ms.owl
type: Ontology
version IRI: ms.owl
namespace-id-rule: * MS:$sequence(7,0,9999999)$
namespace-id-rule: * PEFF:$sequence(7,0,9999999)$
date: 11:02:2026 12:00
default-namespace: MS
has_obo_format_version: 1.2
saved-by: Jonathan Hunter
comment: For any queries contact psidev-ms-vocab@lists.sourceforge.net
comment: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
comment: 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.
comment: URL: http://purl.obolibrary.org/obo/ms/psi-ms.obo
comment: 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
comment: coverage of namespace-id: MS:$sequence(7,4000000,4999999)$: Mass spectrometry quality control metrics
comment: coverage: Mass spectrometer output files and spectra interpretation
comment: creator: Andreas Bertsch <bertsch <-at-> informatik.uni-tuebingen.de>
comment: creator: Chris Bielow <chris.bielow <-at-> fu-berlin.de>
comment: creator: David Cox <david.cox <-at-> sciex.com>
comment: creator: Eric Deutsch <edeutsch <-at-> systemsbiology.org>
comment: creator: Fredrik Levander <fredrik.levander <-at-> immun.lth.se>
comment: creator: Gerhard Mayer <mayerg97 <-at-> rub.de>
comment: creator: Jeroen Van Goey <j.vangoey <-at-> instadeep.com>
comment: creator: Jonathan Hunter <jhunter <-at-> ebi.ac.uk>
comment: creator: Joshua Klein <jaklein <-at-> bu.edu>
comment: creator: Julian Uszkoreit <julian.uszkoreit <-at-> ruhr-uni-bochum.de>
comment: creator: Marius Kallhardt <Marius.Kallhardt <-at-> bdal.de>
comment: creator: Mathias Walzer <walzer <-at-> ebi.ac.uk>
comment: creator: Matt Chambers <matt.chambers <-at-> vanderbilt.edu>
comment: creator: Nils Hoffmann < nils.hoffmann <-at-> cebitec.uni-bielefeld.de>
comment: creator: Nithu Sara John <nithu <-at-> ebi.ac.uk>
comment: creator: Pierre-Alain Binz <pierre-alain.binz <-at-> chuv.ch>
comment: creator: Samuel Wein <sam <-at-> openms.de>
comment: creator: Wout Bittremieux <wout.bittremieux <-at-> uantwerpen.be>
comment: creator: Yasset Perez-Riverol <yperez <-at-> ebi.ac.uk>
comment: namespace: MS
comment: namespace: PEFF
comment: publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group

definition
type: AnnotationProperty

term replaced by
type: AnnotationProperty

namespace-id-rule
type: AnnotationProperty

created by
type: AnnotationProperty

creation date
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

id
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

part_of
type: ObjectProperty
type: TransitiveProperty
database_cross_reference: BFO:0000050
has_obo_namespace: MS
id: part_of
shorthand: part_of

has_column
type: ObjectProperty
has_obo_namespace: MS
id: has_column

has_domain
type: ObjectProperty
has_obo_namespace: MS
id: has_domain

has_metric_category
type: ObjectProperty
has_obo_namespace: MS
id: has_metric_category

has_optional_column
type: ObjectProperty
has_obo_namespace: MS
id: has_optional_column

has_order
type: ObjectProperty
has_obo_namespace: MS
id: has_order

has regexp
type: ObjectProperty
has_obo_namespace: MS
id: has_regexp

has structured representation in format
type: ObjectProperty
definition: 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.
has_obo_namespace: MS
id: has_structured_representation_in_format

has_units
type: ObjectProperty
has_obo_namespace: MS
id: has_units

has_value_concept
type: ObjectProperty
has_obo_namespace: MS
id: has_value_concept

has value type
type: ObjectProperty
definition: 'Entity A' has value type 'Entity B', such as xsd:float.
has_obo_namespace: MS
id: has_value_type

Proteomics Standards Initiative Mass Spectrometry Vocabularies
type: Class
definition: Proteomics Standards Initiative Mass Spectrometry Vocabularies.
has_obo_namespace: MS
id: MS:0000000

