scan rate." [PSI:PI] is_a: MS:1002735 ! feature-level quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002833 name: alternating polarity mode def: "Polarities of the scans of a run are alternating, i.e. both positive and negative mode scans are acquired." [PSI:PI] is_a: MS:1000857 ! run attribute [Term] id: MS:1002834 name: ProteomeDiscoverer:Delta Score def: "The Delta Score reported by Proteome Discoverer version 2." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002835 name: LTQ Orbitrap Classic def: "Thermo Fisher Scientific LTQ Orbitrap Classic." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002836 name: iProX dataset identifier def: "Dataset identifier issued by the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002837 name: iProX dataset URI def: "URI that allows the access to one dataset in the iProX repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002838 name: mzMLb format def: "mzMLb file format, mzML encapsulated within HDF5." [PSI:PI, https://github.com/biospi/mzmlb] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002839 name: Conversion to mzMLb def: "Conversion of a file format to Proteomics Standards Initiative mzMLb file format." [PSI:PI] is_a: MS:1000530 ! file format conversion [Term] id: MS:1002840 name: external reference data def: "Data belonging to an external reference." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1002841 name: external HDF5 dataset def: "The HDF5 dataset location containing the binary data, relative to the dataset containing the mzML. Also indicates that there is no data in the section of the BinaryDataArray." [PSI:PI] is_a: MS:1002840 ! external reference data relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002842 name: external offset def: "The position in the external data where the array begins." [PSI:PI] relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002843 name: external array length def: "Describes how many fields an array contains." [PSI:PI] relationship: has_units UO:0000189 ! Count is_a: MS:1002840 ! external reference data relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002844 name: Experiment additional parameter def: "Root node for terms relating to the description of an Experiment in relation to the PRIDE-XML element ExperimentCollection/Experiment/additional/cvParam." [PSI:PI] is_a: MS:1001458 ! spectrum generation information [Term] id: MS:1002845 name: Associated file URI def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002846 name: Associated raw file URI def: "URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission)." [PSI:PI] is_a: MS:1002845 ! Associated file URI relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002847 name: ProteomeCentral dataset URI def: "URI associated to one PX submission in ProteomeCentral." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002848 name: Result file URI def: "URI of one file labeled as 'Result', associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002849 name: Search engine output file URI def: "URI of one search engine output file associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002850 name: Peak list file URI def: "URI of one of one search engine output file associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002851 name: Other type file URI def: "URI of one file labeled as 'Other', associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002852 name: Dataset FTP location def: "FTP location of one entire PX data set." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002853 name: Dataset with no associated published manuscript def: "A dataset which does not have an associated published manuscript." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002854 name: Peer-reviewed dataset def: "Dataset has been peer-reviewed somehow." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002855 name: Non peer-reviewed dataset def: "Dataset that has not been peer-reviewed by any means." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002856 name: Supported dataset by repository def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. This is usually called a complete submission." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002857 name: Unsupported dataset by repository def: "Dataset for which the identifications and/or spectra/traces are in formats that cannot be parsed by the hosting data repository and thus internal references between identifications and spectra/traces are not browsable at the repository. This is usually called a partial submission." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002858 name: Dataset with its publication pending def: "A dataset which has an associated manuscript pending for publication." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002859 name: Additional associated raw file URI def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE." [PSI:PI] is_a: MS:1002845 ! Associated file URI relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002860 name: Gel image file URI def: "URI of one gel image file associated to one PX submission." [PSI:PI] is_a: MS:1002845 ! Associated file URI relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002861 name: Reprocessed complete dataset def: "All the raw files included in the original dataset (or group of original datasets) have been reanalysed." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002862 name: Reprocessed subset dataset def: "A subset of the raw files included in the original dataset (or group of original datasets) has been reanalysed." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002863 name: Data derived from previous dataset def: "One dataset is a reanalysis of previously published data." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002864 name: No PTMs are included in the dataset def: "No post-translational-modifications are been included in the identified peptides of one dataset." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002865 name: Accepted manuscript def: "A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002866 name: Reference def: "Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002867 name: Experimental information has been refined since this experiment was originally made publicly available def: "This means that the experimental information available has been improved, for instance precursor charges were added." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002868 name: Original data def: "One dataset is not a reanalysis of previously published data." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1002869 name: mzR def: "Bioconductor package mzR for reading and writing mass spectrometry data files." [PSI:PI] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002870 name: MSnbase def: "Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data." [PMID:22113085] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002871 name: CAMERA def: "Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments." [PMID:22111785] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002872 name: Panorama Public dataset identifier def: "Dataset identifier issued by the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002873 name: Panorama Public dataset URI def: "URI that allows the access to one dataset in the Panorama Public repository. A dataset can refer to either a single sample as part of a study, or all samples that are part of the study corresponding to a publication." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:anyURI ! The allowed value-type for this CV term [Term] id: MS:1002874 name: TSQ Altis def: "Thermo Scientific TSQ Altis Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002875 name: TSQ Quantis def: "Thermo Scientific TSQ Quantis Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002876 name: TSQ 9000 def: "Thermo Scientific TSQ 9000 Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002877 name: Q Exactive HF-X def: "Thermo Scientific Q Exactive HF-X Hybrid Quadrupole Orbitrap MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1002878 name: small molecule analysis software def: "Software for the analysis of small molecules." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1002879 name: Progenesis QI def: "Metabolomics analysis software for LC-MS data from Nonlinear Dynamics." [PSI:PI] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002880 name: Compound Discoverer def: "Metabolomics analysis software from Thermo Fisher Scientific." [PSI:PI] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002881 name: MyCompoundID def: "Metabolite identification tool MyCompoundID." [PSI:PI, PMID:23373753] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002882 name: study variable average function def: "Function used to calculate the study variable quantification value." [PSI:PI] is_a: MS:1001184 ! search statistics [Term] id: MS:1002883 name: median def: "Median function." [PSI:PI] is_a: MS:1002882 ! study variable average function [Term] id: MS:1002884 name: study variable variation function def: "Function used to calculate the study variable quantification variation value." [PSI:PI] is_a: MS:1001184 ! search statistics [Term] id: MS:1002885 name: standard error def: "Standard error function." [PSI:PI] is_a: MS:1002884 ! study variable variation function [Term] id: MS:1002886 name: small molecule quantification datatype def: "The value reported in a small molecule quantification." [PSI:PI] is_a: MS:1001805 ! quantification datatype [Term] id: MS:1002887 name: Progenesis QI normalised abundance def: "The normalised abundance produced by Progenesis QI LC-MS." [PSI:PI] is_a: MS:1002886 ! small molecule quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002888 name: small molecule confidence measure def: "The confidence score produced by a small molecule analysis software." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002889 name: Progenesis MetaScope score def: "The confidence score produced by Progenesis QI." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002890 name: fragmentation score def: "The fragmentation confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002891 name: isotopic fit score def: "The isotopic fit confidence score." [PSI:PI] is_a: MS:1002888 ! small molecule confidence measure relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1002892 name: ion mobility attribute def: "An attribute describing ion mobility searches." [PSI:PI] is_a: MS:1000503 ! scan attribute is_a: MS:1002345 ! PSM-level attribute [Term] id: MS:1002893 name: ion mobility array def: "Abstract array of ion mobility data values. A more specific child term concept should be specified in data files to make precise the nature of the data being provided." [PSI:PI] is_a: MS:1000513 ! binary data array [Term] id: MS:1002894 name: InChIKey def: "Unique chemical structure identifier for chemical compounds." [PMID:273343401] is_a: MS:1001405 ! spectrum identification result details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002895 name: small molecule identification attribute def: "Compound identification information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002896 name: compound identification confidence level def: "Confidence level for annotation of identified compounds as defined by the Metabolomics Standards Initiative (MSI). The value slot can have the values 'Level 0' until 'Level 4'." [PMID:29748461] is_a: MS:1002895 ! small molecule identification attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002897 name: isotopomer peak def: "OBSOLETE Identifies a peak when no de-isotoping has been performed. The value slot reports the isotopomer peak, e.g. '2H', '13C', '15N', '18O', '31P'." [PSI:PI] comment: This term was obsoleted because it was replaced by the more exact terms MS:1002956 'isotopic ion MS peak', MS:1002957 'isotopomer MS peak' and MS:1002958 'isotopologue MS peak' instead. is_a: MS:1000231 ! peak is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002898 name: Shimadzu Biotech QTOF nativeID format def: "Native format defined by scan=xsd:nonNegativeInteger." [PSI:PI] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1002899 name: msalign format def: "msalign file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002900 name: feature format def: "TopFD feature file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002901 name: TopPIC def: "TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization." [PMID:27423895, http://proteomics.informatics.iupui.edu/software/toppic/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002902 name: TopFD def: "Top-down mass spectral feature detection." [http://proteomics.informatics.iupui.edu/software/toppic/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002903 name: TopMG def: "A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra." [PMID:28453668, http://proteomics.informatics.iupui.edu/software/topmg/index.html] is_a: MS:1001456 ! analysis software [Term] id: MS:1002904 name: proteoform-level identification attribute def: "Proteoform level information." [PSI:PI] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1002905 name: proteoform-level identification statistic def: "Identification confidence metric for a proteoform." [PSI:PI] is_a: MS:1002904 ! proteoform-level identification attribute [Term] id: MS:1002906 name: search engine specific score for proteoforms def: "Search engine specific proteoform scores." [PSI:PI] is_a: MS:1002905 ! proteoform-level identification statistic [Term] id: MS:1002907 name: proteoform-level global FDR def: "Estimation of the global false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002908 name: proteoform-level local FDR def: "Estimation of the local false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002909 name: proteoform-level statistical threshold def: "Estimated statistical threshold at proteoform-level." [PSI:PI] is_a: MS:1002573 ! spectrum identification statistical threshold [Term] id: MS:1002910 name: proteoform-level global FDR threshold def: "Threshold for the global false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002909 ! proteoform-level statistical threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002911 name: proteoform-level local FDR threshold def: "Threshold for the local false discovery rate of proteoforms." [PSI:PI] is_a: MS:1002909 ! proteoform-level statistical threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002912 name: TopPIC input parameter def: "Search engine input parameters specific to TopPIC." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002913 name: TopPIC:fixed modification def: "Fixed modifications for TopPIC searching." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002914 name: TopPIC:N-term form def: "N-terminal forms of proteins allowed in TopPIC searching." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002915 name: TopPIC:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002916 name: TopPIC:max shift def: "Maximum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002917 name: TopPIC:min shift def: "Minimum value of the mass shift (in Dalton) of an unexpected modification." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002918 name: TopPIC:shift num def: "Maximum number of unexpected modifications in a proteoform spectrum match." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002919 name: TopPIC:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002920 name: TopPIC:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002921 name: TopPIC:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002922 name: TopPIC:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002923 name: TopPIC:generating function def: "P-value and E-value estimation using generating function." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002924 name: TopPIC:combined spectrum number def: "Number of combined spectra." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002925 name: TopPIC:mod file def: "The text file containing the information of common PTMs." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter [Term] id: MS:1002926 name: TopPIC:thread number def: "Number of threads used in TopPIC." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002927 name: TopPIC:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] is_a: MS:1002912 ! TopPIC input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002928 name: TopPIC:spectral E-value def: "TopPIC spectrum-level E-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002353 ! PSM-level e-value relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002929 name: TopPIC:spectral FDR def: "TopPIC spectrum-level FDR." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002351 ! PSM-level local FDR relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002930 name: TopPIC:proteoform-level FDR def: "TopPIC proteoform-level FDR." [PSI:PI] is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002906 ! search engine specific score for proteoforms relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002931 name: TopPIC:spectral p-value def: "TopPIC spectrum-level p-value." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1002352 ! PSM-level p-value relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002932 name: TopPIC:MIScore def: "Modification identification score." [PMID:27291504] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002933 name: TopPIC:MIScore threshold def: "TopPIC:MIScore threshold." [PSI:PI] is_a: MS:1002555 ! PTM localization score threshold relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002934 name: TopMG input parameter def: "Search engine input parameters specific to TopMG." [PSI:PI] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1002935 name: TopMG:fixed modification def: "Fixed modifications for TopMG searching." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002936 name: TopMG:N-term form def: "N-terminal forms of proteins allowed in TopMG searching." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002937 name: TopMG:error tolerance def: "Error tolerance for precursor and fragment masses in PPM." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002938 name: TopMG:max shift def: "Maximum value of the mass shift (in Dalton)." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002939 name: TopMG:spectral cutoff type def: "Spectrum-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002940 name: TopMG:spectral cutoff value def: "Spectrum-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002941 name: TopMG:proteoform-level cutoff type def: "Proteoform-level cutoff type for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002942 name: TopMG:proteoform-level cutoff value def: "Proteoform-level cutoff value for filtering identified proteoform spectrum matches." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002943 name: TopMG:mod file def: "The text file containing the information of common PTMs." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter [Term] id: MS:1002944 name: TopMG:thread number def: "Number of threads used in TopMG." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002945 name: TopMG:use TopFD feature def: "Proteoform identification using TopFD feature file." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002946 name: TopMG:proteoform graph gap size def: "Gap size in constructing proteoform graph." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002947 name: TopMG:variable PTM number def: "Maximum number of variable PTMs." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002948 name: TopMG:variable PTM number in proteoform graph gap def: "Maximum number of variable PTMs in a proteoform graph gap." [PSI:PI] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1002949 name: TopMG:use ASF-DIAGONAL def: "Protein filtering using ASF-DIAGONAL method." [PMID:29327814] is_a: MS:1002934 ! TopMG input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1002950 name: TopMG:spectral E-value def: "TopMG spectrum-level E-value." [PSI:PI] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002951 name: TopMG:spectral FDR def: "TopMG spectrum-level FDR." [PSI:PI] is_a: MS:1002351 ! PSM-level local FDR is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002952 name: TopMG:proteoform-level FDR def: "TopMG proteoform-level FDR." [PSI:PI] is_a: MS:1002908 ! proteoform-level local FDR is_a: MS:1002906 ! search engine specific score for proteoforms relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002953 name: TopMG:spectral p-value def: "TopMG spectrum-level p-value." [PSI:PI] is_a: MS:1002352 ! PSM-level p-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002954 name: collisional cross sectional area def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] is_a: MS:1000861 ! molecular entity property is_a: MS:1000455 ! ion selection attribute relationship: has_units UO:0000324 ! square angstrom relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002955 name: hr-ms compound identification confidence level def: "Refined High Resolution mass spectrometry confidence level for annotation of identified compounds as proposed by Schymanski et al. The value slot can have the values 'Level 1', 'Level 2', 'Level 2a', 'Level 2b', 'Level 3', 'Level 4', and 'Level 5'." [PMID:24476540] is_a: MS:1002895 ! small molecule identification attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002956 name: isotopic ion MS peak def: "A mass spectrometry peak that represents one or more isotopic ions. The value slot contains a description of the represented isotope set, e.g. 'M+1 peak'." [PSI:PI] is_a: MS:1000231 ! peak relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002957 name: isotopomer MS peak def: "The described isotopomer mass spectrometric signal. The value slot contains a description of the represented isotopomer, e.g. '13C peak', '15N peak', '2H peak', '18O peak' or '31P peak'." [PSI:PI] is_a: MS:1002956 ! isotopic ion MS peak relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002958 name: isotopologue MS peak def: "The described isotopologue mass spectrometric signal. The value slot contains a description of the represented isotopologue, e.g. '13C1 peak' or '15N1 peak'." [PSI:PI] is_a: MS:1002956 ! isotopic ion MS peak relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002959 name: isomer def: "One of several species (or molecular entities) that have the same atomic composition (molecular formula) but different line formulae or different stereochemical formulae." [https://goldbook.iupac.org/html/I/I03289.html] is_a: MS:1000859 ! molecule relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002960 name: isotopomer def: "An isomer that differs from another only in the spatial distribution of the constitutive isotopic atoms." [https://goldbook.iupac.org/html/I/I03352.html] is_a: MS:1002959 ! isomer relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002961 name: isotopologue def: "A molecular entity that differs only in isotopic composition (number of isotopic substitutions)." [https://goldbook.iupac.org/html/I/I03351.html] is_a: MS:1002959 ! isomer relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1002962 name: mean def: "The arithmetic mean." [PSI:PI] is_a: MS:1002882 ! study variable average function [Term] id: MS:1002963 name: variation coefficient def: "The coefficient of variation." [PSI:PI] is_a: MS:1002884 ! study variable variation function [Term] id: MS:1002964 name: lipidomics analysis software def: "Lipidomics analysis software." [PSI:PI] is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1002965 name: Lipid Data Analyzer def: "Lipid Data Analyzer software for lipid quantification." [PMID:29058722] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002966 name: chrom format def: "The Lipid Data Analyzer native chrom format." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002967 name: LipidHunter def: "Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets." [PMID:28753264] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002968 name: LipidXplorer def: "Software for consensual cross-platform lipidomics." [PMID:22272252] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002969 name: LipidMatch def: "An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data." [PMID:28693421] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002970 name: Greazy def: "Open-source software for automated phospholipid tandem mass spectrometry identification." [PMID:27186799] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002971 name: LipidBlast def: "LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library." [PMID:28660581] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002972 name: Lipid-Pro def: "A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms." [PMID:25433698] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002973 name: LipidFinder def: "A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets." [PMID:28405621] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002974 name: LipiDex def: "An integrated software package for high-confidence lipid identification." [PMID:29705063] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002975 name: LIQUID def: "An-open source software for identifying lipids in LC-MS/MS-based lipidomics data." [PMID:28158427] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002976 name: ALEX def: "Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1)." [PMID:24244551] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002977 name: ALEX123 def: "Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level." [PMID:29786091] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002978 name: LIMSA def: "Software tool for the quantitative analysis of mass spectrometric lipidome data." [PMID:17165823] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002979 name: LOBSTAHS def: "Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers." [PMID:27322848] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002980 name: LipidQA def: "Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species." [PMID:17720531] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1002981 name: Proline def: "The Proline software suite for mass spectrometry based proteomics." [http://www.profiproteomics.fr/proline/] is_a: MS:1001456 ! analysis software [Term] id: MS:1002982 name: PepNovo def: "PepNovo tool for de novo peptide sequencing." [PMID:15858974] is_a: MS:1001456 ! analysis software [Term] id: MS:1002983 name: pNovo def: "pNovo tool for de novo peptide sequencing and identification using HCD spectra." [PMID:20329752] is_a: MS:1001456 ! analysis software [Term] id: MS:1002984 name: Novor def: "Novor real-time peptide de novo sequencing software tool." [PMID:26122521] is_a: MS:1001456 ! analysis software [Term] id: MS:1002985 name: in-gel digestion def: "Digestion of proteins separated by gel electrophoresis for mass spectrometric characterization of proteins and proteomes." [PSI:PI] is_a: MS:1000831 ! sample preparation [Term] id: MS:1002986 name: in-solution digestion def: "Digestion of proteins in solution for mass spectrometric characterization of proteins and proteomes." [PSI:PI] is_a: MS:1000831 ! sample preparation [Term] id: MS:1002987 name: IdentiPy def: "IdentiPy." [PMID:29682971, https://bitbucket.org/levitsky/identipy] is_a: MS:1001456 ! analysis software [Term] id: MS:1002988 name: IdentiPy:RHNS def: "The IdentiPy result 'RHNS'." [PSI:PI] is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002989 name: IdentiPy:hyperscore def: "The IdentiPy result 'hyperscore'." [PSI:PI] is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002990 name: ms_deisotope def: "ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra." [https://github.com/mobiusklein/ms_deisotope] is_a: MS:1001457 ! data processing software [Term] id: MS:1002991 name: python-psims def: "python-psims, a library for generating mzML and mzIdentML." [https://github.com/mobiusklein/psims] is_a: MS:1002333 ! conversion software [Term] id: MS:1002995 name: Andromeda:PEP def: "Posterior error probability of the best identified peptide of the Andromeda search engine." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1002996 name: Andromeda:apl file format def: "Peak list file format of the Andromeda search engine." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1002997 name: ProteomeXchange dataset identifier reanalysis number def: "Index number of a reanalysis within a ProteomeXchange reprocessed dataset identifier container (RPXD)." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1002998 name: LCMS-9030 def: "Shimadzu Scientific Instruments LCMS-9030 Q-TOF MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1002999 name: LCMS-8060 def: "Shimadzu Scientific Instruments LCMS-8060 MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003000 name: LCMS-8050 def: "Shimadzu Scientific Instruments LCMS-8050 MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003001 name: LCMS-8045 def: "Shimadzu Scientific Instruments LCMS-8045 MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003002 name: LCMS-8040 def: "Shimadzu Scientific Instruments LCMS-8040 MS." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003003 name: LCMS-2020 def: "Shimadzu Scientific Instruments LCMS-2020." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003004 name: maXis II def: "Bruker Daltonics' maXis II." [PSI:MS] is_a: MS:1001547 ! Bruker Daltonics maXis series [Term] id: MS:1003005 name: timsTOF Pro def: "Bruker Daltonics' timsTOF Pro." [PSI:MS] is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003006 name: mean inverse reduced ion mobility array def: "Array of population mean ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003007 name: raw ion mobility array def: "Array of raw ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003008 name: raw inverse reduced ion mobility array def: "Array of raw ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003009 name: Shimadzu Biotech LCD format def: "Shimadzu Biotech LCD file format." [PSI:PI] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1003010 name: LPPtiger def: "Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets." [PMID:29123162] is_a: MS:1002964 ! lipidomics analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1003011 name: pFind def: "Sequence-tag-based search engine pFind." [PMID:30295672] is_a: MS:1001456 ! analysis software [Term] id: MS:1003012 name: KSDP score def: "Kernel mass spectral dot product scoring function." [PMID:15044235] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better [Term] id: MS:1003013 name: i3tms def: "i3-tms search engine and data-analysis software." [PSI:PI] is_a: MS:1001456 ! analysis software [Term] id: MS:1003014 name: MSFragger def: "A database search-based peptide identification tool." [PMID:28394336] is_a: MS:1001456 ! analysis software [Term] id: MS:1003015 name: razor peptide def: "Peptide that is shared between protein groups and assigned to the protein group with the largest number of identified peptides." [PSI:MS] is_a: MS:1000860 ! peptide [Term] id: MS:1003016 name: ProteinProphet:peptide weight def: "Fraction of peptide evidence attributable to a protein or a set of indistinguishable proteins." [PSI:PI] is_a: MS:1002490 ! peptide-level scoring is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003017 name: ProteinProphet:peptide group weight def: "Fraction of peptide evidence attributable to a group of proteins." [PSI:PI] is_a: MS:1002490 ! peptide-level scoring is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003018 name: Philosopher def: "General proteomics processing toolkit for shotgun proteomics." [https://philosopher.nesvilab.org/] is_a: MS:1001456 ! analysis software [Term] id: MS:1003019 name: pressure chromatogram def: "Representation of chromatographic pressure versus time." [PSI:MS] is_a: MS:1000626 ! chromatogram type [Term] id: MS:1003020 name: flow rate chromatogram def: "Representation of the chromatographic flow rate versus time." [PSI:MS] is_a: MS:1000626 ! chromatogram type [Term] id: MS:1003021 name: Fixed modification def: "Post-translational modification which is assumed to be present at each instance of a residue type." [PSI:PI] is_a: MS:1001055 ! modification parameters is_a: MS:1003026 ! named element in mzIdentML [Term] id: MS:1003022 name: Variable modification def: "Post-translational modification which may or may not be present at a residue type." [PSI:PI] is_a: MS:1001055 ! modification parameters is_a: MS:1003026 ! named element in mzIdentML [Term] id: MS:1003023 name: OpenPepXL def: "Cross-Linking MS search engine." [PSI:PI] is_a: MS:1000752 ! TOPP software [Term] id: MS:1003024 name: OpenPepXL:score def: "The OpenPepXL score for a crosslink spectrum match." [PSI:PI] is_a: MS:1001143 ! PSM-level search engine specific statistic is_a: MS:1001153 ! search engine specific score relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003025 name: named element def: "A named element that is an attribute in a proteomics standards file." [PSI:PI] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1003026 name: named element in mzIdentML def: "A named element that is an attribute in a mzIdentML file." [PSI:PI] is_a: MS:1003025 ! named element [Term] id: MS:1003027 name: named element in mzML def: "A named element that is an attribute in a mzML file." [PSI:PI] is_a: MS:1003025 ! named element [Term] id: MS:1003028 name: Orbitrap Exploris 480 def: "Thermo Scientific Orbitrap Exploris 480 Quadrupole Orbitrap MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003029 name: Orbitrap Eclipse def: "Thermo Scientific Orbitrap Eclipse mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003030 name: Mascot:MinNumSigUniqueSeqs def: "Minimum number of significant unique sequences required in a protein hit. The setting is only relevant if the protein grouping strategy is 'family clustering'." [PSI:PI] is_a: MS:1002095 ! Mascot input parameter relationship: has_value_type xsd:nonNegativeInteger ! The allowed value-type for this CV term [Term] id: MS:1003031 name: CPTAC accession number def: "Main identifier of a CPTAC dataset." [PSI:PI] is_a: MS:1000878 ! external reference identifier relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003032 name: compound identification confidence code in MS-DIAL def: "The confidence code to describe the confidence of annotated compounds as defined by the MS-DIAL program." [PMID:25938372, http://prime.psc.riken.jp/Metabolomics_Software/MS-DIAL] is_a: MS:1002895 ! small molecule identification attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003033 name: molecular entity attribute def: "Non-inherent characteristic attributed to a molecular entity." [PSI:PI] relationship: part_of MS:1000881 ! molecular entity [Term] id: MS:1003034 name: atom def: "Smallest constituent unit of ordinary matter that constitutes a chemical element." [https://en.wikipedia.org/wiki/Atom] is_a: MS:1000881 ! molecular entity [Term] id: MS:1003035 name: small molecule def: "Low molecular weight (< 900 daltons) organic compound that may regulate a biological process." [https://en.wikipedia.org/wiki/Small_molecule] is_a: MS:1000859 ! molecule [Term] id: MS:1003036 name: metabolite def: "Small molecule that is the intermediate end product of metabolism." [https://en.wikipedia.org/wiki/Metabolite] is_a: MS:1003035 ! small molecule [Term] id: MS:1003037 name: ribonucleotide def: "Nucleotide containing ribose as its pentose component." [https://en.wikipedia.org/wiki/Ribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003038 name: deoxyribonucleotide def: "Monomer, or single unit, of DNA, or deoxyribonucleic acid." [https://en.wikipedia.org/wiki/Deoxyribonucleotide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003039 name: amino acid def: "Organic molecule that contains amine (-NH2) and carboxyl (-COOH) functional groups, along with a side chain (R group) that is specific to each amino acid." [https://en.wikipedia.org/wiki/Amino_acid] is_a: MS:1003035 ! small molecule [Term] id: MS:1003040 name: monosaccharide def: "Simplest form of sugar and the most basic units of carbohydrate that cannot be further hydrolyzed to a simpler molecule." [https://en.wikipedia.org/wiki/Monosaccharide] is_a: MS:1003035 ! small molecule [Term] id: MS:1003041 name: nucleic acid def: "Molecule composed of a chain of nucleotides." [https://en.wikipedia.org/wiki/Nucleic_acid] is_a: MS:1000859 ! molecule [Term] id: MS:1003042 name: polysaccharide def: "Polymeric carbohydrate molecules composed of long chains of monosaccharide units bound together by glycosidic linkages." [https://en.wikipedia.org/wiki/Polysaccharide] is_a: MS:1000859 ! molecule [Term] id: MS:1003043 name: number of residues def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003044 name: number of missed cleavages def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003045 name: peptide-to-protein mapping def: "Process of mapping a peptide sequence to a protein sequence." [PSI:PI] is_a: MS:1000887 ! peptide attribute [Term] id: MS:1003046 name: peptide-to-protein mapping attribute def: "Nonphysical characteristic attributed to the result of peptide-to-protein mapping." [PSI:PI] is_a: MS:1003045 ! peptide-to-protein mapping [Term] id: MS:1003047 name: protein sequence offset def: "Offset in number of residues from the n terminus of the protein at which the peptide begins. Use 1 when the first residue of the peptide sequence is the first residue of the protein sequence." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003048 name: number of enzymatic termini def: "Total number of termini that match standard rules for the cleavage agent, 2 when both termini match cleavage agent rules, 1 when only one terminus does, and 0 if neither terminus matches cleavage agent rules." [PSI:PI] is_a: MS:1003046 ! peptide-to-protein mapping attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003049 name: peptidoform def: "Peptide that contains zero or more mass modifications on the termini or side chains of its amino acid residues, and may be differentiated from other peptidoforms with the same peptide sequence but different mass modification configurations." [PSI:PI] is_a: MS:1000860 ! peptide [Term] id: MS:1003050 name: peptidoform attribute def: "Non-inherent characteristic attributed to a peptidoform." [PSI:PI] relationship: part_of MS:1003049 ! peptidoform [Term] id: MS:1003051 name: peptidoform ion def: "Peptidoform that has formed an adduct with an ion, thereby rendering it potentially detectable with a mass spectrometer. Commonly called a 'precursor' or 'precursor ion' or 'parent ion'." [PSI:PI] is_a: MS:1003049 ! peptidoform synonym: "precursor" RELATED [] synonym: "precursor ion" RELATED [] synonym: "parent ion" RELATED [] [Term] id: MS:1003052 name: peptidoform ion property def: "Inherent or measurable characteristic of a peptidoform ion." [PSI:PI] relationship: part_of MS:1003051 ! peptidoform ion [Term] id: MS:1003053 name: theoretical monoisotopic m/z def: "Mass-to-charge ratio of a peptidoform ion composed of the most common isotope of each atom computed from the putative knowledge of its molecular constituents." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003054 name: theoretical average m/z def: "Mass-to-charge ratio of a peptidoform ion computed from the putative knowledge of its molecular constituents, averaged over the distribution of naturally occurring isotopes." [PSI:PI] is_a: MS:1003052 ! peptidoform ion property relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003055 name: adduct def: "Product of a direct addition of two or more distinct molecules, resulting in a single reaction product containing all atoms of all components. The resultant is considered a distinct molecular species." [https://en.wikipedia.org/wiki/Adduct] is_a: MS:1000859 ! molecule [Term] id: MS:1003056 name: adduct ion property def: "Physical measurable characteristic of an adduct ion." [PSI:PI] relationship: part_of MS:1000353 ! adduct ion [Term] id: MS:1003057 name: scan number def: "Ordinal number of the scan indicating its order of acquisition within a mass spectrometry acquisition run." [PSI:PI] is_a: MS:1000503 ! scan attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003058 name: spectrum property def: "Inherent or measurable characteristic of a spectrum." [PSI:PI] relationship: part_of MS:1000442 ! spectrum [Term] id: MS:1003059 name: number of peaks def: "Number of peaks or features in a spectrum. For a peak-picked spectrum, this will correspond to the number of data points. For a non-peak-picked spectrum, this corresponds to the number of features discernable in the spectrum, which will be fewer than the number of data points." [PSI:PI] is_a: MS:1003058 ! spectrum property relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003060 name: number of data points def: "Number of data points in a spectrum. For a peak-picked spectrum, this will correspond to the number of peaks. For a non-peak-picked spectrum, this corresponds to the number of values in the data array, which are not all peaks." [PSI:PI] is_a: MS:1003058 ! spectrum property relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003061 name: library spectrum name def: "Label attached to a spectrum uniquely naming it within a collection of spectra, often in a spectral library. It is often a string combination of peptide sequence, charge, mass modifications, collision energy, but will obviously be different for small molecules or unidentified spectra. It must be unique within a collection." [PSI:PI] is_a: MS:1000499 ! spectrum attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term synonym: "spectrum name" EXACT [] [Term] id: MS:1003062 name: library spectrum index def: "Integer index value that indicates the spectrum's ordered position within a spectral library. By custom, index counters should begin with 0." [PSI:PI] is_a: MS:1003234 ! library spectrum attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003063 name: universal spectrum identifier def: "PSI universal spectrum identifier (USI) multipart key that uniquely identifies a spectrum available in a ProteomeXchange datasets or spectral library." [PSI:PI] is_a: MS:1000499 ! spectrum attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term synonym: "USI" EXACT [] [Term] id: MS:1003064 name: spectrum aggregation attribute def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003065 name: spectrum aggregation type def: "Categorization of a spectrum based on its type of aggregation (e.g., individual spectrum, consensus spectrum, best replicate spectrum, etc.)." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003066 name: singleton spectrum def: "Spectrum that is not the result of some aggregation process." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003067 name: consensus spectrum def: "Spectrum that is the result of merging several replicate spectra to form a spectrum that is more representative of its class and ideally less noisy that any of its source replicates." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003068 name: best replicate spectrum def: "Spectrum that is considered the most representative from a pool of replicate spectra." [PSI:PI] is_a: MS:1003065 ! spectrum aggregation type [Term] id: MS:1003069 name: number of replicate spectra available def: "Number of replicate spectra available for use during the aggregation process." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003070 name: number of replicate spectra used def: "Number of replicate spectra used during the aggregation process. This is generally applicable when there are many replicates available, but some are discarded as being low S/N, blended, or otherwise unsuitable, and the remaining set is then used for merging via a consensus algorithm." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003071 name: spectrum origin attribute def: "Non-inherent characteristic attributed to spectrum aggregation." [PSI:PI] is_a: MS:1000499 ! spectrum attribute [Term] id: MS:1003072 name: spectrum origin type def: "Categorization of a spectrum based on its origin (e.g., observed spectrum, predicted spectrum, demultiplexed spectrum, etc.)." [PSI:PI] is_a: MS:1003071 ! spectrum origin attribute [Term] id: MS:1003073 name: observed spectrum def: "Spectrum that originates from an analysis attempt of a single analyte species on an instrument." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003074 name: predicted spectrum def: "Spectrum that originates from a compututational algorithm that attempts to predict spectra." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003075 name: demultiplexed spectrum def: "Spectrum that originates from an attempted extraction of a single ion spieces from a multiplexed spectrum that contains multiple ion species." [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003076 name: uninterpreted spectrum def: "Spectrum provided in the form of plain numerical values without any information pertaining to the interpretation of features." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003077 name: interpreted spectrum def: "Spectrum provided in a form where specific features of the spectrum are interpreted to provide putative explanations for some feature." [PSI:PI] is_a: MS:1000442 ! spectrum [Term] id: MS:1003078 name: interpreted spectrum attribute def: "Non-inherent characteristic attributed to an interpreted spectrum." [PSI:PI] relationship: part_of MS:1003077 ! interpreted spectrum [Term] id: MS:1003079 name: total unassigned intensity fraction def: "Fraction of intensity summed from all unassigned peaks divided by the intensity summed from all peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003080 name: top 20 peak unassigned intensity fraction def: "Fraction of intensity summed from unassigned peaks among the top 20 divided by the intensity summed from all top 20 peaks in the spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003081 name: unidentified modification monoisotopic mass delta def: "Monoisotopic mass delta in Daltons of an amino acid residue modification whose atomic composition or molecular identity has not been determined. This term should not be used for modifications of known molecular identity such as those available in Unimod, RESID or PSI-MOD. This term MUST NOT be used inside the element in mzIdentML." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_units UO:0000221 ! dalton relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003082 name: MS-DIAL def: "Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors." [PMID:25938372] is_a: MS:1002878 ! small molecule analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1003083 name: raw data file def: "Data file that contains original data as generated by an instrument, although not necessarily in the original data format (i.e. an original raw file converted to a different format is still a raw data file)." [PSI:MS] is_a: MS:1000577 ! source data file [Term] id: MS:1003084 name: processed data file def: "File that contains data that has been substantially processed or transformed from what was originally acquired by an instrument." [PSI:MS] is_a: MS:1000577 ! source data file relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003085 name: previous MSn-1 scan precursor intensity def: "Intensity of the precursor ion in the previous MSn-1 scan (prior in time to the referencing MSn scan). For an MS2 scan, this means the MS1 precursor intensity. It is unspecified on whether this is an apex (across m/z) intensity, integrated (across m/z) intensity, a centroided peak intensity of unknown origin, or even summed across several isotopes." [PSI:MS] is_a: MS:1001141 ! intensity of precursor ion is_a: MS:1000499 ! spectrum attribute relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003086 name: precursor apex intensity def: "Intensity of the precursor ion current as measured by its apex point over time and m/z. It is unspecified whether this is the intensity of the selected isotope or the most intense isotope." [PSI:MS] is_a: MS:1001141 ! intensity of precursor ion is_a: MS:1000499 ! spectrum attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003087 name: supported by repository but incomplete data and/or metadata def: "Dataset for which the identifications and/or spectra/traces are in formats that can be parsed by the hosting data repository such that internal references between identifications and spectra/traces are preserved and browsable at the repository. However, some metadata is not properly described due to lack of CV terms or some auxiliary data, such as data used to create a spectral library or a sequence search database crucial to the analysis, is not available." [PSI:PI] is_a: MS:1002844 ! Experiment additional parameter [Term] id: MS:1003088 name: truncation and zlib compression def: "Data array compression using mantissa bit truncation followed by zlib compression." [https://github.com/biospi/pwiz] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1003089 name: truncation, delta prediction and zlib compression def: "Data array compression using mantissa bit truncation, delta prediction and zlib compression." [https://github.com/biospi/pwiz] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1003090 name: truncation, linear prediction and zlib compression def: "Data array compression using mantissa bit truncation, linear prediction and zlib compression." [https://github.com/biospi/pwiz] is_a: MS:1000572 ! binary data compression type [Term] id: MS:1003091 name: binary data compression parameter def: "Settable parameter for a binary data compression event." [PSI:MS] relationship: part_of MS:1000442 ! spectrum relationship: part_of MS:1000625 ! chromatogram [Term] id: MS:1003092 name: number of mantissa bits truncated def: "Number of extraneous mantissa bits truncated to improve subsequent compression." [PSI:MS] is_a: MS:1003091 ! binary data compression parameter relationship: has_value_type xsd:positiveInteger ! The allowed value-type for this CV term [Term] id: MS:1003093 name: Lys-N def: "Metalloendopeptidase found in the mushroom Grifola frondosa that cleaves proteins on the amino side of lysine residues." [https://en.wikipedia.org/wiki/Lys-N] is_a: MS:1001045 ! cleavage agent name relationship: has_regexp MS:1001335 ! (?=K) [Term] id: MS:1003094 name: Orbitrap Exploris 240 def: "Thermo Scientific Orbitrap Exploris 240 Quadrupole Orbitrap MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003095 name: Orbitrap Exploris 120 def: "Thermo Scientific Orbitrap Exploris 120 Quadrupole Orbitrap MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003096 name: LTQ Orbitrap Velos Pro def: "Thermo Scientific LTQ Orbitrap Velos Pro, often just referred to as the Orbitrap Velos Pro." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003097 name: MaxQuant protein group-level score def: "The probability based MaxQuant protein group score." [PSI:MS] is_a: MS:1002368 ! search engine specific score for protein groups relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003098 name: Andromeda peptide PEP def: "Peptide probability from Andromeda." [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003099 name: MaxQuant-DIA peptide PEP def: "Peptide probability from MaxQuant-DIA algorithm." [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003100 name: MaxQuant-DIA score def: "PSM evidence score from MaxQuant-DIA algorithm." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003101 name: MaxQuant-DIA PEP def: "PSM evidence PEP probability from MaxQuant-DIA algorithm." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003102 name: NIST msp comment def: "Term for a comment field withing the NIST msp file format" [PSI:MS] is_a: MS:1000499 ! spectrum attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003103 name: ion annotation format def: "Annotation format used for annotating individual spectrum ion peaks." [PSI:MS] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003104 name: mzPAF peptide ion annotation format def: "Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS] is_a: MS:1003103 ! ion annotation format synonym: "peptide ion annotation format" EXACT [] [Term] id: MS:1003105 name: crosslinked peptide ion annotation format def: "Annotation format designed specifically for crosslinked peptide ion peaks." [PSI:MS] synonym: "cross-linked peptide ion annotation format" EXACT [] is_a: MS:1003103 ! ion annotation format [Term] id: MS:1003106 name: glycan ion annotation format def: "Annotation format designed specifically for glycan ion peaks." [PSI:MS] is_a: MS:1003103 ! ion annotation format [Term] id: MS:1003107 name: lipid ion annotation format def: "Annotation format designed specifically for lipid ion peaks." [PSI:MS] is_a: MS:1003103 ! ion annotation format [Term] id: MS:1003108 name: PatternLab def: "PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data." [PSI:MS] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1003109 name: SIM-XL def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1003110 name: SIM-XL score def: "SIM-XL identification search engine score" [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003111 name: QUIN-XL def: "Quantification of crosslinked peptides in complex protein mixtures" [PSI:MS] is_a: MS:1001139 ! quantitation software name [Term] id: MS:1003112 name: Orbitrap ID-X def: "Thermo Scientific Orbitrap ID-X mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003113 name: OpenMS:ConsensusID PEP def: "The OpenMS ConsesusID tool posterior error probability" [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003114 name: OpenMS:Best PSM Score def: "The score of the best PSM selected by the underlying identification tool" [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003115 name: OpenMS:Target-decoy PSM q-value def: "The OpenMS Target-decoy q-values at PSM level" [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003116 name: OpenMS:Target-decoy peptide q-value def: "The OpenMS Target-decoy q-values at peptide sequence level" [PSI:MS] is_a: MS:1002358 ! search engine specific peptide sequence-level identification statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003117 name: OpenMS:Target-decoy protein q-value def: "The OpenMS Target-decoy q-values at protein level" [PSI:MS] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003118 name: EPIFANY def: "A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework" [PSI:MS] is_a: MS:1001456 ! analysis software is_a: MS:1000752 ! TOPP software [Term] id: MS:1003119 name: EPIFANY:Protein posterior probability def: "Protein Posterior probability calculated by EPIFANY protein inference algorithm" [PSI:MS] is_a: MS:1002363 ! search engine specific score for proteins relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003120 name: OpenMS:LFQ intensity def: "The data type LFQ intensity produced by OpenMS." [PSI:MS] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003121 name: OpenMS:LFQ spectral count def: "The data type LFQ spectral count produced by OpenMS." [PSI:MS] is_a: MS:1001805 ! quantification datatype relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003122 name: rapifleX def: "Bruker Daltonics' rapiflex: MALDI TOF/TOF." [PSI:MS] is_a: MS:1001534 ! Bruker Daltonics flex series [Term] id: MS:1003123 name: Bruker Daltonics timsTOF series def: "Bruker Daltonics timsTOF series" [PSI:MS] is_a: MS:1000122 ! Bruker Daltonics instrument model [Term] id: MS:1003124 name: timsTOF fleX def: "Bruker Daltonics' timsTOF fleX" [PSI:MS] is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003125 name: ProSight:spectral Q-value def: "ProSight spectrum-level Q-value." [PSI:MS] is_a: MS:1002354 ! PSM-level q-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003126 name: ProSight:spectral P-score def: "ProSight spectrum-level P-score." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003127 name: ProSight:spectral E-value def: "ProSight spectrum-level E-value." [PSI:MS] is_a: MS:1002353 ! PSM-level e-value is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003128 name: ProSight:spectral C-score def: "ProSight spectrum-level C-score." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_order MS:1002108 ! higher score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003129 name: proteoform-level Q-value def: "Estimation of the Q-value for proteoforms." [PSI:MS] is_a: MS:1002905 ! proteoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003130 name: ProSight:proteoform Q-value def: "ProSight proteoform-level Q-value." [PSI:MS] is_a: MS:1003129 ! proteoform-level Q-value relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003131 name: isoform-level identification attribute def: "Isoform level information." [PSI:MS] is_a: MS:1002694 ! single identification result attribute [Term] id: MS:1003132 name: isoform-level identification statistic def: "Identification confidence metric for a isoform." [PSI:MS] is_a: MS:1003131 ! isoform-level identification attribute [Term] id: MS:1003133 name: isoform-level Q-value def: "Estimation of the Q-value for isoforms." [PSI:MS] is_a: MS:1003132 ! isoform-level identification statistic relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003134 name: ProSight:isoform Q-value def: "ProSight isoform-level Q-value." [PSI:MS] is_a: MS:1003133 ! isoform-level Q-value relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003135 name: ProSight:protein Q-value def: "ProSight protein-level Q-value." [PSI:MS] is_a: MS:1001869 ! protein-level q-value relationship: has_order MS:1002109 ! lower score better relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003136 name: ProSight input parameter def: "Search engine input parameters specific to ProSight." [PSI:MS] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1003137 name: TDPortal input parameter def: "Search engine input parameters specific to TDPortal." [PSI:MS] is_a: MS:1001302 ! search engine specific input parameter [Term] id: MS:1003138 name: ProSight:Run delta m mode def: "If true, runs delta m mode in ProSight." [PSI:MS] is_a: MS:1003136 ! ProSight input parameter is_a: MS:1003137 ! TDPortal input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003139 name: ProSight:Run Subsequence Search mode def: "If true, runs Subsequence Search mode in ProSight." [PSI:MS] is_a: MS:1003136 ! ProSight input parameter is_a: MS:1003137 ! TDPortal input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003140 name: ProSight:Run Annotated Proteoform Search mode def: "If true, runs Annotated Proteoform Search mode in ProSight." [PSI:MS] is_a: MS:1003136 ! ProSight input parameter is_a: MS:1003137 ! TDPortal input parameter relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003141 name: ProSight def: "ProSight: Database search engine for top-down proteomics." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1003142 name: TDPortal def: "TDPortal: Database search engine for top-down proteomics." [PSI:MS] is_a: MS:1001456 ! analysis software [Term] id: MS:1003143 name: mass array def: "A data array of mass values." [PSI:MS] xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units UO:0000221 ! dalton [Term] id: MS:1003144 name: Triple Quad 7500 def: "SCIEX Triple Quad 7500." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1003145 name: ThermoRawFileParser def: "Cross-platform software to convert Thermo RAW files to a number of open formats." [DOI:10.1021/acs.jproteome.9b00328, PMID:31755270] is_a: MS:1001457 ! data processing software [Term] id: MS:1003146 name: pyteomics def: "Python module that helps handling various proteomics data analysis tasks." [DOI:10.1021/acs.jproteome.8b00717, PMID:30576148] is_a: MS:1001456 ! analysis software [Term] id: MS:1003147 name: PTMProphet probability def: "Probability that one mass modification has been correctly localized to a specific residue as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring [Term] id: MS:1003148 name: PTMProphet mean best probability def: "PSM-specific average of the m best site probabilities over all potential sites where m is the number of modifications of a specific type, as computed by PTMProphet." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring [Term] id: MS:1003149 name: PTMProphet normalized information content def: " PTMProphet-computed PSM-specific normalized (0.0 - 1.0) measure of information content across all modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring [Term] id: MS:1003150 name: PTMProphet information content def: " PTMProphet-computed PSM-specific measure of information content per modification type ranging from 0 to m, where m is the number of modifications of a specific type." [DOI:10.1021/acs.jproteome.9b00205, PMID:31290668] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring [Term] id: MS:1003151 name: SHA-256 def: "SHA-256 (member of Secure Hash Algorithm-2 family) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity." [PSI:MS] is_a: MS:1000561 ! data file checksum type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003152 name: GCMS-QP2010SE def: "Shimadzu Scientific Instruments GCMS-QP2010SE." [PSI:MS] is_a: MS:1000603 ! Shimadzu Scientific Instruments instrument model [Term] id: MS:1003153 name: raw ion mobility drift time array def: "Array of raw ion mobility values from a drift time device, reported in seconds (or milliseconds), corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003154 name: deconvoluted ion mobility array def: "Array of ion mobility values (K or K0) based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003155 name: deconvoluted inverse reduced ion mobility array def: "Array of ion mobility values based on ion separation in gaseous phase due to different ion mobilities under an electric field based on ion size, m/z and shape, normalized for the local conditions and reported in volt-second per square centimeter, as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units MS:1002814 ! volt-second per square centimeter relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003156 name: deconvoluted ion mobility drift time array def: "Array of mean ion mobility values from a drift time device, reported in seconds (or milliseconds), as an average property of an analyte post peak-detection, weighted charge state reduction, and/or adduct aggregation, corresponding to a spectrum of individual peaks encoded with an m/z array." [PSI:MS] is_a: MS:1002893 ! ion mobility array relationship: has_units UO:0000028 ! millisecond relationship: has_units UO:0000010 ! second relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003157 name: scanning quadrupole position lower bound m/z array def: "Array of m/z values representing the lower bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] is_a: MS:1000513 ! binary data array relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003158 name: scanning quadrupole position upper bound m/z array def: "Array of m/z values representing the upper bound m/z of the quadrupole position at each point in the spectrum." [PSI:MS] is_a: MS:1000513 ! binary data array relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003159 name: isolation window full range def: "Indicates an acquisition mode in which the isolation window is a full range, rather than a subset of the full range." [PSI:MS] is_a: MS:1000792 ! isolation window attribute [Term] id: MS:1003160 name: mzQC format def: "Proteomics Standards Initiative mzQC format for quality control data." [PSI:MS] is_a: MS:1003161 ! quality control data format [Term] id: MS:1003161 name: quality control data format def: "Grouping term for quality control data formats." [PSI:MS] is_a: MS:1001459 ! file format [Term] id: MS:1003162 name: PTX-QC def: "Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization." [DOI:10.1021/acs.jproteome.5b00780, PMID:26653327, https://github.com/cbielow/PTXQC/] is_a: MS:1001456 ! analysis software synonym: "PTXQC" EXACT [] [Term] id: MS:1003163 name: analyte mixture members def: "The set of analyte identifiers that compose an interpretation of a spectrum." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type MS:1002712 ! list of integers [Term] id: MS:1003164 name: QuaMeter IDFree def: "QuaMeter IDFree software for QC metric calculation." [DOI:10.1021/ac4034455, PMID:24494671] is_a: MS:1001456 ! analysis software synonym: "QuaMeter" EXACT [] [Term] id: MS:1003165 name: iMonDB def: "iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files." [DOI:10.1021/acs.jproteome.5b00127, PMID:25798920, https://github.com/bittremieux/iMonDB] is_a: MS:1001456 ! analysis software [Term] id: MS:1003166 name: assigned intensity fraction def: "Fraction of intensity summed from all peaks that can be attributed to expected fragments of the analyte, divided by the intensity summed from all peaks in the spectrum" [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003167 name: MSn-1 isolation window precursor purity def: "The fraction of total intensities in the isolation window in the previous round of MS (i.e. the MSn-1 scan) that can be assigned to this identified analyte" [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003168 name: library spectrum comment def: "A free-text string providing additional information of the library spectrum not encoded otherwise, usually for human use and not parsed by software tools." [PSI:PI] is_a: MS:1003234 ! library spectrum attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003169 name: proforma peptidoform sequence def: "Sequence string describing the amino acids and mass modifications of a peptidoform using the PSI ProForma notation" [PSI:PI] is_a: MS:1000889 ! peptidoform sequence relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003170 name: spectral library def: "A collection of spectra organized by their originating analyte, compiled deliberately for use in MS data analysis in future experiments" [PSI:PI] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1003171 name: spectral library attribute def: "An attribute of a spectral library" [PSI:PI] relationship: part_of MS:1003170 ! spectral library [Term] id: MS:1003172 name: library spectrum def: "An entry in a spectral library representing a spectrum" [PSI:PI] relationship: part_of MS:1003170 ! spectral library [Term] id: MS:1003173 name: numeric attribute def: "An attribute that takes on a numeric value" [PSI:PI] is_a: MS:1000547 ! object attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003174 name: attribute maximum def: "The maximum value for this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003175 name: attribute minimum def: "The minimum value for this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003176 name: attribute mean def: "The arithmetic mean value for this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003177 name: attribute standard deviation def: "The standard deviation (exact value of population, or estimate from sample) of this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003178 name: attribute coefficient of variation def: "The coefficient of variation of this attribute, i.e. standard deviation divided by the mean" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003179 name: attribute summary value def: "The most appropriate summary value of the attribute, usually but not necessarily the mean" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003180 name: attribute median def: "The median of this attribute" [PSI:PI] relationship: part_of MS:1003171 ! numeric attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003181 name: combined dissociation method def: "Combination of two or more dissociation methods that are known by a special term." [PSI:PI] is_a: MS:1000044 ! dissociation method [Term] id: MS:1003182 name: electron-transfer/collision-induced dissociation def: "Dissociation process combining electron-transfer dissociation (ETD) and collision-induced dissociation (CID)." [PSI:PI] synonym: "ETciD" EXACT [] is_a: MS:1003181 ! combined dissociation method [Term] id: MS:1003183 name: Synapt XS def: "Waters oa-ToF based Synapt XS." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003184 name: SELECT SERIES Cyclic IMS def: "Waters oa-ToF based SELECT SERIES Cyclic IMS." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003185 name: SELECT SERIES MRT def: "Waters oa-ToF based SELECT SERIES MRT." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003186 name: library format version def: "Version number of the [PSI] library format specification" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003187 name: library identifier def: "Short identifier for the library for easy reference, preferably but not necessarily globally unique" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003188 name: library name def: "A short name identifying the library to potential users. The same name may refer to multiple versions of the same continually updated library." [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003189 name: library description def: "Extended free-text description of the library" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003190 name: library version def: "Version number of the library, usually refering to a certain release of a continually updated library " [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003191 name: library URI def: "URI or URL that uniquely identifies the library" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003192 name: decoy spectrum def: "A spectrum deliberately introduced into a spectral library that necessarily produces incorrect identifications when matched, for the purpose of error control in spectral library searching" [PSI:PI] is_a: MS:1003072 ! spectrum origin type [Term] id: MS:1003193 name: shuffle-and-reposition decoy spectrum def: "A decoy spectrum generated from a real spectrum, by shuffling the amino acid sequence of the identification of the real spectrum, followed by re-positioning annotated peaks to match the shuffled sequence." [PSI:PI] is_a: MS:1003192 ! decoy spectrum [Term] id: MS:1003194 name: precursor shift decoy spectrum def: "A decoy spectrum generated from a real spectrum, by changing the precursor m/z value of the real spectrum." [PSI:PI] is_a: MS:1003192 ! decoy spectrum [Term] id: MS:1003195 name: unnatural peptidoform decoy spectrum def: "A decoy spectrum that is either a real spectrum of an unnatural peptidoform (e.g. a synthetic peptide that cannot be found in nature), or an artificial spectrum predicted for such unnatural peptidoform" [PSI:PI] is_a: MS:1003192 ! decoy spectrum [Term] id: MS:1003196 name: unrelated species decoy spectrum def: "A decoy spectrum that is a real spectrum of a naturally occuring peptidoform of an unrelated species that should not be found in the sample" [PSI:PI] is_a: MS:1003192 ! decoy spectrum [Term] id: MS:1003197 name: license URI def: "URI of the license controlling use of the library (e.g. https://creativecommons.org/publicdomain/zero/1.0/)" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003198 name: copyright notice def: "Notice of statutorily prescribed form that informs users of the underlying claim to copyright ownership in a published work" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003199 name: change log def: "Extended free-text description of the difference from the previous version" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003200 name: software version def: "Version number of the software package used for library creation" [PSI:PI] is_a: MS:1003171 ! spectral library attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003201 name: library provenance attribute def: "Abstract term containing several different types of provenance information" [PSI:PI] is_a: MS:1003171 ! spectral library attribute [Term] id: MS:1003202 name: BiblioSpec def: "A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington" [PSI:PI] is_a: MS:1001456 ! analysis software is_a: MS:1003207 ! library creation software [Term] id: MS:1003203 name: constituent spectrum file def: "Spectrum data file from which (at least) a subset of spectra were extracted from. Should use USI notation mzspec:PXDxxxx:msRunName if possible, or a URI if USI notation is not possible." [PSI:PI] is_a: MS:1003201 ! library provenance attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003204 name: constituent identification file def: "Identification file where (at least) a subset of identifications were extracted from. Should use a URI if possible" [PSI:PI] is_a: MS:1003201 ! library provenance attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003205 name: constituent library file def: "Source library URI which(at least) a subset of spectra were extracted from." [PSI:PI] is_a: MS:1003201 ! library provenance attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003206 name: library creation log def: "String of logging information generated when the library was constructed from its constituent files. Multiple lines should be separated with escaped \n" [PSI:PI] is_a: MS:1003201 ! library provenance attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003207 name: library creation software def: "Library creation software" [PSI:MS] is_a: MS:1000531 ! software is_a: MS:1003171 ! spectral library attribute [Term] id: MS:1003208 name: experimental precursor monoisotopic m/z def: "The measured or inferred m/z (as reported by the mass spectrometer acquisition software or post-processing software) of the monoisotopic peak of the precursor ion based on the MSn-1 spectrum." [PSI:MS] is_a: MS:1000455 ! ion selection attribute is_a: MS:1003295 ! summary statistics of replicates relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003209 name: monoisotopic m/z deviation def: "The measured monoisotopic m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical monoisotopic m/z of the analyte assigned to the spectrum." [PSI:MS] is_a: MS:1003078 ! interpreted spectrum attribute is_a: MS:1003295 ! summary statistics of replicates relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000169 ! parts per million relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003210 name: average m/z deviation def: "The measured average m/z (as reported by the mass spectrometer acquisition software or post-processing software) minus the theoretical average m/z of the analyte assigned to the spectrum." [PSI:MS] is_a: MS:1003078 ! interpreted spectrum attribute is_a: MS:1003295 ! summary statistics of replicates relationship: has_units MS:1000040 ! m/z relationship: has_units UO:0000169 ! parts per million relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003211 name: library spectrum attribute set def: "A set of spectrum-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] is_a: MS:1003171 ! spectral library attribute [Term] id: MS:1003212 name: library attribute set name def: "A name to refer to a library attribute set" [PSI:PI] relationship: part_of MS:1003211 ! library spectrum attribute set relationship: part_of MS:1003238 ! library analyte attribute set relationship: part_of MS:1003239 ! library interpretation attribute set relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003213 name: mass spectrometry acquisition method def: "Mode of running a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS] is_a: MS:1000524 ! data file content is_a: MS:1001954 ! acquisition parameter relationship: part_of MS:1003350 ! mass spectrometry proteomics [Term] id: MS:1003214 name: mass spectrometry acquisition method aspect def: "Specific aspect of a mass spectrometer method by which mass ranges are selected and possibly dissociated." [PSI:MS] is_a: MS:1001458 ! spectrum generation information relationship: part_of MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1003215 name: data-independent acquisition def: "Mass spectrometer data acquisition method wherein mass selection for fragmentation is configured according to a pre-determined program, rather than based on any detected precursor ions." [PSI:MS] synonym: "DIA" EXACT [] is_a: MS:1003214 ! mass spectrometry acquisition method aspect [Term] id: MS:1003216 name: dissociation of full mass range def: "Mass spectrometer data acquisition method wherein all precursor ions of which the instrument is capable are fragmented at once.." [PSI:MS] is_a: MS:1003214 ! mass spectrometry acquisition method aspect [Term] id: MS:1003217 name: dissociation of scanning quadrupole across a specified mass range def: "Mass spectrometer data acquisition method wherein ????." [PSI:MS] is_a: MS:1003214 ! mass spectrometry acquisition method aspect [Term] id: MS:1003218 name: dissociation of sequential mass ranges def: "Mass spectrometer data acquisition method wherein a series of limited mass range fragmentation selection windows are preconfigured." [PSI:MS] is_a: MS:1003214 ! mass spectrometry acquisition method aspect [Term] id: MS:1003219 name: ion mobility separation def: "Mass spectrometer data acquisition method wherein precursor ions are separated by their ion mobility properties prior to measurement." [PSI:MS] is_a: MS:1003214 ! mass spectrometry acquisition method aspect [Term] id: MS:1003220 name: adduct deconvolution def: "Data processing action of merging of the measurements of potentially multiple adducts into a single representation that is independent of the small ion that adds charge to a larger molecule." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1003221 name: data-dependent acquisition def: "Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run." [PSI:MS] is_a: MS:1003214 ! mass spectrometry acquisition method aspect is_a: MS:1003213 ! mass spectrometry acquisition method synonym: "DDA" EXACT [] [Term] id: MS:1003222 name: ion mobility deconvolution def: "Data processing action of merging multiple ion peaks acquired at different ion mobility steps into a single mass spectrum representing a single analyte." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1003224 name: data independent acquisition from dissociation of sequential mass ranges def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented. Examples of such an approach include SWATH-MS, FT-ARM, HRM, and PAcIFIC." [PSI:MS] is_a: MS:1003218 ! dissociation of sequential mass ranges is_a: MS:1003215 ! data-independent acquisition is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1003225 name: data independent acquisition from dissociation of sequential mass ranges after ion mobility separation def: "Data independent mass spectrometer acquisition method wherein a preconfigured sequence of mass ranges are fragmented after being separated by ion mobility. An example of such an approach is Bruker diaPASEF." [PSI:MS] is_a: MS:1003218 ! dissociation of sequential mass ranges is_a: MS:1003219 ! ion mobility separation is_a: MS:1003215 ! data-independent acquisition is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1003226 name: data independent acquisition from dissociation of full mass range after ion mobility separation def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented after being separated by ion mobility. Examples of such an approach include HDMS^E and IMS-AIF." [PSI:MS] is_a: MS:1003216 ! dissociation of full mass range is_a: MS:1003219 ! ion mobility separation is_a: MS:1003215 ! data-independent acquisition is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1003227 name: data independent acquisition from dissociation of full mass range def: "Data independent mass spectrometer acquisition method wherein the full mass range is fragmented. Examples of such an approach include MS^E, AIF, and bbCID." [PSI:MS] is_a: MS:1003216 ! dissociation of full mass range is_a: MS:1003219 ! ion mobility separation is_a: MS:1003215 ! data-independent acquisition is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1003228 name: data independent acquisition from dissociation of scanning quadrupole across mass range def: "Data independent mass spectrometer acquisition method wherein ???. An example of such an approach is Waters SONAR." [PSI:MS] is_a: MS:1003215 ! data-independent acquisition is_a: MS:1003217 ! dissociation of scanning quadrupole across a specified mass range is_a: MS:1003213 ! mass spectrometry acquisition method [Term] id: MS:1003229 name: timsTOF def: "Bruker Daltonics' timsTOF." [PSI:MS] is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003230 name: timsTOF Pro 2 def: "Bruker Daltonics' timsTOF Pro 2." [PSI:MS] is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003231 name: timsTOF SCP def: "Bruker Daltonics' timsTOF SCP." [PSI:MS] is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003232 name: PeakForest def: "comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB)." [https://peakforest.org/] is_a: MS:1001456 ! analysis software is_a: MS:1003207 ! library creation software is_a: MS:1002878 ! small molecule analysis software [Term] id: MS:1003234 name: library spectrum attribute def: "An attribute that describes information about an entry in a spectral library" [PSI:PI] relationship: part_of MS:1003172 ! library spectrum [Term] id: MS:1003235 name: paper spray ionization def: "The ionization of analytes from a piece of paper by applying a solvent and voltage." [PSI:MS] is_a: MS:1000008 ! ionization type [Term] id: MS:1003237 name: library spectrum key def: "An ordinal number uniquely identifying a spectrum in a library. Library spectrum keys should start at 1. Library spectrum keys SHOULD not change if entries are re-ordered or removed from a library." [PSI:PI] is_a: MS:1003234 ! library spectrum attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003238 name: library analyte attribute set def: "A set of analyte-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] is_a: MS:1003171 ! spectral library attribute [Term] id: MS:1003239 name: library interpretation attribute set def: "A set of interpretation-related attributes that is shared by a subset of spectra within the same spectral library" [PSI:PI] is_a: MS:1003171 ! spectral library attribute [Term] id: MS:1003240 name: peak intensity transform def: "A mathematical transformation applied to peak intensities, for example, as a way to modify the weight put on each peak when computing spectral match scores" [PSI:PI] is_a: MS:1000543 ! data processing action [Term] id: MS:1003241 name: square root transform def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their square roots" [PSI:PI] is_a: MS:1003240 ! peak intensity transform [Term] id: MS:1003242 name: rank transform def: "A mathematical transformation applied to peak intensities, in which peak intensities are replaced by their ranks" [PSI:PI] is_a: MS:1003240 ! peak intensity transform [Term] id: MS:1003243 name: adduct ion mass def: "The theoretical mass of the adduct ion (e.g. for a singly-charged protonated peptide ion, this value would be the neutral peptide molecule's mass plus the mass of a proton)" [PSI:PI] is_a: MS:1003056 ! adduct ion property relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003244 name: peptide accession number def: "Accession number (e.g. in PeptideAtlas) of the peptide sequence" [PSI:PI] is_a: MS:1003050 ! peptidoform attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003245 name: Q Exactive UHMR def: "Thermo Scientific Q Exactive UHMR (Ultra High Mass Range) Hybrid Quadrupole Orbitrap MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003246 name: ultraviolet photodissociation def: "Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple UV photons." [PSI:MS] synonym: "UVPD" EXACT [] is_a: MS:1000435 ! photodissociation [Term] id: MS:1003247 name: negative electron transfer dissociation def: "A process to fragment ions in a mass spectrometer by inducing fragmentation of anions (e.g. peptides or proteins) by transferring electrons to a radical-cation." [DOI:10.1016/j.jasms.2005.01.015, PSI:MS] synonym: "NETD" EXACT [] is_a: MS:1000044 ! dissociation method [Term] id: MS:1003248 name: proton transfer reaction def: "Process to transfer a proton from a hydronium ion (H3O+) to neutral analyte, leading to a protonated analyte, which typically does not lead to fragmentation." [DOI:10.1002/mas.20048, PSI:MS] synonym: "PTR" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1003249 name: proton transfer charge reduction def: "Process to transfer one or more protons from a multiply charged cation (peptide or protein ion) to a proton acceptor anion or neutral basic compound, thereby reducing the charge of the original analyte." [PSI:MS] synonym: "PTCR" EXACT [] is_a: MS:1000008 ! ionization type [Term] id: MS:1003250 name: count of identified peptidoforms def: "The number of peptidoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] is_a: MS:1002702 ! peptide sequence-level result list attribute is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1003251 name: count of identified spectra def: "The number of spectra that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] is_a: MS:1002700 ! PSM-level result list attribute is_a: MS:4000003 ! single value relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_metric_category MS:4000008 ! ID based metric [Term] id: MS:1003252 name: Xevo G2-XS QTof def: "Waters Corporation Xevo G2-XS QTof quadrupole time-of-flight mass spectrometer." [PSI:PI] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003253 name: DIA-NN def: "A universal software for data-independent acquisition (DIA) proteomics data processing" [PMID:31768060, https://github.com/vdemichev/DiaNN] is_a: MS:1001139 ! quantitation software name is_a: MS:1001456 ! analysis software [Term] id: MS:1003254 name: peak attribute def: "An attribute of a peak in a mass spectrum other than its m/z, intensity, and annotation. " [PSI:PI] relationship: part_of MS:1000231 ! peak [Term] id: MS:1003255 name: pre-decharged charge state def: "For a de-charged spectrum, the original charge state of the ion observed in a mass spectrum determined by charge deconvolution. " [PSI:PI] is_a: MS:1003254 ! peak attribute [Term] id: MS:1003256 name: peptidoform ion attribute def: "Non-inherent characteristic attributed to a peptidoform" [PSI:PI] relationship: part_of MS:1003051 ! peptidoform ion [Term] id: MS:1003257 name: library spectrum cross reference def: "A link from one spectrum to another spectrum of interest " [PSI:PI] is_a: MS:1003234 ! library spectrum attribute [Term] id: MS:1003258 name: related spectrum def: "A cross reference to another spectrum that has some relationship with this one, but is not necessarily spectrally similar. " [PSI:PI] is_a: MS:1003257 ! library spectrum cross reference [Term] id: MS:1003259 name: related spectrum keys def: "A list of cross references to a related spectrum in the same library, in the form of the library spectrum key. " [PSI:PI] is_a: MS:1003258 ! related spectrum relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term [Term] id: MS:1003260 name: related spectrum USI def: "A cross reference to a related spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] is_a: MS:1003258 ! related spectrum relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003261 name: related spectrum description def: "A free-text string describing the related spectrum and/or its relationship to this spectrum" [PSI:PI] relationship: part_of MS:1003258 ! related spectrum relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003262 name: similar spectrum def: "A cross reference to another spectrum that has high spectral similarity with this one, usually assumed to originate from the same analyte ion." [PSI:PI] is_a: MS:1003257 ! library spectrum cross reference [Term] id: MS:1003263 name: similar spectrum keys def: "A list of cross references to a similar spectrum in the same library, in the form of the library spectrum key. " [PSI:PI] is_a: MS:1003262 ! similar spectrum relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term [Term] id: MS:1003264 name: similar spectrum USI def: "A cross reference to a similar spectrum in the form of a PSI Universal Spectrum Identifier" [PSI:PI] is_a: MS:1003262 ! similar spectrum relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003265 name: spectrum cluster def: "A group of spectra that are spectrally similar to each other" [PSI:PI] relationship: part_of MS:1003170 ! spectral library [Term] id: MS:1003266 name: spectrum cluster attribute def: "A non-inherent characteristic of a spectrum cluster" [PSI:PI] relationship: part_of MS:1003265 ! spectrum cluster [Term] id: MS:1003267 name: spectrum cluster key def: "An ordinal number uniquely identifying a spectrum cluster. It should start with 1." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003268 name: spectrum cluster member spectrum keys def: "A list of integers corresponding to the library spectrum keys of the members of this cluster. These members must be in the same library." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term [Term] id: MS:1003269 name: spectrum cluster member USI def: "A member of this cluster external to the library, specified using a PSI Universal Spectrum Identifier." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003270 name: proforma peptidoform ion notation def: "A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type." [PSI:PI] is_a: MS:1003256 ! peptidoform ion attribute [Term] id: MS:1003271 name: peak annotation def: "The molecular identity(-ies) of the ion(s) producing this peak, inferred manually or computationally based on its m/z and the molecular interpretation of the spectrum." [PSI:PI] relationship: part_of MS:1000231 ! peak [Term] id: MS:1003272 name: peak annotation string def: "A string representing the peak annotation, in a defined format specified by the attribute 'ion annotation format'." [PSI:PI] relationship: part_of MS:1003271 ! peak annotation relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003273 name: peak annotation confidence def: "A confidence value of assigning a peak annotation to a peak, as defined by the attribute 'peak annotation confidence metric'." [PSI:PI] relationship: part_of MS:1003271 ! peak annotation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003274 name: peak annotation confidence metric def: "A confidence metric of assigning a peak annotation to a peak. By default, this should range from 0 (no confidence) to 1 (certain), and if there are multiple annotations of the same peak, the sum of their confidence levels should be no more than 1." [PSI:PI] is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003275 name: other attribute name def: "A user-provided name for a user-defined value describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003276 to provide the attribute's value" [PSI:MS] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003276 name: other attribute value def: "A user-provided value for a user-defined name describing a trait not covered by an existing controlled vocabulary term. This term should be used sparingly, preferring existing terms that describe the specific concept. Should be used with MS:1003275 to provide the attribute's name" [PSI:MS] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:string ! The allowed value-type for this CV term relationship: has_value_type xsd:integer ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_type MS:1002711 ! The allowed value-type for this CV term relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term relationship: has_value_type MS:1002713 ! The allowed value-type for this CV term [Term] id: MS:1003277 name: value between -1 and 1 inclusive def: "Value range for signed normalized score values." [PSI:PI] is_a: MS:1002304 ! domain range [Term] id: MS:1003278 name: m/z variability of peak def: "A measure of the statistical variability of the m/z value of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI] is_a: MS:1003254 ! peak attribute [Term] id: MS:1003279 name: observation frequency of peak def: "The frequency at which this peak is observed among replicate spectra of the same analyte." [PSI:PI] is_a: MS:1003254 ! peak attribute relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003280 name: intensity variability of peak def: "A measure of the statistical variability of the intensity of this peak, usually estimated from replicate spectra of the same analyte." [PSI:PI] is_a: MS:1003254 ! peak attribute [Term] id: MS:1003281 name: Casanovo def: "Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/." [https://github.com/Noble-Lab/casanovo/] is_a: MS:1001456 ! analysis software [Term] id: MS:1003282 name: Bruker TSF format def: "Bruker TSF raw file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1003283 name: Bruker TSF nativeID format def: "Native format defined by frame=xsd:nonNegativeInteger." [PSI:MS] is_a: MS:1000767 ! native spectrum identifier format [Term] id: MS:1003284 name: Bruker TSF nativeID format, combined spectra def: "Bruker TSF comma separated list of spectra that have been combined prior to searching or interpretation." [PSI:PI] is_a: MS:1002646 ! native spectrum identifier format, combined spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003285 name: standard deviation of m/z values of peak among replicates def: "The standard deviation of the m/z values of this peak among the replicate spectra of the same analyte." [PSI:PI] is_a: MS:1003278 ! m/z variability of peak relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003286 name: coefficient of variation of intensity of peak among replicates def: "The coefficient of variation (standard deviation divided by mean) of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI] is_a: MS:1003280 ! intensity variability of peak relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003287 name: standard deviation of intensity of peak among replicates def: "The standard deviation of the intensities of this peak among the replicate spectra of the same analyte." [PSI:PI] is_a: MS:1003280 ! intensity variability of peak relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003288 name: number of unassigned peaks def: "The number of unassigned peaks in the spectrum." [NIST] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003289 name: intensity of highest unassigned peak def: "The intensity of the highest unassigned peak in the spectrum." [NIST] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003290 name: number of unassigned peaks among top 20 peaks def: "The number of unassigned peaks among the most intense 20 peaks in the spectrum." [NIST] is_a: MS:1003078 ! interpreted spectrum attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003291 name: Luciphor deltaScore def: "Luciphor phosphosite localization score" [PSI:MS] is_a: MS:1001968 ! PTM localization PSM-level statistic relationship: has_regexp MS:1002505 ! regular expression for modification localization scoring [Term] id: MS:1003292 name: TSQ Altis Plus def: "Thermo Scientific TSQ Altis Plus Triple Quadrupole MS." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003293 name: ZenoTOF 7600 def: "SCIEX ZenoTOF 7600." [PSI:MS] is_a: MS:1000121 ! SCIEX instrument model [Term] id: MS:1003294 name: electron activated dissociation def: "A process to fragment ions in a high intensity electron beam which results in a dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins." [PSI:MS] synonym: "EAD" EXACT [] is_a: MS:1000250 ! electron capture dissociation [Term] id: MS:1003295 name: summary statistics of replicates def: "Summary statistics of an attribute among all replicates that are aggregated to generate this spectrum." [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute [Term] id: MS:1003296 name: number of replicates spectra used from source def: "The number of replicate spectra used during the aggregation process that originate from a specified source (e.g. a file, a dataset, a sample type, etc.). This term must appear in a group alongside a source term, which is one of: 'ProteomeXchange accession number', 'constituent spectrum file', or 'sample name'" [PSI:PI] is_a: MS:1003064 ! spectrum aggregation attribute relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003297 name: contributing replicate spectrum def: "A cross reference to another spectrum that is a replicate spectrum of the same analyte and contributes to the generation of this aggregated spectrum." [PSI:PI] is_a: MS:1003257 ! library spectrum cross reference [Term] id: MS:1003298 name: contributing replicate spectrum keys def: "A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys." [PSI:PI] relationship: part_of MS:1003297 ! contributing replicate spectrum [Term] id: MS:1003299 name: contributing replicate spectrum USI def: "A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers." [PSI:PI] relationship: part_of MS:1003297 ! contributing replicate spectrum [Term] id: MS:1003300 name: spectrum match def: "Result of a comparison of a spectrum to another spectrum, usually to assess the plausibility that the two spectra originate from the same analyte." [PSI:PI] relationship: part_of MS:1001000 ! spectrum interpretation [Term] id: MS:1003301 name: peptide-spectrum match def: "Result of a comparison of an observed fragment ion spectrum to the theoretically predicted fragmentation pattern of a peptide sequence, to assess the plausibility that the observed spectrum originates from the putative peptide sequence." [PSI:PI] is_a: MS:1003300 ! spectrum match synonym: "PSM" EXACT [] [Term] id: MS:1003302 name: spectrum-spectrum match def: "Result of a comparison of an observed fragment ion spectrum to another observed fragment ion spectrum, to assess the plausibility that two spectra originate from the same analyte, e.g., in spectral library searching and spectrum clustering." [PSI:PI] is_a: MS:1003300 ! spectrum match synonym: "SSM" EXACT [] [Term] id: MS:1003303 name: spectral similarity def: "A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone." [PSI:PI] is_a: MS:1002694 ! single identification attribute relationship: part_of MS:1003302 ! spectrum-spectrum match [Term] id: MS:1003304 name: spectral dot product def: "The dot (inner) product of two vectorized spectra divided by the product of their vector norms. It ranges from 0 (orthogonal vectors) to 1 (collinear vectors). Also known as cosine similarity." [PSI:PI] is_a: MS:1003303 ! spectral similarity synonym: "cosine similarity" EXACT [] relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003305 name: spectral Euclidean distance def: "The Euclidean distance between a pair of points representing two vectorized spectra in high-dimensional space." [PSI:PI] is_a: MS:1003303 ! spectral similarity relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003306 name: shared peak count def: "The number of peaks with closely matching m/z values that are common to two spectra." [PSI:PI] is_a: MS:1003303 ! spectral similarity relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003307 name: normalized spectral angle def: "The angle subtended by two vectorized spectra in high-dimensional space. It is equal to the 1 - (2 * inverse cosine of the spectral dot product) / pi." [https://doi.org/10.1074/mcp.O113.036475] is_a: MS:1003303 ! spectral similarity relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003308 name: spectral Pearson correlation def: "The Pearson's rho statistic between a pair of points representing two vectorized spectra." [PSI:PI] is_a: MS:1003303 ! spectral similarity relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003309 name: Goslin def: "The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature." [PMID:32589019, https://github.com/lifs-tools/goslin] is_a: MS:1001457 ! data processing software is_a: MS:1002414 ! postprocessing software is_a: MS:1002964 ! lipidomics analysis software [Term] id: MS:1003310 name: Lipid shorthand identification confidence level def: "Identification confidence levels based on the updated lipid shorthand nomenclature. The value slot can have the values 'Category', 'Class', 'Species', 'Phosphate-position', 'Molecular species', 'sn-position', 'DBE position', 'Structure defined', 'Full structure', 'Complete structure'." [PMID:33037133] is_a: MS:1002895 ! small molecule identification attribute [Term] id: MS:1003311 name: Lipid empirical score def: "The lipid empirical score is a point-based lipid class-specific scoring system based on MS and other evidence sources as defined by the Lipidomics Standards Initiative (LSI). The score has a numeric value between 0 and 100. Score values are lipid class-specific and are therefore not immediately comparable between lipid classes." [] is_a: MS:1002888 ! small molecule confidence measure relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003312 name: Lipid shorthand identification confidence - Category def: "Lipid shorthand identification confidence level 'Category'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003313 name: Lipid shorthand identification confidence - Class def: "Lipid shorthand identification confidence level 'Class'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003314 name: Lipid shorthand identification confidence - Species def: "Lipid shorthand identification confidence level 'Species'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003315 name: Lipid shorthand identification confidence - Phosphate-position def: "Lipid shorthand identification confidence level 'Phosphate-position'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003316 name: Lipid shorthand identification confidence - Molecular species def: "Lipid shorthand identification confidence level 'Molecular species'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003317 name: Lipid shorthand identification confidence - sn-position def: "Lipid shorthand identification confidence level 'sn-position'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003318 name: Lipid shorthand identification confidence - DBE pos def: "Lipid shorthand identification confidence level 'DBE pos'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003319 name: Lipid shorthand identification confidence - Structure defined def: "Lipid shorthand identification confidence level 'Structure defined'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003320 name: spectrum cluster size def: "The number of spectra in a spectrum cluster." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute relationship: has_value_type xsd:integer [Term] id: MS:1003321 name: summary statistics of clustered spectra def: "Summary statistics of an attribute among all spectra of a spectrum cluster." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute [Term] id: MS:1003322 name: spectrum cluster best representative def: "Cross reference to the spectrum that is considered the most representative among spectra in a cluster, either as a library spectrum key if the best representative is in the same library, or a universal spectrum identifier if it is not." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute relationship: has_value_type xsd:string [Term] id: MS:1003323 name: spectrum cluster consensus spectrum def: "Cross reference to a consensus spectrum that is constructed from aggregating spectra in a cluster, either as a library spectrum key if the consensus spectrum is in the same library, or a universal spectrum identifier if it is not." [PSI:PI] is_a: MS:1003266 ! spectrum cluster attribute relationship: has_value_type xsd:string [Term] id: MS:1003324 name: spectral dot product to aggregated spectrum def: "Spectral similarity measured by the spectral dot product between a replicate to its corresponding aggregated (e.g. consensus) spectrum." [PSI:PI] is_a: MS:1003295 ! summary statistics of replicates is_a: MS:1003304 ! spectral dot product relationship: has_value_type xsd:float [Term] id: MS:1003325 name: Lipid shorthand identification confidence - Full structure def: "Lipid shorthand identification confidence level 'Full structure'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003326 name: Lipid shorthand identification confidence - Complete structure def: "Lipid shorthand identification confidence level 'Complete structure'." [PMID:33037133] is_a: MS:1003310 ! Lipid shorthand identification confidence level [Term] id: MS:1003327 name: number of identified protein groups def: "The number of protein groups that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] is_a: MS:1002405 ! protein group-level result list attribute is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] id: MS:1003328 name: number of identified proteoforms def: "The number of proteoforms that pass the threshold to be considered identified with sufficient confidence." [PSI:PI] is_a: MS:1001085 ! protein-level identification attribute is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] id: MS:1003329 name: looplink spectrum identification item def: "Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink." [PSI:MS] synonym: "loop-link spectrum identification item" EXACT [] is_a: MS:1002508 ! crosslinking attribute [Term] id: MS:1003330 name: noncovalently associated peptides search def: "Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions." [PSI:MS] is_a: MS:1002489 ! special processing [Term] id: MS:1003331 name: noncovalently associated peptides spectrum identification item def: "Noncovalently associated peptides spectrum identification item." [PSI:MS] is_a: MS:1002508 ! crosslinking attribute relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:1003332 name: identification based on multiple spectra def: "Provides an identifier to encode identifications based on multiple spectra." [PSI:MS] is_a: MS:1002345 ! PSM-level attribute relationship: has_regexp MS:1003333 ! regular expression for encoding identifications based on multiple spectra. relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003333 name: regular expression for encoding identifications based on multiple spectra. def: "^(?[0-9]+)(?::(?P|C))$" [PSI:MS] is_a: MS:1002479 ! regular expression [Term] id: MS:1003334 name: parent term for PSM-level scores for identifications based on multiple spectra def: "Parent term for PSM-level scores for identifications based on multiple spectra." [PSI:MS] is_a: MS:1002347 ! PSM-level identification statistic is_a: MS:1002483 ! PSM-level statistical threshold relationship: has_regexp MS:1003335 ! regular expression for PSM-level scores for identifications based on multiple spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003335 name: regular expression for PSM-level scores for identifications based on multiple spectra def: "^(?[0-9]+):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+))$" [PSI:MS] is_a: MS:1002479 ! regular expression [Term] id: MS:1003336 name: posterior error probability from identification based on multiple spectra def: "PEP score for identifications based on multiple spectra." [PSI:MS] is_a: MS:1003334 ! Parent term for PSM-level scores for identifications based on multiple spectra relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003337 name: crosslinked PSM-level global FDR def: "Estimation of the global false discovery rate of crosslinked peptide spectrum matches." [PSI:MS] is_a: MS:1002701 ! PSM-level result list statistic is_a: MS:1002483 ! PSM-level statistical threshold is_a: MS:1002664 ! interaction score derived from crosslinking relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003338 name: peptide-pair sequence-level global FDR def: "Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides." [PSI:MS] is_a: MS:1002703 ! peptide sequence-level result list statistic is_a: MS:1002484 ! peptide-level statistical threshold is_a: MS:1002664 ! interaction score derived from crosslinking relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003339 name: peptide-pair passes threshold def: "Peptide-pair passes threshold. Applicable in the case of crosslinked peptides or noncovalently associated peptides." [PSI:MS] is_a: MS:1001105 ! peptide sequence-level identification attribute relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003340 name: residue-pair passes threshold def: "Residue-pair passes threshold. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI)." [PSI:MS] is_a: MS:1001060 ! quality estimation method details relationship: has_regexp MS:1003342 ! regular expression for whether interaction score derived from crosslinking passes threshold relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003341 name: protein-protein interaction passes threshold def: "Protein-protein interaction passes threshold." [PSI:MS] is_a: MS:1001060 ! quality estimation method details relationship: has_regexp MS:1003342 ! regular expression for whether interaction score derived from crosslinking passes threshold relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003342 name: regular expression for whether interaction score derived from crosslinking passes threshold def: "^((?[0-9]+):(?true|false))$" [PSI:MS] is_a: MS:1002479 ! regular expression [Term] id: MS:1003343 name: FDR applied separately to self crosslinks and protein heteromeric crosslinks def: "States whether FDR was applied separately to self crosslinks (crosslinks between peptides within one protein sequence) and protein heteromeric crosslinks (crosslinks between distinct protein sequences)." [PSI:MS] is_a: MS:1002489 ! special processing relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: MS:1003344 name: residue-pair ref def: "Reference to a residue-pair supported by this identification item, the value is the identifier for the residue-pair. In the context of crosslinking experiments, a residue-pair is a unique pair of crosslinked residues, irrespective of the peptides identified (A level of consolidation higher than unique peptide but lower than PPI)." [PSI:MS] is_a: MS:1002508 ! crosslinking attribute relationship: has_regexp MS:1003345 ! regular expression for residue-pair ref relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003345 name: regular expression for residue-pair ref def: "^(([0-9]+).(a|b))$" [PSI:MS] is_a: MS:1002479 ! regular expression [Term] id: MS:1003346 name: cleavable crosslinker stub def: "This term indicates that a given protein modification is a derivative of a cleavable crosslinker." [PSI:MS] is_a: MS:1001471 ! peptide modification details [Term] id: MS:1003347 name: Unimod derivative code def: "The single letter code in Unimod that identifies a specific derivative of a modification. For example, in UNIMOD:1842 (http://www.unimod.org/modifications_view.php?editid1=1842) the letter ‘W’ represents the derivative ‘water quenched monolink’." [PSI:MS] is_a: MS:1001471 ! peptide modification details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003348 name: proteomics def: "large-scale study of proteins and proteomes." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:1003349 name: affinity proteomics def: "large-scale study of proteins and proteomes via the use of affinity reagents." [PSI:MS] is_a: MS:1003348 ! proteomics [Term] id: MS:1003350 name: mass spectrometry proteomics def: "large-scale study of proteins and proteomes via the use of mass spectrometers to measure the masses and abundances of charged proteins or protein fragments." [PSI:MS] is_a: MS:1003348 ! proteomics [Term] id: MS:1003351 name: top-down proteomics def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact proteins." [PSI:MS] is_a: MS:1003350 ! mass spectrometry proteomics [Term] id: MS:1003352 name: native top-down proteomics def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact folded proteins." [PSI:MS] is_a: MS:1003351 ! top-down proteomics [Term] id: MS:1003353 name: non-native top-down proteomics def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of charged intact denatured proteins." [PSI:MS] is_a: MS:1003351 ! top-down proteomics [Term] id: MS:1003354 name: middle-down proteomics def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins." [PSI:MS] is_a: MS:1003350 ! mass spectrometry proteomics [Term] id: MS:1003355 name: bottom-up proteomics def: "study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins." [PSI:MS] is_a: MS:1003350 ! mass spectrometry proteomics [Term] id: MS:1003356 name: Orbitrap Ascend def: "Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003357 name: ANN-SoLo def: "ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart." [doi:10.1021/acs.jproteome.8b00359, doi:10.1021/acs.jproteome.9b00291] is_a: MS:1001456 ! analysis software [Term] id: MS:1003358 name: XCorr rank def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score." [PSI:MS] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003359 name: exact p-value def: "A p-value for the XCorr score, calculated using dynamic programming." [PMID:24895379] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003360 name: refactored XCorr def: "A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum." [PMID:30221945] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003361 name: res-ev score def: "The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks." [PMID:30221945] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003362 name: res-ev rank def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score." [PMID:30221945] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003363 name: res-ev p-value def: "The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure." [PMID:30221945] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003364 name: combined p-value def: "A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them." [PMID:30221945] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003365 name: combined p-value rank def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value." [PMID:30221945] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003366 name: tailor score def: "A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum." [PMID:32175744] is_a: MS:1001143 ! PSM-level search engine specific statistic relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] id: MS:1003367 name: monoisotopic mass deisotoping def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] is_a: MS:1000033 ! deisotoping [Term] id: MS:1003368 name: most abundant mass deisotoping def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] is_a: MS:1000033 ! deisotoping [Term] id: MS:1003369 name: average mass deisotoping def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] is_a: MS:1000033 ! deisotoping [Term] id: MS:1003370 name: reduction to summed singly charged peak list def: "The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] id: MS:1003371 name: SelexION compensation voltage def: "The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer." [PSI:MS] is_a: MS:1002892 ! ion mobility attribute is_a: MS:1000455 ! ion selection attribute is_a: MS:1003254 ! peak attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003372 name: specification document extension version def: "The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies relationship: has_regexp MS:1003384 ! semantic version regexp [Term] id: MS:1003373 name: mzIdentML extension version def: "The versioning of an mzIdentML extension document." [PSI:PI] is_a: MS:1003372 ! specification document extension version relationship: part_of MS:1002073 ! mzIdentML format [Term] id: MS:1003374 name: Open Chromatography Binary OCB format def: "ChemClipse/OpenChrom file format." [PSI:MS] is_a: MS:1000560 ! mass spectrometer file format [Term] id: MS:1003375 name: Conversion to OCB def: "Conversion of a file format to Open Chromatography Binary OCB file format." [PSI:MS] is_a: MS:1000530 ! file format conversion [Term] id: MS:1003376 name: ChemClipse def: "ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH." [https://projects.eclipse.org/projects/science.chemclipse] synonym: "chemclipse" EXACT [] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1003377 name: OpenChrom def: "OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse." [PMID:20673335, DOI:10.1186/1471-2105-11-405, https://www.openchrom.net/] synonym: "openchrom" EXACT [] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1003378 name: Orbitrap Astral def: "Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer." [PSI:MS] is_a: MS:1000494 ! Thermo Scientific instrument model [Term] id: MS:1003379 name: asymmetric track lossless time-of-flight analyzer def: "A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution." [PSI:MS] synonym: "Astral" EXACT [] is_a: MS:1000084 ! time-of-flight [Term] id: MS:1003380 name: Xevo G3 QTof def: "Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003381 name: ACQUITY RDa Detector def: "Waters Corporation RDa time-of-flight mass detector." [PSI:MS] is_a: MS:1000126 ! Waters instrument model [Term] id: MS:1003382 name: waters_connect def: "Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing." [PSI:MS] is_a: MS:1000694 ! Waters software is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1003383 name: timsTOF Ultra def: "Bruker Daltonics' timsTOF Ultra." [PSI:MS] is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003384 name: semantic version regexp def: "v?(\d+)\.(\d+)\.