Axiom
annotated source: Proteomics Standards Initiative Mass Spectrometry Vocabularies
annotated property: definition
annotated target: Proteomics Standards Initiative Mass Spectrometry Vocabularies.
database_cross_reference: PSI:MS

sample number
type: Class
subclass of: sample attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A reference number relevant to the sample under study.
has_obo_namespace: MS
id: MS:1000001

Axiom
annotated source: sample number
annotated property: definition
annotated target: A reference number relevant to the sample under study.
database_cross_reference: PSI:MS

sample name
type: Class
subclass of: sample attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A reference string relevant to the sample under study.
has_obo_namespace: MS
id: MS:1000002

Axiom
annotated source: sample name
annotated property: definition
annotated target: A reference string relevant to the sample under study.
database_cross_reference: PSI:MS

sample state
type: Class
subclass of: sample attribute
definition: The chemical phase of a pure sample, or the state of a mixed sample.
has_obo_namespace: MS
id: MS:1000003

Axiom
annotated source: sample state
annotated property: definition
annotated target: The chemical phase of a pure sample, or the state of a mixed sample.
database_cross_reference: PSI:MS

sample mass
type: Class
subclass of: sample attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000021
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Total mass of sample used.
has_obo_namespace: MS
id: MS:1000004

Axiom
annotated source: sample mass
annotated property: definition
annotated target: Total mass of sample used.
database_cross_reference: PSI:MS

sample volume
type: Class
subclass of: sample attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000098
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Total volume of solution used.
has_obo_namespace: MS
id: MS:1000005

Axiom
annotated source: sample volume
annotated property: definition
annotated target: Total volume of solution used.
database_cross_reference: PSI:MS

sample concentration
type: Class
subclass of: sample attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000175
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
has_obo_namespace: MS
id: MS:1000006

Axiom
annotated source: sample concentration
annotated property: definition
annotated target: Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
database_cross_reference: PSI:MS

inlet type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source
definition: The nature of the sample inlet.
has_obo_namespace: MS
id: MS:1000007

Axiom
annotated source: inlet type
annotated property: definition
annotated target: The nature of the sample inlet.
database_cross_reference: PSI:MS

ionization type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source
definition: The method by which gas phase ions are generated from the sample.
has_obo_namespace: MS
id: MS:1000008

Axiom
annotated source: ionization type
annotated property: definition
annotated target: The method by which gas phase ions are generated from the sample.
database_cross_reference: PSI:MS

ionization mode
type: Class
definition: OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer.
has_obo_namespace: MS
id: MS:1000009
comment: This term was made obsolete because it was replaced by scan polarity (MS:1000465).
deprecated: true

Axiom
annotated source: ionization mode
annotated property: definition
annotated target: OBSOLETE Whether positive or negative ions are selected for analysis by the spectrometer.
database_cross_reference: PSI:MS

analyzer type
type: Class
definition: OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted.
has_obo_namespace: MS
id: MS:1000010
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: analyzer type
annotated property: definition
annotated target: OBSOLETE The common name of the particular analyzer stage being described. Synonym of mass analyzer, should be obsoleted.
database_cross_reference: PSI:MS

mass resolution
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height.
has_obo_namespace: MS
id: MS:1000011

Axiom
annotated source: mass resolution
annotated property: definition
annotated target: Smallest mass difference between two equal magnitude peaks so that the valley between them is a specified fraction of the peak height.
database_cross_reference: PSI:MS

resolution measurement method
type: Class
subclass of: measurement method
definition: Which of the available standard measures is used to define whether two peaks are separate.
has_obo_namespace: MS
id: MS:1000012

Axiom
annotated source: resolution measurement method
annotated property: definition
annotated target: Which of the available standard measures is used to define whether two peaks are separate.
database_cross_reference: PSI:MS

resolution type
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000013
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: resolution type
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

accuracy
type: Class
subclass of: mass analyzer attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has_units
  some values from: UO_0000169
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Accuracy is the degree of conformity of a measured mass to its actual value.
has_obo_namespace: MS
id: MS:1000014

Axiom
annotated source: accuracy
annotated property: definition
annotated target: Accuracy is the degree of conformity of a measured mass to its actual value.
database_cross_reference: PSI:MS

scan rate
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: Th/s
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Rate in Th/sec for scanning analyzers.
has_obo_namespace: MS
id: MS:1000015

Axiom
annotated source: scan rate
annotated property: definition
annotated target: Rate in Th/sec for scanning analyzers.
database_cross_reference: PSI:MS

scan start time
type: Class
subclass of: scan attribute
subclass of: MS_1002345
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The time that an analyzer started a scan, relative to the start of the MS run.
has_obo_namespace: MS
id: MS:1000016

Axiom
annotated source: scan start time
annotated property: definition
annotated target: The time that an analyzer started a scan, relative to the start of the MS run.
database_cross_reference: PSI:MS

Scan Function
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000017
comment: OBSOLETE This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: Scan Function
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

scan direction
type: Class
subclass of: Restriction
  on property: part_of
  some values from: scan
definition: Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low).
has_obo_namespace: MS
id: MS:1000018

Axiom
annotated source: scan direction
annotated property: definition
annotated target: Direction in terms of m/z of the scan for scanning analyzers (low to high, or high to low).
database_cross_reference: PSI:MS

scan law
type: Class
subclass of: Restriction
  on property: part_of
  some values from: scan
definition: 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.
has_obo_namespace: MS
id: MS:1000019

Axiom
annotated source: scan law
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

scanning method
type: Class
definition: Describes the acquisition data type produced by a tandem mass spectrometry experiment.
has_obo_namespace: MS
has_related_synonym: Tandem Scanning Method
id: MS:1000020
comment: OBSOLETE This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: scanning method
annotated property: definition
annotated target: Describes the acquisition data type produced by a tandem mass spectrometry experiment.
database_cross_reference: PSI:MS

reflectron state
type: Class
subclass of: mass analyzer attribute
definition: Status of the reflectron, turned on or off.
has_obo_namespace: MS
id: MS:1000021

Axiom
annotated source: reflectron state
annotated property: definition
annotated target: Status of the reflectron, turned on or off.
database_cross_reference: PSI:MS

TOF Total Path Length
type: Class
subclass of: mass analyzer attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000008
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The length of the field free drift space in a time of flight mass spectrometer.
has_obo_namespace: MS
id: MS:1000022

Axiom
annotated source: TOF Total Path Length
annotated property: definition
annotated target: The length of the field free drift space in a time of flight mass spectrometer.
database_cross_reference: PSI:MS

isolation width
type: Class
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion.
has_obo_namespace: MS
id: MS:1000023
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: isolation width
annotated property: definition
annotated target: OBSOLETE The total width (i.e. not half for plus-or-minus) of the gate applied around a selected precursor ion.
database_cross_reference: PSI:MS

final MS exponent
type: Class
subclass of: mass analyzer attribute
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Final MS level achieved when performing PFF with the ion trap (e.g. MS E10).
has_obo_namespace: MS
id: MS:1000024

Axiom
annotated source: final MS exponent
annotated property: definition
annotated target: Final MS level achieved when performing PFF with the ion trap (e.g. MS E10).
database_cross_reference: PSI:MS

magnetic field strength
type: Class
subclass of: mass analyzer attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000228
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_exact_synonym: B
has_obo_namespace: MS
has_related_synonym: Magnetic Field
id: MS:1000025

Axiom
annotated source: magnetic field strength
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

detector type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: detector
definition: Type of detector used in the mass spectrometer.
has_obo_namespace: MS
id: MS:1000026

Axiom
annotated source: detector type
annotated property: definition
annotated target: Type of detector used in the mass spectrometer.
database_cross_reference: PSI:MS

detector acquisition mode
type: Class
subclass of: Restriction
  on property: part_of
  some values from: detector
definition: Method by which detector signal is acquired by the data system.
has_obo_namespace: MS
id: MS:1000027