(\d+)(?:-(\S+))?" [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1003385 name: mzIdentML crosslinking extension document version def: "The versioning of the crosslinking mzIdentML extension document." [PSI:PI] is_a: MS:1003373 ! mzIdentML extension version relationship: has_value_type xsd:string [Term] id: MS:1003386 name: Spectra def: "Bioconductor package Spectra for mass spectrometry data representation and processing." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.Spectra] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1003387 name: MetaboAnnotation def: "Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.MetaboAnnotation, https://doi.org/10.3390/metabo12020173, PMID:35208247] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software [Term] id: MS:1003388 name: CompoundDb def: "Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.CompoundDb, https://doi.org/10.3390/metabo12020173, PMID:35208247] is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software is_a: MS:1003207 ! library creation software [Term] id: MS:1003389 name: mzTab-M def: "Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence." [PMID:30688441, PMID:31525911, https://www.psidev.info/mztab] is_a: MS:1000914 ! tab delimited text format [Term] id: MS:1003390 name: crosslinker cleavage characteristics def: "Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_regexp MS:1003391 ! crosslinker cleavage regular expression relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003391 name: crosslinker cleavage regular expression def: "^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$" [PSI:PI] is_a: MS:1002479 ! regular expression [Term] id: MS:1003392 name: search modification id def: "A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003393 name: search modification id ref def: "A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance." [PSI:PI] is_a: MS:1001471 ! peptide modification details relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003394 name: SelexION separation voltage def: "RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF." [PSI:MS] is_a: MS:1002892 ! ion mobility attribute is_a: MS:1000455 ! ion selection attribute is_a: MS:1003254 ! peak attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:1003395 name: Q Exactive GC Orbitrap def: "Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer." [PSI:MS] is_a: MS:1000483 ! Thermo Fisher Scientific instrument model [Term] id: MS:1003396 name: 8890 GC/MS def: "Agilent 8890 Gas Chromatograph System." [PSI:MS] is_a: MS:1000490 ! Agilent instrument model [Term] id: MS:1003397 name: timsTOF fleX MALDI-2 def: "Bruker Daltonics' timsTOF fleX MALDI-2." [PSI:MS] is_a: MS:1003123 ! Bruker Daltonics timsTOF series [Term] id: MS:1003398 name: deconvoluted data def: "The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file." [PSI:MS] is_a: MS:1000524 ! data file content [Term] id: MS:1003399 name: quality control software def: "Software that creates or manipulates QC-related data." [PSI:MS] is_a: MS:1001457 ! data processing software [Term] id: MS:1003400 name: rmzqc def: "An R package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/rmzqc] is_a: MS:1003399 ! quality control software [Term] id: MS:1003401 name: jmzqc def: "A Java package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/jmzqc] is_a: MS:1003399 ! quality control software [Term] id: MS:1003402 name: pymzqc def: "A Python package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/pymzqc] is_a: MS:1003399 ! quality control software [Term] id: MS:1003403 name: InChI def: "IUPAC International Chemical Identifier." [PMID:26136848] is_a: MS:1001405 ! spectrum identification result details is_a: MS:1000867 ! structural formula relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:4000000 name: PSI-MS CV Quality Control Vocabulary def: "PSI Quality Control controlled vocabulary term." [PSI:MS] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: MS:4000001 name: QC metric def: "Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations." [PSI:MS] relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary [Term] id: MS:4000002 name: QC metric value type def: "The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix." [PSI:MS] relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary [Term] id: MS:4000003 name: single value def: "Metrics consisting of a single value. The value must have a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS] is_a: MS:4000002 ! QC metric value type [Term] id: MS:4000004 name: n-tuple def: "Metrics consisting of multiple values, with the number of values implicitly specified by length of the JSON array (e.g. length 4 for quartiles). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the tuple must have the same unit and type (if applicable)." [PSI:MS] is_a: MS:4000002 ! QC metric value type [Term] id: MS:4000005 name: table def: "Metrics consisting of a table or data frame. The values of the table may have different types in each column (in contrast to a matrix). Each column must have a unit (identical for all entries of this column) and may have a value type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value)." [PSI:MS] comment: The actual structure of the table is defined in the mzQC specification document. In short: it must have at least one column, and MAY have optional columns. is_a: MS:4000002 ! QC metric value type [Term] id: MS:4000006 name: matrix def: "A matrix is a rectangular array of values of the same type (in contrast to a table). All values must be given a unit (e.g. UO:0000221 ! dalton or UO:0000187 ! percent), and optionally a type (e.g. STATO:0000574 ! median or MS:1002354 ! PSM-level q-value). All values in the matrix must have the same unit and type (if applicable)." [PSI:MS] comment: The actual structure of the matrix is defined in the mzQC specification document. is_a: MS:4000002 ! QC metric value type [Term] id: MS:4000007 name: QC metric category def: "Categorization of the QC metric." [PSI:MS] relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary [Term] id: MS:4000008 name: ID based metric def: "QC metric based on identification results." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000009 name: ID free metric def: "QC metric not based on identification results." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000010 name: quantification based metric def: "QC metric based on quantification results." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000012 name: single run based metric def: "QC metric calculated from a single run (e.g. one .raw file)." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000013 name: multiple runs based metric def: "QC metric calculated from multiple runs (e.g. multiple .raw files)." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000014 name: single spectrum based metric def: "QC metric calculated from a single spectrum." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000015 name: multiple spectra based metric def: "QC metric calculated from multiple spectra." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000016 name: retention time metric def: "QC metric related to retention time." [PSI:MS] is_a: MS:4000001 ! QC metric [Term] id: MS:4000017 name: chromatogram metric def: "QC metric related to a chromatogram." [PSI:MS] is_a: MS:4000001 ! QC metric [Term] id: MS:4000018 name: XIC metric def: "QC metric related to an extracted ion chromatogram." [PSI:MS] is_a: MS:4000017 ! chromatogram metric [Term] id: MS:4000019 name: MS metric def: "QC metric related to the mass spectrometry acquisition." [PSI:MS] is_a: MS:4000001 ! QC metric [Term] id: MS:4000020 name: ion source metric def: "QC metric related to events in the ion source." [PSI:MS] is_a: MS:4000019 ! MS metric [Term] id: MS:4000021 name: MS1 metric def: "QC metric based on MS1 events." [PSI:MS] is_a: MS:4000019 ! MS metric [Term] id: MS:4000022 name: MS2 metric def: "QC metric based on MS2 events." [PSI:MS] is_a: MS:4000019 ! MS metric [Term] id: MS:4000023 name: sample preparation metric def: "QC metric related to the sample preparation." [PSI:MS] is_a: MS:4000001 ! QC metric [Term] id: MS:4000024 name: environment metric def: "QC metric related to measurements of the ambient environment, such as the laboratory." [PSI:MS] is_a: MS:4000001 ! QC metric [Term] id: MS:4000050 name: XIC50 fraction def: "The number of XIC that account for the top half of all XIC-FWHM divided by the number of all XIC." [PSI:MS] comment: This metric characterises the distribution of precursor peak widths, much as the N50 characterises contig sizes in genome assembly. synonym: "XIC-WideFrac" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept UO:0000191 ! fraction [Term] id: MS:4000051 name: XIC-FWHM quantiles def: "The first to n-th quantile of peak widths for XICs. A metric's value triplet represents the related QuaMeter metrics of XIC-FWHM-Q1,Q2,Q3." [PSI:MS] synonym: "XIC-FWHM-Q1" RELATED [PMID:24494671] synonym: "XIC-FWHM-Q2" RELATED [PMID:24494671] synonym: "XIC-FWHM-Q3" RELATED [PMID:24494671] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000018 ! XIC metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept MS:1000086 ! full width at half-maximum relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000010 ! second [Term] id: MS:4000052 name: XIC-Height quartile ratios def: "The log ratio of successive XIC height quartiles. The metric's value triplet represents the log ratios of XIC-height-Q2 to XIC-height-Q1, XIC-height-Q3 to XIC-height-Q2, XIC-height max to XIC-height-Q3." [PSI:MS] synonym: "XIC-Height-Q2" RELATED [PMID:24494671] synonym: "XIC-Height-Q3" RELATED [PMID:24494671] synonym: "XIC-Height-Q4" RELATED [PMID:24494671] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000018 ! XIC metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept STATO:0000105 ! log signal intensity ratio relationship: has_value_concept UO:0000191 ! fraction [Term] id: MS:4000053 name: chromatography duration def: "The retention time duration of the chromatography in seconds." [PSI:MS] comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. synonym: "RT-Duration" RELATED [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C25330 ! Duration relationship: has_units UO:0000010 ! second [Term] id: MS:4000054 name: TIC quarters RT fraction def: "The interval when the respective quarter of the TIC accumulates divided by retention time duration." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run. synonym: "RT-TIC-Q1" RELATED [PMID:24494671] synonym: "RT-TIC-Q2" RELATED [PMID:24494671] synonym: "RT-TIC-Q3" RELATED [PMID:24494671] synonym: "RT-TIC-Q4" RELATED [PMID:24494671] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000191 ! fraction [Term] id: MS:4000055 name: MS1 quarter RT fraction def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type. synonym: "RT-MS-Q1" RELATED [PMID:24494671] synonym: "RT-MS-Q2" RELATED [PMID:24494671] synonym: "RT-MS-Q3" RELATED [PMID:24494671] synonym: "RT-MS-Q4" RELATED [PMID:24494671] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000191 ! fraction [Term] id: MS:4000056 name: MS2 quarter RT fraction def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. synonym: "RT-MSMS-Q1" RELATED [PMID:24494671] synonym: "RT-MSMS-Q2" RELATED [PMID:24494671] synonym: "RT-MSMS-Q3" RELATED [PMID:24494671] synonym: "RT-MSMS-Q4" RELATED [PMID:24494671] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000191 ! fraction [Term] id: MS:4000057 name: MS1 TIC-change quartile ratios def: "The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3" [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation.This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant. synonym: "MS1-TIC-Change-Q2" RELATED [PMID:24494671] synonym: "MS1-TIC-Change-Q3" RELATED [PMID:24494671] synonym: "MS1-TIC-Change-Q4" RELATED [PMID:24494671] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept STATO:0000105 ! log signal intensity ratio [Term] id: MS:4000058 name: MS1 TIC quartile ratios def: "The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples. synonym: "MS1-TIC-Q2" RELATED [PMID:24494671] synonym: "MS1-TIC-Q3" RELATED [PMID:24494671] synonym: "MS1-TIC-Q4" RELATED [PMID:24494671] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept STATO:0000105 ! log signal intensity ratio [Term] id: MS:4000059 name: number of MS1 spectra def: "The number of MS1 events in the run." [PSI:MS] comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. synonym: "MS1-Count" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000060 name: number of MS2 spectra def: "The number of MS2 events in the run." [PSI:MS] comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. synonym: "MS2-Count" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000061 name: MS1 density quantiles def: "The first to n-th quantile of MS1 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS1 density. The number of values in the tuple implies the quantile mode." [PSI:MS] synonym: "MS1-Density-Q1" RELATED [PMID:24494671] synonym: "MS1-Density-Q2" RELATED [PMID:24494671] synonym: "MS1-Density-Q3" RELATED [PMID:24494671] synonym: "MS1 peak density distribution - quantiles" EXACT [] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C45781 ! Density relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000062 name: MS2 density quantiles def: "The first to n-th quantile of MS2 peak density (scan peak counts). A value triplet represents the original QuaMeter metrics, the quartiles of MS2 density. The number of values in the tuple implies the quantile mode." [PSI:MS] synonym: "MS2-Density-Q1" RELATED [PMID:24494671] synonym: "MS2-Density-Q2" RELATED [PMID:24494671] synonym: "MS2-Density-Q3" RELATED [PMID:24494671] synonym: "MS2 peak density distribution - quantiles" EXACT [] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C45781 ! Density relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000063 name: MS2 known precursor charges fractions def: "The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher." [PSI:MS] comment: the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2. synonym: "MS2-PrecZ-1" NARROW [PMID:24494671] synonym: "MS2-PrecZ-2" NARROW [PMID:24494671] synonym: "MS2-PrecZ-3" NARROW [PMID:24494671] synonym: "MS2-PrecZ-4" NARROW [PMID:24494671] synonym: "MS2-PrecZ-5" NARROW [PMID:24494671] synonym: "MS2-PrecZ-more" NARROW [PMID:24494671] synonym: "IS-3A" RELATED [PMID:19837981] synonym: "IS-3B" RELATED [PMID:19837981] synonym: "IS-3C" RELATED [PMID:19837981] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_column MS:1000041 ! charge state relationship: has_column UO:0000191 ! fraction [Term] id: MS:4000064 name: MS2 unknown and likely precursor charges fractions def: "The fractions of inferred charge state of MS/MS precursors. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. Charge 0 represents unknown charge states." [PSI:MS] synonym: "MS2-PrecZ-likely-1" RELATED [PMID:24494671] synonym: "MS2-PrecZ-likely-multi" RELATED [PMID:24494671] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_column MS:1000041 ! charge state relationship: has_column UO:0000191 ! fraction [Term] id: MS:4000065 name: fastest frequency for MS level 1 collection def: "Fastest frequency for MS level 1 collection" [PSI:MS] comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. synonym: "MS1-Freq-Max" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000106 ! hertz [Term] id: MS:4000066 name: fastest frequency for MS level 2 collection def: "Fastest frequency for MS level 2 collection" [PSI:MS] comment: Spectrum acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. synonym: "MS2-Freq-Max" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units UO:0000106 ! hertz [Term] id: MS:4000067 name: MS run duration def: "The duration of the mass spectrometry acquisition (as measured by the time between the last scan and first scan) in seconds." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000019 ! MS metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C25330 ! Duration relationship: has_units UO:0000010 ! second [Term] id: MS:4000068 name: spectra half-TIC def: "The minimal proportion of peaks needed to account for at least 50% of the total ion current in each individual spectrum considered, recorded in a mandatory fraction column. Either USI or native spectrum identifier columns must be present as well." [PSI:MS] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_optional_column MS:1003063 ! universal spectrum identifier relationship: has_optional_column MS:1000767 ! native spectrum identifier format relationship: has_column UO:0000191 ! fraction relationship: has_relation MS:1000285 ! total ion current [Term] id: MS:4000069 name: m/z acquisition range def: "Upper and lower limit of m/z precursor values at which MSn spectra are recorded." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition. Based on the used MS instrument configuration, the values should be similar. Variations between measurements may arise when employing acquisition in DDA mode. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000019 ! MS metric relationship: has_units MS:1000040 ! m/z relationship: has_value_concept STATO:0000035 ! range [Term] id: MS:4000070 name: retention time acquisition range def: "Upper and lower limit of retention time at which spectra are recorded." [PSI:MS] comment: An unusual low range may indicate incomplete sampling and/or a premature or failed LC run. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_units UO:0000010 ! second relationship: has_value_concept STATO:0000035 ! range [Term] id: MS:4000071 name: number of chromatograms def: "The number of chromatograms recorded for the run." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000072 name: observed mass accuracy def: "Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000014 ! single spectrum based metric relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_units UO:0000169 ! parts per million relationship: has_value_concept MS:1000014 ! accuracy [Term] id: MS:4000073 name: QC sample metric def: "A QC metric based on a QC sample of known content." [PSI:MS] is_a: MS:4000007 ! QC metric category [Term] id: MS:4000074 name: high complexity QC sample metric def: "A QC metric based on a QC sample of known and high complexity content." [PSI:MS] is_a: MS:4000073 ! QC sample metric [Term] id: MS:4000075 name: low complexity QC sample metric def: "A QC metric based on a QC sample of known and low complexity content." [PSI:MS] is_a: MS:4000073 ! QC sample metric [Term] id: MS:4000076 name: QC2 sample metric def: "A QC metric based on the results of a QC2 sample measurement. A QC2 sample is made from Pierce HeLa protein digest standard, see Pichler et al. Chiva et al. for details on QC sample design." [PSI:MS, PMID:23088386, PMID:29324744] comment: Expected peptides from QC2 sample measurement are: 'YAEAVTR','STLTDSLVC(Carbamidomethyl)K','SLADELALVDVLEDK','NPDDITNEEYGEFYK','LAVDEEENADNNTK','FEELNMDLFR','EAALSTALSEK','DDVAQTDLLQIDPNFGSK','RFPGYDSESK','EATTEFSVDAR','EQFLDGDGWTSR','TPAQFDADELR','LGDLYEEEMR','EVSTYIK','FAFQAEVNR' is_a: MS:4000074 ! high complexity QC sample metric [Term] id: MS:4000077 name: QC1 sample metric def: "A QC metric based on the results of a QC1 sample measurement. A QC1 sample is made from trypsin-digested BSA MS Standard (CAM modified), see Pichler et al. Chiva et al. for details on QC sample design)." [PSI:MS, PMID:23088386, PMID:29324744] comment: Expected peptides from QC1 sample measurement are: 'LVNELTEFAK','HLVDEPQNLIK','VPQVSTPTLVEVSR','EAC(Carbamidomethyl)FAVEGPK','EYEATLEEC(Carbamidomethyl)C(Carbamidomethyl)AK','EC(Carbamidomethyl)C(Carbamidomethyl)HGDLLEC(Carbamidomethyl)ADDR','SLHTLFGDELC(Carbamidomethyl)K','TC(Carbamidomethyl)VADESHAGC(Carbamidomethyl)EK','YIC(Carbamidomethyl)DNQDTISSK','NEC(Carbamidomethyl)FLSHK' is_a: MS:4000075 ! low complexity QC sample metric [Term] id: MS:4000078 name: QC2 sample mass accuracies def: "Observed mass accuracy for the peptides of a QC2 sample measurement. The table should contain the peptides as described in the QC2 sample metric term, missing are interpreted as not detected." [PSI:MS] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000076 ! QC2 sample metric relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_column MS:1003169 ! proforma peptidoform sequence relationship: has_column MS:4000072 ! observed mass accuracy [Term] id: MS:4000079 name: QC2 sample intensities def: "Observed intensities for the peptides of a QC2 sample measurement within 5 ppm and +/- 240 s RT tolerance. Different metrics of observed intensities are possible, at least one must be present. The table should contain the peptides as defined in the parent QC2 sample metric term, missing are interpreted as not detected." [PSI:MS] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000076 ! QC2 sample metric relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_column MS:1003169 ! proforma peptidoform sequence relationship: has_optional_column MS:1001858 ! XIC area relationship: has_optional_column MS:1001859 ! normalized XIC area relationship: has_optional_column MS:1001844 ! MS1 feature area relationship: has_optional_column MS:1001843 ! MS1 feature maximum intensity relationship: has_optional_column MS:1003085 ! previous MSn-1 scan precursor intensity [Term] id: MS:4000080 name: QC non-metric term def: "QC terms associated but not directly metrics themselves." [PSI:MS] relationship: part_of MS:4000000 ! PSI-MS CV Quality Control Vocabulary [Term] id: MS:4000081 name: first principal component def: "Data from the first principal component of a PCA." [PSI:MS] relationship: has_value_concept NCIT:C60694 ! Principal Component is_a: MS:4000080 ! QC non-metric term synonym: "1st PC" EXACT [] [Term] id: MS:4000082 name: second principal component def: "Data from the second principal component of a PCA." [PSI:MS] relationship: has_value_concept NCIT:C60694 ! Principal Component is_a: MS:4000080 ! QC non-metric term synonym: "2nd PC" EXACT [] [Term] id: MS:4000083 name: third principal component def: "Data from the third principal component of a PCA." [PSI:MS] relationship: has_value_concept NCIT:C60694 ! Principal Component is_a: MS:4000080 ! QC non-metric term synonym: "3rd PC" EXACT [] [Term] id: MS:4000084 name: fourth principal component def: "Data from the fourth principal component of a PCA." [PSI:MS] relationship: has_value_concept NCIT:C60694 ! Principal Component is_a: MS:4000080 ! QC non-metric term synonym: "4th PC" EXACT [] [Term] id: MS:4000085 name: fifth principal component def: "Data from the fifth principal component of a PCA." [PSI:MS] relationship: has_value_concept NCIT:C60694 ! Principal Component is_a: MS:4000080 ! QC non-metric term synonym: "5th PC" EXACT [] [Term] id: MS:4000086 name: mzQC input reference def: "Used to refer to data elements of input sections in mzQC, either inputFile names or metadata labels." [PSI:MS] is_a: MS:4000080 ! QC non-metric term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:4000087 name: mzQC plot label def: "Used to supply alternative labels for plotting figures." [PSI:MS] is_a: MS:4000080 ! QC non-metric term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:4000088 name: batch label def: "Used to supply batch label information with any string value." [PSI:MS] is_a: MS:4000080 ! QC non-metric term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:4000089 name: injection sequence label def: "Used to supply injection sequence information with consecutive