Axiom
annotated source: detector acquisition mode
annotated property: definition
annotated target: Method by which detector signal is acquired by the data system.
database_cross_reference: PSI:MS

detector resolution
type: Class
subclass of: detector attribute
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000028

Axiom
annotated source: detector resolution
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

sampling frequency
type: Class
subclass of: detector attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000106
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The rate of signal sampling (measurement) with respect to time.
has_narrow_synonym: ADC Sampling Frequency
has_obo_namespace: MS
id: MS:1000029

Axiom
annotated source: sampling frequency
annotated property: definition
annotated target: The rate of signal sampling (measurement) with respect to time.
database_cross_reference: PSI:MS

vendor
type: Class
definition: OBSOLETE Name of instrument vendor.
has_obo_namespace: MS
id: MS:1000030
comment: This term was made obsolete because it was replaced by instrument model (MS:1000031).
deprecated: true

Axiom
annotated source: vendor
annotated property: definition
annotated target: OBSOLETE Name of instrument vendor.
database_cross_reference: PSI:MS

instrument model
type: Class
subclass of: Restriction
  on property: part_of
  some values from: instrument
definition: Instrument model name not including the vendor's name.
has_obo_namespace: MS
id: MS:1000031

Axiom
annotated source: instrument model
annotated property: definition
annotated target: Instrument model name not including the vendor's name.
database_cross_reference: PSI:MS

customization
type: Class
subclass of: instrument attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Free text description of a single customization made to the instrument; for several modifications, use several entries.
has_obo_namespace: MS
id: MS:1000032

Axiom
annotated source: customization
annotated property: definition
annotated target: Free text description of a single customization made to the instrument; for several modifications, use several entries.
database_cross_reference: PSI:MS

deisotoping
type: Class
subclass of: data processing action
definition: 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.
has_obo_namespace: MS
id: MS:1000033

Axiom
annotated source: deisotoping
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge deconvolution
type: Class
subclass of: data processing action
definition: The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions.
has_obo_namespace: MS
id: MS:1000034

Axiom
annotated source: charge deconvolution
annotated property: definition
annotated target: The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions.
database_cross_reference: PSI:MS

peak picking
type: Class
subclass of: data processing action
definition: Spectral peak processing conducted on the acquired data to convert profile data to centroided data.
has_obo_namespace: MS
id: MS:1000035

Axiom
annotated source: peak picking
annotated property: definition
annotated target: Spectral peak processing conducted on the acquired data to convert profile data to centroided data.
database_cross_reference: PSI:MS

scan mode
type: Class
definition: OBSOLETE.
has_obo_namespace: MS
id: MS:1000036
comment: This term was made obsolete because .
deprecated: true

Axiom
annotated source: scan mode
annotated property: definition
annotated target: OBSOLETE.
database_cross_reference: PSI:MS

polarity
type: Class
definition: OBSOLETE Terms to describe the polarity setting of the instrument.
has_obo_namespace: MS
id: MS:1000037
comment: This term was made obsolete because it was redundant with the Pato Ontology term polarity (UO:0002186).
deprecated: true

Axiom
annotated source: polarity
annotated property: definition
annotated target: OBSOLETE Terms to describe the polarity setting of the instrument.
database_cross_reference: PSI:MS

minute
type: Class
definition: OBSOLETE Acquisition time in minutes.
has_obo_namespace: MS
id: MS:1000038
comment: This term was made obsolete because it was redundant with Unit Ontology minute (UO:0000031).
deprecated: true

Axiom
annotated source: minute
annotated property: definition
annotated target: OBSOLETE Acquisition time in minutes.
database_cross_reference: PSI:MS

second
type: Class
definition: OBSOLETE Acquisition time in seconds.
has_obo_namespace: MS
id: MS:1000039
comment: This term was made obsolete because it was redundant with Unit Ontology second (UO:0000010).
deprecated: true

Axiom
annotated source: second
annotated property: definition
annotated target: OBSOLETE Acquisition time in seconds.
database_cross_reference: PSI:MS

m/z
type: Class
subclass of: UO_0000000
definition: 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.
has_exact_synonym: Th
has_exact_synonym: mass-to-charge ratio
has_exact_synonym: thomson
has_obo_namespace: MS
id: MS:1000040

Axiom
annotated source: m/z
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge state
type: Class
subclass of: ion selection attribute
subclass of: ion property
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Number of net charges, positive or negative, on an ion.
has_exact_synonym: z
has_obo_namespace: MS
id: MS:1000041

Axiom
annotated source: charge state
annotated property: definition
annotated target: Number of net charges, positive or negative, on an ion.
database_cross_reference: PSI:MS

peak intensity
type: Class
subclass of: ion selection attribute
subclass of: Restriction
  on property: part_of
  some values from: peak
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
subclass of: Restriction
  on property: has_units
  some values from: UO_0000269
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Intensity of ions as measured by the height or area of a peak in a mass spectrum.
has_obo_namespace: MS
id: MS:1000042

Axiom
annotated source: peak intensity
annotated property: definition
annotated target: Intensity of ions as measured by the height or area of a peak in a mass spectrum.
database_cross_reference: PSI:MS

intensity unit
type: Class
subclass of: UO_0000000
definition: Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors.
has_obo_namespace: MS
id: MS:1000043

Axiom
annotated source: intensity unit
annotated property: definition
annotated target: Intensity units are commonly arbitrary. Detected in counts per second (cps) when using counting detectors, but measured in volts when using analog detectors.
database_cross_reference: PSI:MS

dissociation method
type: Class
subclass of: Restriction
  on property: part_of
  some values from: precursor activation
definition: Fragmentation method used for dissociation or fragmentation.
has_obo_namespace: MS
has_related_synonym: Activation Method
id: MS:1000044

Axiom
annotated source: dissociation method
annotated property: definition
annotated target: Fragmentation method used for dissociation or fragmentation.
database_cross_reference: PSI:MS

collision energy
type: Class
subclass of: precursor activation attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000266
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion.
has_obo_namespace: MS
id: MS:1000045

Axiom
annotated source: collision energy
annotated property: definition
annotated target: Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion.
database_cross_reference: PSI:MS

energy unit
type: Class
subclass of: UO_0000000
definition: OBSOLETE Energy units are represented in either eV or Joules.
has_obo_namespace: MS
id: MS:1000046
comment: This term was made obsolete because it was redundant with the Unit Ontology term energy unit (UO:0000111).
deprecated: true

Axiom
annotated source: energy unit
annotated property: definition
annotated target: OBSOLETE Energy units are represented in either eV or Joules.
database_cross_reference: PSI:MS

emulsion
type: Class
subclass of: sample state
definition: State if the sample is in emulsion form.
has_obo_namespace: MS
id: MS:1000047

Axiom
annotated source: emulsion
annotated property: definition
annotated target: State if the sample is in emulsion form.
database_cross_reference: PSI:MS

gaseous sample state
type: Class
subclass of: sample state
definition: State if the sample is in gaseous form.
has_obo_namespace: MS
id: MS:1000048

Axiom
annotated source: gaseous sample state
annotated property: definition
annotated target: State if the sample is in gaseous form.
database_cross_reference: PSI:MS

liquid sample state
type: Class
subclass of: sample state
definition: State if the sample is in liquid form.
has_obo_namespace: MS
id: MS:1000049

Axiom
annotated source: liquid sample state
annotated property: definition
annotated target: State if the sample is in liquid form.
database_cross_reference: PSI:MS

solid sample state
type: Class
subclass of: sample state
definition: State if the sample is in solid form.
has_obo_namespace: MS
id: MS:1000050

Axiom
annotated source: solid sample state
annotated property: definition
annotated target: State if the sample is in solid form.
database_cross_reference: PSI:MS

solution
type: Class
subclass of: sample state
definition: State if the sample is in solution form.
has_obo_namespace: MS
id: MS:1000051