whole numbers." [PSI:MS] is_a: MS:4000080 ! QC non-metric term relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: MS:4000090 name: principal component analysis of MaxQuant's protein group raw intensities def: "A table with the PCA results of MaxQuant's protein group raw intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"} is_a: MS:4000005 ! table relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_metric_category MS:4000013 ! multiple runs based metric relationship: has_column MS:4000081 ! first principal component relationship: has_column MS:4000086 ! mzQC input reference relationship: has_optional_column MS:4000082 ! second principal component relationship: has_optional_column MS:4000083 ! third principal component relationship: has_optional_column MS:4000084 ! fourth principal component relationship: has_optional_column MS:4000085 ! fifth principal component [Term] id: MS:4000091 name: principal component analysis of MaxQuant's protein group lfq intensities def: "A table with the PCA results of MaxQuant's protein group lfq intensities." [PSI:MS] {http://coxdocs.org/doku.php?id="maxquant:table:directory&s[]=output"} is_a: MS:4000005 ! table relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_metric_category MS:4000013 ! multiple runs based metric relationship: has_column MS:4000081 ! first principal component relationship: has_column MS:4000086 ! mzQC input reference relationship: has_optional_column MS:4000082 ! second principal component relationship: has_optional_column MS:4000083 ! third principal component relationship: has_optional_column MS:4000084 ! fourth principal component relationship: has_optional_column MS:4000085 ! fifth principal component [Term] id: MS:4000092 name: identified MS1 feature area principal component analysis result def: "A table with the PCA results of identified MS1 feature areas." [PSI:MS] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_metric_category MS:4000013 ! multiple runs based metric relationship: has_column MS:4000081 ! first principal component relationship: has_column MS:4000086 ! mzQC input reference relationship: has_optional_column MS:4000082 ! second principal component relationship: has_optional_column MS:4000083 ! third principal component relationship: has_optional_column MS:4000084 ! fourth principal component relationship: has_optional_column MS:4000085 ! fifth principal component relationship: has_optional_column MS:4000087 ! mzQC plot label relationship: has_optional_column MS:4000088 ! batch label relationship: has_optional_column MS:4000089 ! injection sequence label [Term] id: MS:4000093 name: unidentified MS1 feature area principal component analysis result def: "A table with the PCA results of unidentified but multiple-run-matched MS1 feature areas." [PSI:MS] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_metric_category MS:4000013 ! multiple runs based metric relationship: has_column MS:4000081 ! first principal component relationship: has_column MS:4000086 ! mzQC input reference relationship: has_optional_column MS:4000082 ! second principal component relationship: has_optional_column MS:4000083 ! third principal component relationship: has_optional_column MS:4000084 ! fourth principal component relationship: has_optional_column MS:4000085 ! fifth principal component relationship: has_optional_column MS:4000087 ! mzQC plot label relationship: has_optional_column MS:4000088 ! batch label relationship: has_optional_column MS:4000089 ! injection sequence label [Term] id: MS:4000094 name: batch-corrected identified MS1 feature area principal component analysis result def: "A table with the PCA results of identified MS1 feature areas after batch-correction." [PSI:MS] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_metric_category MS:4000013 ! multiple runs based metric relationship: has_column MS:4000081 ! first principal component relationship: has_column MS:4000086 ! mzQC input reference relationship: has_optional_column MS:4000082 ! second principal component relationship: has_optional_column MS:4000083 ! third principal component relationship: has_optional_column MS:4000084 ! fourth principal component relationship: has_optional_column MS:4000085 ! fifth principal component relationship: has_optional_column MS:4000087 ! mzQC plot label relationship: has_optional_column MS:4000088 ! batch label relationship: has_optional_column MS:4000089 ! injection sequence label [Term] id: MS:4000095 name: slowest frequency for MS level 1 collection def: "The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_units UO:0000106 ! hertz relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_metric_category MS:4000021 ! MS1 metric [Term] id: MS:4000096 name: slowest frequency for MS level 2 collection def: "The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_units UO:0000106 ! hertz relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_metric_category MS:4000022 ! MS2 metric [Term] id: MS:4000097 name: MS1 signal jump (10x) count def: "The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans." [PSI:MS] comment: An unusual high count of signal jumps or falls may indicate ESI stability issues. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_units UO:0000189 ! count unit relationship: has_value_type xsd:integer ! The allowed value-type for this CV term synonym: "IS-1A" RELATED [] [Term] id: MS:4000098 name: MS1 signal fall (10x) count def: "The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans." [PSI:MS] comment: An unusual high count of signal jumps or falls may indicate ESI stability issues. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_units UO:0000189 ! count unit relationship: has_value_type xsd:integer ! The allowed value-type for this CV term synonym: "IS-1B" RELATED [] [Term] id: MS:4000099 name: number of empty MS1 scans def: "Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_units UO:0000189 ! count unit relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:4000100 name: number of empty MS2 scans def: "Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_units UO:0000189 ! count unit relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:4000101 name: number of empty MS3 scans def: "Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_units UO:0000189 ! count unit relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:4000102 name: number of detected quantification data points def: "The number of data points detected for quantification purposes within the run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000103 name: number of identified quantification data points def: "The number of identified data points for quantification purposes within the run after user defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000104 name: total ion currents def: "Tabular representation of the total ion current detected in each of a series of mass spectra." [PSI:MS] is_a: MS:4000005 ! table is_a: MS:1000235 ! total ion current chromatogram relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_column MS:1000767 ! native spectrum identifier format relationship: has_optional_column MS:1000894 ! retention time relationship: has_optional_column MS:1003059 ! number of peaks relationship: has_column MS:1000285 ! total ion current [Term] id: MS:4000105 name: ion injection parameters def: "Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition." [PSI:MS] is_a: MS:4000005 ! table relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_column MS:1000767 ! native spectrum identifier format relationship: has_column MS:1000927 ! ion injection time relationship: has_optional_column MS:1000511! ms level relationship: has_optional_column MS:1000465 ! scan polarity relationship: has_optional_column MS:1000500 ! scan window upper limit relationship: has_optional_column MS:1000501 ! scan window lower limit [Term] id: MS:4000106 name: MS1 frequency in equal parts of subsequent RT def: "Average MS1 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)" [PSI:MS] comment: Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_units UO:0000106 ! hertz relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000107 name: MS2 frequency in equal parts of subsequent RT def: "Average MS2 frequency during retention time periods between adjacent retention time quantiles. (Four values implies values for 1st, 2nd, 3rd, 4th quarter.)" [PSI:MS] comment: Acquisition frequency can be used to gauge the suitability of instrument settings depending on the sample content. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_units UO:0000106 ! hertz relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000108 name: MS1 peak density distribution mean def: "From the distribution of peak densities in MS1, the mean" [PSI:MS] comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000109 name: MS1 peak density distribution sigma def: "From the distribution of peak densities in MS1, the sigma value" [PSI:MS] comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000110 name: MS1 peak density distribution low outliers def: "From the distribution of peak densities in MS1, the list of outliers below a in-file defined threshold" [PSI:MS] comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000111 name: MS1 peak density distribution high outliers def: "From the distribution of peak densities in MS1, the list of outliers above a in-file defined threshold" [PSI:MS] comment: The distribution of peak densities in MS1 can provide insight into the presence of nuisance factors. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000112 name: MS2 peak density distribution mean def: "From the distribution of peak densities in MS2, the mean" [PSI:MS] comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000113 name: MS2 peak density distribution sigma def: "From the distribution of peak densities in MS2, the sigma value" [PSI:MS] comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000114 name: MS2 peak density distribution low outliers def: "From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold" [PSI:MS] comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000115 name: MS2 peak density distribution high outliers def: "From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold" [PSI:MS] comment: The distribution of peak densities in MS2 can provide insight into the instruments ion selection settings. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000116 name: MS2 precursor intensity distribution def: "From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3." [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000117 name: MS2 precursor intensity distribution mean def: "From the distribution of MS2 precursor intensities, the mean" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000118 name: MS2 precursor intensity distribution sigma def: "From the distribution of MS2 precursor intensities, the sigma value" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000119 name: MS2 precursor intensity distribution low outliers def: "From the distribution of precursor intensities, the list of outliers below a in-file defined threshold" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000120 name: MS2 precursor intensity distribution high outliers def: "From the distribution of precursor intensities, the list of outliers above a in-file defined threshold" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000121 name: MS1 signal-to-noise ratio quantiles def: "From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] comment: The Signal-to-noise ratio in MS1 distribution can provide insight to the presence of nuisance factors. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000122 name: MS1 signal-to-noise ratio mean def: "From the distribution of signal-to-noise ratio in MS1, the mean" [PSI:MS] comment: The signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000123 name: MS1 signal-to-noise ratio sigma def: "From the distribution of signal-to-noise ratio in MS1, the sigma value" [PSI:MS] comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000124 name: MS1 signal-to-noise ratio low outliers def: "From the distribution of signal-to-noise ratio in MS1, the list of outliers below a in-file defined threshold" [PSI:MS] comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000125 name: MS1 signal-to-noise ratio high outliers def: "From the distribution of signal-to-noise ratio in MS1, the list of outliers above a in-file defined threshold" [PSI:MS] comment: The Signal-to-noise ratio in MS1 distribution can provide insight into the presence of nuisance factors. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000126 name: MS2 signal-to-noise ratio quantiles def: "From the distribution of signal-to-noise ratio in MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000127 name: MS2 signal-to-noise ratio mean def: "From the distribution of signal-to-noise ratio in MS2, the mean" [PSI:MS] comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000128 name: MS2 signal-to-noise ratio sigma def: "From the distribution of signal-to-noise ratio in MS2, the sigma value" [PSI:MS] comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000129 name: MS2 signal-to-noise ratio low outliers def: "From the distribution of signal-to-noise ratio in MS2, the list of outliers below a in-file defined threshold" [PSI:MS] comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000130 name: MS2 signal-to-noise ratio high outliers def: "From the distribution of signal-to-noise ratio in MS2, the list of outliers above a in-file defined threshold" [PSI:MS] comment: A high signal-to-noise ratio in MS2 distribution can explain a high rate of unidentified spectra. Comparisons will likely only make local sense where the same method of S/N calculation is applied (or overall the same software to calculate this metric, see mzQC 'analysisSoftware'). is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000131 name: MS1 ion collection time quantiles def: "From the distribution of ion injection times (MS:1000927) for MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000132 name: MS1 ion collection time mean def: "From the distribution of ion injection times (MS:1000927) for MS1, the mean" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000133 name: MS1 ion collection time sigma def: "From the distribution of ion injection times (MS:1000927) for MS1, the sigma value" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000134 name: MS1 ion collection time low outliers def: "From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers below a in-file defined threshold" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000135 name: MS1 ion collection time high outliers def: "From the distribution of ion injection times (MS:1000927) for MS1, the list of outliers above a in-file defined threshold" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000136 name: MS2 ion collection time quantiles def: "From the distribution of ion injection times (MS:1000927) for MS2, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000137 name: MS2 ion collection time mean def: "From the distribution of ion injection times (MS:1000927) for MS2, the mean" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000138 name: MS2 ion collection time sigma def: "From the distribution of ion injection times (MS:1000927) for MS2, the sigma value" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000139 name: MS2 ion collection time low outliers def: "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000140 name: MS2 ion collection time high outliers def: "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold" [PSI:MS] comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000141 name: outlier threshold criterion def: "The definition of the outlier criteria applied." [PSI:MS] is_a: MS:4000080 ! QC non-metric term [Term] id: MS:4000142 name: Tukey's fence def: "Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000143 name: Tukey's fence high outliers def: "Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000144 name: Tukey's fence low outliers def: "Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000145 name: Z-score threshold def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000146 name: Z-score threshold high outliers def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000147 name: Z-score threshold low outliers def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000148 name: algorithmical threshold def: "Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000149 name: iRT calibration formula def: "A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc." [PSI:MS] is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000150 name: iRT calibration adjusted r-squared def: "The goodness of fit statistic between observed retention times and iRT calibrated retention times." [PSI:MS] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000151 name: MsQuality def: "MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data." [DOI:10.1101/2023.05.12.540477, https://github.com/tnaake/MsQuality/] is_a: MS:1001456 ! analysis software [Term] id: MS:4000152 name: MS2 precursor median m/z of identified quantification data points def: "Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The m/z distribution informs about the dynamic range of the acquisition. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_units MS:1000040 ! m/z [Term] id: MS:4000153 name: interquartile RT period for identified quantification data points def: "The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_units UO:0000010 ! second synonym: "C-2A" RELATED [PMID:19837981] [Term] id: MS:4000154 name: rate of the interquartile RT period for identified quantification data points def: "The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: Higher rates may indicate a more efficient sampling and identification. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_units UO:0000106 ! hertz synonym: "C-2B" RELATED [PMID:19837981] [Term] id: MS:4000155 name: area under TIC def: "The area under the total ion chromatogram." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free relationship: has_metric_category MS:4000017 ! chromatogram metric [Term] id: MS:4000156 name: area under TIC RT quantiles def: "The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. Differences between samples of an experiment may indicate differences in chromatographic performance, differences in the dynamic range and/or in the sample content. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free relationship: has_metric_category MS:4000017 ! chromatogram metric [Term] id: MS:4000157 name: extent of identified MS2 precursor intensity def: "Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "MS1-3A" RELATED [PMID:19837981] [Term] id: MS:4000158 name: median of TIC values in the RT range in which the middle half of quantification data points are identified def: "Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric [Term] id: MS:4000159 name: median of TIC values in the shortest RT range in which half of the quantification data points are identified def: "Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric synonym: "MS1-2B" RELATED [PMID:19837981] [Term] id: MS:4000160 name: MS2 precursor intensity range def: "Minimum and maximum MS2 precursor intensity recorded." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free relationship: has_metric_category MS:4000022 ! MS2 metric [Term] id: MS:4000161 name: identified MS2 precursor intensity distribution def: "From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000162 name: unidentified MS2 precursor intensity distribution def: "From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000163 name: identified MS2 precursor intensity distribution mean def: "From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000164 name: unidentified MS2 precursor intensity distribution mean def: "From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000165 name: identified MS2 precursor intensity distribution sigma def: "From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000166 name: unidentified MS2 precursor intensity distribution sigma def: "From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000167 name: ratio of 1+ over 2+ of all MS2 known precursor charges def: "The ratio of 1+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "IS-3A" RELATED [PMID:19837981] synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] [Term] id: MS:4000168 name: ratio of 1+ over 2+ of identified MS2 known precursor charges def: "The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "IS-3A" RELATED [PMID:19837981] synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] [Term] id: MS:4000169 name: ratio of 3+ over 2+ of all MS2 known precursor charges def: "The ratio of 3+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "IS-3B" RELATED [PMID:19837981] synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] [Term] id: MS:4000170 name: ratio of 3+ over 2+ of identified MS2 known precursor charges def: "The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "IS-3B" RELATED [PMID:19837981] synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] [Term] id: MS:4000171 name: ratio of 4+ over 2+ of all MS2 known precursor charges def: "The ratio of 4+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "IS-3C" RELATED [PMID:19837981] synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] [Term] id: MS:4000172 name: ratio of 4+ over 2+ of identified MS2 known precursor charges def: "The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "IS-3C" RELATED [PMID:19837981] synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] [Term] id: MS:4000173 name: mean MS2 precursor charge in all spectra def: "Mean MS2 precursor charge in all spectra" [PSI:MS] comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] [Term] id: MS:4000174 name: mean MS2 precursor charge in identified spectra def: "Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] [Term] id: MS:4000175 name: median MS2 precursor charge in all spectra def: "Median MS2 precursor charge in all spectra" [PSI:MS] comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] [Term] id: MS:4000176 name: median MS2 precursor charge in identified spectra def: "Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides in relation to identifiability. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000020 ! ion source metric relationship: has_metric_category MS:4000022 ! MS2 metric synonym: "MS2 known precursor charges fractions" RELATED [] synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] [Term] id: PEFF:0000001 name: PEFF CV term def: "PSI Extended FASTA Format controlled vocabulary term." [PSI:PEFF] relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies [Term] id: PEFF:0000002 name: PEFF file header section term def: "CV term that may appear in a PEFF file header section." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000003 name: PEFF file sequence entry term def: "CV term that may appear in a description line of a PEFF file individual sequence entry." [PSI:PEFF] is_a: PEFF:0000001 ! PEFF CV term [Term] id: PEFF:0000008 name: DbName def: "PEFF keyword for the sequence database name." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000009 name: Prefix def: "PEFF keyword for the sequence database prefix." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000010 name: DbDescription def: "PEFF keyword for the sequence database short description." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000011 name: Decoy def: "PEFF keyword for the specifying whether the sequence database is a decoy database." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:boolean ! The allowed value-type for this CV term [Term] id: PEFF:0000012 name: DbSource def: "PEFF keyword for the source of the database file." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000013 name: DbVersion def: "PEFF keyword for the database version (release date) according to database provider." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000014 name: DbDate def: "OBSOLETE PEFF keyword for the database date (release or file date of the source) according to database provider." [PSI:PEFF] comment: This term was obsoleted. is_a: PEFF:0000002 ! PEFF file header section term is_obsolete: true [Term] id: PEFF:0000015 name: NumberOfEntries def: "PEFF keyword for the sumber of sequence entries in the database." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: PEFF:0000016 name: Conversion def: "PEFF keyword for the description of the conversion from original format to this current one." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000017 name: SequenceType def: "PEFF keyword for the molecular type of the sequences." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_regexp PEFF:1002002 ! regular expression for PEFF molecular sequence type relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000018 name: SpecificKey def: "PEFF keyword for database specific keywords not included in the current controlled vocabulary." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000019 name: SpecificValue def: "PEFF keyword for the specific values for a custom key." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000020 name: DatabaseDescription def: "PEFF keyword for the short description of the PEFF file." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000021 name: GeneralComment def: "PEFF keyword for a general comment." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000022 name: ProteoformDb def: "PEFF keyword that when set to 'true' indicates that the database contains complete proteoforms." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000023 name: OptionalTagDef def: "PEFF keyword for the short tag (abbreviation) and longer definition used to annotate a sequence annotation (such as variant or modification) in the OptionalTag location." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0000024 name: HasAnnotationIdentifiers def: "PEFF keyword that when set to 'true' indicates that entries in the database have identifiers for each annotation." [PSI:PEFF] is_a: PEFF:0000002 ! PEFF file header section term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001001 name: DbUniqueId def: "OBSOLETE Sequence database unique identifier." [PSI:PEFF] comment: This term was made obsolete because decided in Heidelberg 2018-04 that this is redundant. is_a: PEFF:0000003 ! PEFF file sequence entry term is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001002 name: PName def: "PEFF keyword for the protein full name." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001003 name: NcbiTaxId def: "PEFF keyword for the NCBI taxonomy identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: PEFF:0001004 name: TaxName def: "PEFF keyword for the taxonomy name (latin or common name)." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001005 name: GName def: "PEFF keyword for the gene name." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001006 name: Length def: "PEFF keyword for the sequence length." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: PEFF:0001007 name: SV def: "PEFF keyword for the sequence version." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001008 name: EV def: "PEFF keyword for the entry version." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001009 name: PE def: "PEFF keyword for the Protein Evidence; A UniProtKB code 1-5." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:int ! The allowed value-type for this CV term [Term] id: PEFF:0001010 name: Processed def: "PEFF keyword for information on how the full length original protein sequence can be processed into shorter components such as signal peptides and chains." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001011 name: Variant def: "OBSOLETE Sequence variation (substitution, insertion, deletion)." [PSI:PEFF] comment: This term was made obsolete in favor of VariantSimple and VariantComplex. is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment is_obsolete: true relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001012 name: ModResPsi def: "PEFF keyword for the modified residue with PSI-MOD identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001013 name: ModRes def: "PEFF keyword for the modified residue without aPSI-MOD or UniMod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001014 name: AltAC def: "PEFF keyword for the Alternative Accession Code." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001015 name: SeqStatus def: "PEFF keyword for the sequence status. Complete or Fragment." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002003 ! regular expression for PEFF sequence status relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001016 name: CC def: "PEFF keyword for the entry associated comment." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001017 name: KW def: "PEFF keyword for the entry associated keyword(s)." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001018 name: GO def: "PEFF keyword for the Gene Ontology code." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001019 name: XRef def: "PEFF keyword for the cross-reference to an external resource." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001020 name: mature protein def: "Portion of a newly synthesized protein that contributes to a final structure after other components such as signal peptides are removed." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001021 name: signal peptide def: "Short peptide present at the N-terminus of a newly synthesized protein that is cleaved off and is not part of the final mature protein." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001022 name: transit peptide def: "Short peptide present at the N-terminus of a newly synthesized protein that helps the protein through the membrane of its destination organelle." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001023 name: Conflict def: "PEFF keyword for the sequence conflict; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001024 name: Crc64 def: "PEFF keyword for the Sequence checksum in crc64." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001025 name: Domain def: "PEFF keyword for the sequence range of a domain." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001026 name: ID def: "PEFF keyword for the UniProtKB specific Protein identifier ID; a UniProtKB term." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001027 name: ModResUnimod def: "PEFF keyword for the modified residue with UniMod identifier." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001028 name: VariantSimple def: "PEFF keyword for the simple sequence variation of a single amino acid change. A change to a stop codon is permitted with a * symbol. More complex variations must be encoded with the VariantComplex term." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001029 name: VariantComplex def: "PEFF keyword for a sequence variation that is more complex than a single amino acid change or change to a stop codon." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001030 name: Proteoform def: "PEFF keyword for the proteoforms of this protein, constructed as a set of annotation identifiers." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001031 name: DisulfideBond def: "PEFF keyword for the disulfide bonds in this protein, constructed as a sets of annotation identifiers of two half-cystine modifications." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001032 name: PEFF molecule processing keyword def: "PEFF keyword describing the type of processing event being described." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term [Term] id: PEFF:0001033 name: Comment def: "PEFF keyword for the individual protein entry comment. It is discouraged to put parsable information here. This is only for free-text commentary." [PSI:PEFF] is_a: PEFF:0000003 ! PEFF file sequence entry term relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001034 name: propeptide def: "Short peptide that is cleaved off a newly synthesized protein and generally immediately degraded in the process of protein maturation, and is not a signal peptide or transit peptide." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:0001035 name: initiator methionine def: "N-terminal methionine residue of a protein that can be co-translationally cleaved." [PSI:PEFF] is_a: PEFF:0001032 ! PEFF molecule processing keyword relationship: has_regexp PEFF:1002001 ! regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: PEFF:1002001 name: regular expression for a value in a key-value pair of a PEFF description line describing one sequence position followed by one PEFF term name and one optional comment def: "([0-9]+|[A-Z*](|.+)?)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002002 name: regular expression for PEFF molecular sequence type def: "(AA|NA|DNA|cDNA|RNA|RNAi|tRNA|rRNA|siRNA|mDNA|mRNA|snoRNA|ncRNA|EST|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: PEFF:1002003 name: regular expression for PEFF sequence status def: "(Complete|Fragment|[a-z0-9A-Z]+)." [PSI:PEFF] is_a: MS:1002479 ! regular expression [Term] id: UO:0000000 name: unit namespace: unit.ontology def: "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] created_by: george gkoutos [Term] id: UO:0000001 name: length unit namespace: unit.ontology def: "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0001708 created_by: george gkoutos [Term] id: UO:0000002 name: mass unit namespace: unit.ontology def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0000125 relationship: is_unit_of PATO:0000128 created_by: george gkoutos [Term] id: UO:0000003 name: time unit namespace: unit.ontology alt_id: UO:0000149 def: "A unit which is a standard measure of the dimension in which events occur in sequence." [Wikipedia:Wikipedia] subset: unit_group_slim synonym: "time derived unit" EXACT [] is_a: UO:0000000 relationship: is_unit_of PATO:0000165 relationship: is_unit_of PATO:0001309 created_by: george gkoutos [Term] id: UO:0000005 name: temperature unit namespace: unit.ontology alt_id: UO:0000126 def: "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [Wikipedia:Wikipedia] subset: unit_group_slim synonym: "temperature derived unit" EXACT [] is_a: UO:0000000 relationship: is_unit_of PATO:0000146 created_by: george gkoutos [Term] id: UO:0000008 name: meter namespace: unit.ontology def: "A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second." [BIPM:BIPM, NIST:NIST] subset: unit_slim synonym: "m" EXACT [] synonym: "metre" EXACT [] is_a: UO:0000001 is_a: UO:0000045 created_by: george gkoutos [Term] id: UO:0000010 name: second namespace: unit.ontology def: "A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom." [BIPM:BIPM, NIST:NIST] subset: unit_slim synonym: "s" EXACT [] is_a: UO:0000003 is_a: UO:0000045 created_by: george gkoutos [Term] id: UO:0000012 name: kelvin namespace: unit.ontology def: "A thermodynamic temperature unit which is equal to the fraction 1/273.16 of the thermodynamic temperature of the triple point of water." [BIPM:BIPM, NIST:NIST] subset: unit_slim synonym: "K" EXACT [] is_a: UO:0000005 is_a: UO:0000045 created_by: george gkoutos [Term] id: UO:0000017 name: micrometer namespace: unit.ontology def: "A length unit which is equal to one millionth of a meter or 10^[-6] m." [NIST:NIST] subset: unit_slim synonym: "micrometre" EXACT [] synonym: "micron" EXACT [] synonym: "um" EXACT [] is_a: UO:0000001 created_by: george gkoutos [Term] id: UO:0000018 name: nanometer namespace: unit.ontology def: "A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m." [NIST:NIST] subset: unit_slim synonym: "nanometre" EXACT [] synonym: "nm" EXACT [] is_a: UO:0000001 created_by: george gkoutos [Term] id: UO:0000021 name: gram namespace: unit.ontology def: "A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg." [NIST:NIST] subset: unit_slim synonym: "g" EXACT [] is_a: UO:0000002 created_by: george gkoutos [Term] id: UO:0000027 name: degree Celsius namespace: unit.ontology def: "A temperature unit which is equal to one kelvin degree. However, they have their zeros at different points. The centigrade scale has its zero at 273.15 K." [NIST:NIST] subset: unit_slim synonym: "C" EXACT [] is_a: UO:0000005 created_by: george gkoutos [Term] id: UO:0000028 name: millisecond namespace: unit.ontology def: "A time unit which is equal to one thousandth of a second or 10^[-3] s." [NIST:NIST] subset: unit_slim synonym: "ms" EXACT [] is_a: UO:0000003 created_by: george gkoutos [Term] id: UO:0000031 name: minute namespace: unit.ontology def: "A time unit which is equal to 60 seconds." [Wikipedia:Wikipedia] subset: unit_slim synonym: "min" EXACT [] is_a: UO:0000003 created_by: george gkoutos [Term] id: UO:0000045 name: base unit namespace: unit.ontology def: "A unit which is one of a particular measure to which all measures of that type can be related." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 created_by: george gkoutos [Term] id: UO:0000047 name: area unit namespace: unit.ontology def: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0001709 created_by: george gkoutos [Term] id: UO:0000052 name: mass density unit namespace: unit.ontology def: "A density unit which is a standard measure of the mass of a substance in a given volume." [UOC:GVG] subset: unit_group_slim synonym: "mass per unit volume" EXACT [] is_a: UO:0000182 relationship: is_unit_of PATO:0001353 created_by: george gkoutos [Term] id: UO:0000095 name: volume unit namespace: unit.ontology def: "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0001710 created_by: george gkoutos [Term] id: UO:0000098 name: milliliter namespace: unit.ontology def: "A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter." [NIST:NIST] subset: unit_slim synonym: "millilitre" EXACT [] synonym: "ml" EXACT [] is_a: UO:0000095 created_by: george gkoutos [Term] id: UO:0000105 name: frequency unit namespace: unit.ontology def: "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0000044 created_by: george gkoutos [Term] id: UO:0000106 name: hertz namespace: unit.ontology def: "A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second." [NIST:NIST] subset: unit_slim synonym: "Hz" EXACT [] synonym: "s^1" EXACT [] is_a: UO:0000105 created_by: george gkoutos [Term] id: UO:0000109 name: pressure unit namespace: unit.ontology def: "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0001025 created_by: george gkoutos [Term] id: UO:0000110 name: pascal namespace: unit.ontology def: "A pressure unit which is equal to the pressure or stress on a surface caused by a force of 1 newton spread over a surface of 1 m^[2]." [NIST:NIST] subset: unit_slim synonym: "Pa" EXACT [] is_a: UO:0000109 created_by: george gkoutos [Term] id: UO:0000111 name: energy unit namespace: unit.ontology def: "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0001021 relationship: is_unit_of PATO:0001026 created_by: george gkoutos [Term] id: UO:0000112 name: joule namespace: unit.ontology def: "An energy unit which is equal to the energy required when a force of 1 newton moves an object 1 meter in the direction of the force." [NIST:NIST] subset: unit_slim synonym: "J" EXACT [] is_a: UO:0000111 created_by: george gkoutos [Term] id: UO:0000121 name: angle unit namespace: unit.ontology def: "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0000133 created_by: george gkoutos [Term] id: UO:0000122 name: plane angle unit namespace: unit.ontology def: "A unit which is a standard measure of the angle formed by two straight lines in the same plane." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000121 created_by: george gkoutos [Term] id: UO:0000150 name: nanosecond namespace: unit.ontology def: "A time unit which is equal to one thousandth of one millionth of a second or 10^[-9] s." [NIST:NIST] subset: unit_slim synonym: "ns" EXACT [] is_a: UO:0000003 created_by: george gkoutos [Term] id: UO:0000166 name: parts per notation unit namespace: unit.ontology def: "A dimensionless concentration notation which describes the amount of one substance in another. It is the ratio of the amount of the substance of interest to the amount of that substance plus the amount of the substance." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000186 created_by: george gkoutos [Term] id: UO:0000169 name: parts per million namespace: unit.ontology def: "A dimensionless concentration notation which denotes the amount of a given substance in a total amount of 1,000,000 regardless of the units of measure used as long as they are the same or 1 part in 10^[6]." [UOC:GVG] subset: unit_slim synonym: "10^[-6]" EXACT [] synonym: "ppm" EXACT [] is_a: UO:0000166 created_by: george gkoutos [Term] id: UO:0000175 name: gram per liter namespace: unit.ontology def: "A mass unit density which is equal to mass of an object in grams divided by the volume in liters." [UOC:GVG] subset: unit_slim synonym: "g/L" EXACT [] synonym: "gram per litre" EXACT [] is_a: UO:0000052 created_by: george gkoutos [Term] id: UO:0000182 name: density unit namespace: unit.ontology def: "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0001019 created_by: george gkoutos [Term] id: UO:0000185 name: degree namespace: unit.ontology def: "A plane angle unit which is equal to 1/360 of a full rotation or 1.7453310^[-2] rad." [Wikipedia:Wikipedia] subset: unit_slim is_a: UO:0000122 created_by: george gkoutos [Term] id: UO:0000186 name: dimensionless unit namespace: unit.ontology def: "A unit which is a standard measure of physical quantity consisting of only a numerical number without any units." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 created_by: george gkoutos [Term] id: UO:0000187 name: percent namespace: unit.ontology def: "A dimensionless ratio unit which denotes numbers as fractions of 100." [Wikipedia:Wikipedia] subset: unit_group_slim synonym: "%" EXACT [] is_a: UO:0000190 created_by: george gkoutos [Term] id: UO:0000189 name: count unit namespace: unit.ontology def: "A dimensionless unit which denotes a simple count of things." [MGED:MGED] subset: unit_group_slim synonym: "count" EXACT [] is_a: UO:0000186 created_by: george gkoutos [Term] id: UO:0000190 name: ratio namespace: unit.ontology def: "A dimensionless unit which denotes an amount or magnitude of one quantity relative to another." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000186 created_by: george gkoutos [Term] id: UO:0000191 name: fraction namespace: unit.ontology def: "A dimensionless ratio unit which relates the part (the numerator) to the whole (the denominator)." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000190 created_by: george gkoutos [Term] id: UO:0000217 name: electric potential difference unit namespace: unit.ontology def: "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 relationship: is_unit_of PATO:0001464 created_by: george gkoutos [Term] id: UO:0000218 name: volt namespace: unit.ontology def: "An electric potential difference unit which is equal to the work per unit charge. One volt is the potential difference required to move one coulomb of charge between two points in a circuit while using one joule of energy." [Wikipedia:Wikipedia] subset: unit_slim synonym: "V" EXACT [] is_a: UO:0000217 created_by: george gkoutos [Term] id: UO:0000221 name: dalton namespace: unit.ontology def: "An independently to the base SI units defined mass unit which is equal to one twelfth of the mass of an unbound atom of the carbon-12 nuclide, at rest and in its ground state." [Wikipedia:Wikipedia] subset: unit_slim synonym: "amu" EXACT [] synonym: "Da" EXACT [] synonym: "u" EXACT [] synonym: "unified atomic mass unit" EXACT [] is_a: UO:0000002 created_by: george gkoutos [Term] id: UO:0000222 name: kilodalton namespace: unit.ontology def: "A mass unit which is equal to one thousand daltons." [Wikipedia:Wikipedia] subset: unit_slim synonym: "kDa" EXACT [] is_a: UO:0000002 created_by: george gkoutos [Term] id: UO:0000227 name: magnetic flux density unit namespace: unit.ontology def: "A unit which is a standard measure of the strength of a magnetic field." [allnet:allnet] subset: unit_group_slim synonym: "B" EXACT [] is_a: UO:0000000 created_by: george gkoutos [Term] id: UO:0000228 name: tesla namespace: unit.ontology def: "A magnetic flux density unit which is equal to one weber per square meter." [WordNet:WordNet] subset: unit_slim synonym: "T" EXACT [] synonym: "Wb/m2" EXACT [] is_a: UO:0000227 created_by: george gkoutos [Term] id: UO:0000266 name: electronvolt namespace: unit.ontology def: "A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J." [Wikipedia:Wikipedia] subset: unit_slim synonym: "electron volt" EXACT [] synonym: "eV" EXACT [] is_a: UO:0000111 created_by: george gkoutos [Term] id: UO:0000267 name: electric field strength unit namespace: unit.ontology def: "The electric field strength is a unit which is a measure of the potential difference between two points some distance apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] subset: unit_group_slim synonym: "E-field strength " EXACT [] is_a: UO:0000000 created_by: george gkoutos creation_date: 2009-03-03T12:23:16Z [Term] id: UO:0000268 name: volt per meter namespace: unit.ontology def: "The volt per meter is a unit of electric field strength equal to the a potential difference of 1 volt existing between two points that are 1 meter apart." [Wikipedia:http\://en.wikipedia.org/wiki/Electric_field] subset: unit_slim synonym: "V/m" EXACT [] synonym: "volt per metre" EXACT [] is_a: UO:0000267 created_by: george gkoutos creation_date: 2009-03-03T12:28:17Z [Term] id: UO:0000269 name: absorbance unit namespace: unit.ontology def: "A dimensionless logarithmic unit assigned to a measure of absorbance of light through a partially absorbing substance, defined as -log10(I/I_0) where I = transmitted light and I_0 = incident light." [Wikipedia:http\://en.wikipedia.org/wiki/Absorbance] subset: unit_slim synonym: "AU" EXACT [] is_a: UO:0000186 created_by: george gkoutos creation_date: 2009-07-14T12:33:48Z [Term] id: UO:0000270 name: volumetric flow rate unit namespace: unit.ontology def: "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 created_by: george gkoutos [Term] id: UO:0000271 name: microliters per minute namespace: unit.ontology def: "A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute." [UOC:GVG] subset: unit_slim synonym: "microlitres per minute" EXACT [] synonym: "uL/min" EXACT [] is_a: UO:0000270 relationship: is_unit_of PATO:0001574 created_by: george gkoutos [Term] id: UO:0000324 name: square angstrom namespace: unit.ontology def: "An area unit which is equal to an area enclosed by a square with sides each 1 angstrom long." [UOC:GVG] synonym: "A^[2]" RELATED [] is_a: UO:0000047 created_by: gkoutos creation_date: 2013-06-27T05:06:40Z