Axiom
annotated source: solution
annotated property: definition
annotated target: State if the sample is in solution form.
database_cross_reference: PSI:MS

suspension
type: Class
subclass of: sample state
definition: State if the sample is in suspension form.
has_obo_namespace: MS
id: MS:1000052

Axiom
annotated source: suspension
annotated property: definition
annotated target: State if the sample is in suspension form.
database_cross_reference: PSI:MS

sample batch
type: Class
subclass of: sample attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Sample batch lot identifier.
has_obo_namespace: MS
id: MS:1000053

Axiom
annotated source: sample batch
annotated property: definition
annotated target: Sample batch lot identifier.
database_cross_reference: PSI:MS

chromatography
type: Class
definition: OBSOLETE Chromatographic conditions used to obtain the sample.
has_obo_namespace: MS
id: MS:1000054
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: chromatography
annotated property: definition
annotated target: OBSOLETE Chromatographic conditions used to obtain the sample.
database_cross_reference: PSI:MS

continuous flow fast atom bombardment
type: Class
subclass of: inlet type
definition: Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix.
has_exact_synonym: CF-FAB
has_obo_namespace: MS
id: MS:1000055

Axiom
annotated source: continuous flow fast atom bombardment
annotated property: definition
annotated target: Fast atom bombardment ionization in which the analyte in solution is entrained in a flowing liquid matrix.
database_cross_reference: PSI:MS

direct inlet
type: Class
subclass of: inlet type
definition: The sample is directly inserted into the ion source, usually on the end of a heatable probe.
has_obo_namespace: MS
id: MS:1000056

Axiom
annotated source: direct inlet
annotated property: definition
annotated target: The sample is directly inserted into the ion source, usually on the end of a heatable probe.
database_cross_reference: PSI:MS

electrospray inlet
type: Class
subclass of: inlet type
definition: Inlet used for introducing the liquid sample into an electrospray ionization source.
has_obo_namespace: MS
id: MS:1000057

Axiom
annotated source: electrospray inlet
annotated property: definition
annotated target: Inlet used for introducing the liquid sample into an electrospray ionization source.
database_cross_reference: PSI:MS

flow injection analysis
type: Class
subclass of: inlet type
definition: A sample introduction method in which a discrete sample aliquot is injected into a continuous carrier solvent stream and transported to the ionization source without separation, producing a transient analytical signal.
has_exact_synonym: FIA
has_obo_namespace: MS
id: MS:1000058

Axiom
annotated source: flow injection analysis
annotated property: definition
annotated target: A sample introduction method in which a discrete sample aliquot is injected into a continuous carrier solvent stream and transported to the ionization source without separation, producing a transient analytical signal.
database_cross_reference: PSI:MS

inductively coupled plasma
type: Class
subclass of: inlet type
definition: A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction.
has_obo_namespace: MS
id: MS:1000059

Axiom
annotated source: inductively coupled plasma
annotated property: definition
annotated target: A gas discharge ion source in which the energy to the plasma is supplied by electromagnetic induction.
database_cross_reference: PSI:MS

infusion
type: Class
subclass of: inlet type
definition: A sample introduction method in which a sample solution is continuously delivered to the ionization source at a constant flow rate without separation.
has_exact_synonym: direct infusion
has_obo_namespace: MS
id: MS:1000060

Axiom
annotated source: infusion
annotated property: definition
annotated target: A sample introduction method in which a sample solution is continuously delivered to the ionization source at a constant flow rate without separation.
database_cross_reference: PSI:MS

jet separator
type: Class
subclass of: inlet type
definition: A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity.
has_obo_namespace: MS
id: MS:1000061

Axiom
annotated source: jet separator
annotated property: definition
annotated target: A device that separates carrier gas from gaseous analyte molecules on the basis of diffusivity.
database_cross_reference: PSI:MS

membrane separator
type: Class
subclass of: inlet type
definition: A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane.
has_obo_namespace: MS
id: MS:1000062

Axiom
annotated source: membrane separator
annotated property: definition
annotated target: A device to separate carrier molecules from analyte molecules on the basis of ease of diffusion across a semipermeable membrane.
database_cross_reference: PSI:MS

moving belt
type: Class
subclass of: inlet type
definition: Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules.
has_obo_namespace: MS
id: MS:1000063

Axiom
annotated source: moving belt
annotated property: definition
annotated target: Continuous moving surface in the form of a belt which passes through an ion source carrying analyte molecules.
database_cross_reference: PSI:MS

moving wire
type: Class
subclass of: inlet type
definition: Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules.
has_obo_namespace: MS
id: MS:1000064

Axiom
annotated source: moving wire
annotated property: definition
annotated target: Continuous moving surface in the form of a wire which passes through an ion source carrying analyte molecules.
database_cross_reference: PSI:MS

open split
type: Class
subclass of: inlet type
definition: A division of flowing stream of liquid into two streams.
has_obo_namespace: MS
id: MS:1000065

Axiom
annotated source: open split
annotated property: definition
annotated target: A division of flowing stream of liquid into two streams.
database_cross_reference: PSI:MS

particle beam
type: Class
subclass of: inlet type
definition: Method for generating ions from a solution of an analyte.
has_obo_namespace: MS
id: MS:1000066

Axiom
annotated source: particle beam
annotated property: definition
annotated target: Method for generating ions from a solution of an analyte.
database_cross_reference: PSI:MS

reservoir
type: Class
subclass of: inlet type
definition: A sample inlet method involving a reservoir.
has_obo_namespace: MS
id: MS:1000067

Axiom
annotated source: reservoir
annotated property: definition
annotated target: A sample inlet method involving a reservoir.
database_cross_reference: PSI:MS

septum
type: Class
subclass of: inlet type
definition: A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber.
has_obo_namespace: MS
id: MS:1000068

Axiom
annotated source: septum
annotated property: definition
annotated target: A disc composed of a flexible material that seals the entrance to the reservoir. Can also be entrance to the vacuum chamber.
database_cross_reference: PSI:MS

thermospray inlet
type: Class
subclass of: inlet type
definition: A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample.
has_obo_namespace: MS
id: MS:1000069

Axiom
annotated source: thermospray inlet
annotated property: definition
annotated target: A method for generating gas phase ions from a solution of an analyte by rapid heating of the sample.
database_cross_reference: PSI:MS

atmospheric pressure chemical ionization
type: Class
subclass of: atmospheric pressure ionization
definition: Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization.
has_exact_synonym: APCI
has_obo_namespace: MS
id: MS:1000070

Axiom
annotated source: atmospheric pressure chemical ionization
annotated property: definition
annotated target: Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization.
database_cross_reference: PSI:MS

chemical ionization
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: CI
has_obo_namespace: MS
id: MS:1000071

Axiom
annotated source: chemical ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Electronic Ionization
type: Class
definition: 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.
has_exact_synonym: EI
has_obo_namespace: MS
id: MS:1000072
comment: This term was made obsolete because it was replaced by electron ionization (MS:1000389).
deprecated: true

Axiom
annotated source: Electronic Ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

electrospray ionization
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: ESI
has_obo_namespace: MS
id: MS:1000073

Axiom
annotated source: electrospray ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

fast atom bombardment ionization
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: FAB
has_obo_namespace: MS
id: MS:1000074

Axiom
annotated source: fast atom bombardment ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

matrix-assisted laser desorption ionization
type: Class
subclass of: desorption ionization
definition: 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.
has_exact_synonym: MALDI
has_obo_namespace: MS
id: MS:1000075

Axiom
annotated source: matrix-assisted laser desorption ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

negative polarity acquisition
type: Class
subclass of: MS_1003776
definition: Polarities of the scans of a run are all negative.
has_obo_namespace: MS
id: MS:1000076

Axiom
annotated source: negative polarity acquisition
annotated property: definition
annotated target: Polarities of the scans of a run are all negative.
database_cross_reference: PSI:MS

positive polarity acquisition
type: Class
subclass of: MS_1003776
definition: Polarities of the scans of a run are all positive.
has_obo_namespace: MS
id: MS:1000077

Axiom
annotated source: positive polarity acquisition
annotated property: definition
annotated target: Polarities of the scans of a run are all positive.
database_cross_reference: PSI:MS

axial ejection linear ion trap
type: Class
subclass of: linear ion trap
definition: A linear ion trap mass analyzer where ions are ejected along the axis of the analyzer.
has_obo_namespace: MS
id: MS:1000078

Axiom
annotated source: axial ejection linear ion trap
annotated property: definition
annotated target: A linear ion trap mass analyzer where ions are ejected along the axis of the analyzer.
database_cross_reference: PSI:MS

fourier transform ion cyclotron resonance
type: Class
subclass of: mass analyzer type
subclass of: MS_1003761
definition: A device 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.
has_exact_synonym: FT_ICR
has_obo_namespace: MS
id: MS:1000079

Axiom
annotated source: fourier transform ion cyclotron resonance
annotated property: definition
annotated target: A device 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.
database_cross_reference: PSI:MS

magnetic sector
type: Class
subclass of: mass analyzer type
subclass of: MS_1003761
definition: 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.
has_obo_namespace: MS
id: MS:1000080

Axiom
annotated source: magnetic sector
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

quadrupole
type: Class
subclass of: mass analyzer type
subclass of: MS_1003761
definition: A device 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.
has_obo_namespace: MS
id: MS:1000081

Axiom
annotated source: quadrupole
annotated property: definition
annotated target: A device 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.
database_cross_reference: PSI:MS

quadrupole ion trap
type: Class
subclass of: ion trap
definition: 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.
has_exact_synonym: Paul Ion trap
has_exact_synonym: QIT
has_exact_synonym: Quistor
has_obo_namespace: MS
id: MS:1000082

Axiom
annotated source: quadrupole ion trap
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

radial ejection linear ion trap
type: Class
subclass of: linear ion trap
definition: A linear ion trap mass analyzer where ions are ejected along the radius of the analyzer.
has_obo_namespace: MS
id: MS:1000083

Axiom
annotated source: radial ejection linear ion trap
annotated property: definition
annotated target: A linear ion trap mass analyzer where ions are ejected along the radius of the analyzer.
database_cross_reference: PSI:MS

time-of-flight
type: Class
subclass of: mass analyzer type
subclass of: MS_1003761
definition: Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy.
has_exact_synonym: TOF
has_obo_namespace: MS
id: MS:1000084

Axiom
annotated source: time-of-flight
annotated property: definition
annotated target: Instrument that separates ions by m/z in a field-free region after acceleration to a fixed acceleration energy.
database_cross_reference: PSI:MS

baseline
type: Class
subclass of: resolution measurement method
definition: An attribute of resolution when recording the detector response in absence of the analyte.
has_obo_namespace: MS
id: MS:1000085

Axiom
annotated source: baseline
annotated property: definition
annotated target: An attribute of resolution when recording the detector response in absence of the analyte.
database_cross_reference: PSI:MS

full width at half-maximum
type: Class
subclass of: resolution measurement method
definition: A measure of resolution represented as width of the peak at half peak height.
has_exact_synonym: FWHM
has_obo_namespace: MS
id: MS:1000086

Axiom
annotated source: full width at half-maximum
annotated property: definition
annotated target: A measure of resolution represented as width of the peak at half peak height.
database_cross_reference: PSI:MS

ten percent valley
type: Class
subclass of: resolution measurement method
definition: An attribute of resolution when the ratio between adjacent signals is 10% of the signal height.
has_obo_namespace: MS
id: MS:1000087

Axiom
annotated source: ten percent valley
annotated property: definition
annotated target: An attribute of resolution when the ratio between adjacent signals is 10% of the signal height.
database_cross_reference: PSI:MS

constant
type: Class
definition: OBSOLETE When resolution is constant with respect to m/z.
has_obo_namespace: MS
id: MS:1000088
comment: This child of the former purgatory term resolution type was made obsolete.
deprecated: true

Axiom
annotated source: constant
annotated property: definition
annotated target: OBSOLETE When resolution is constant with respect to m/z.
database_cross_reference: PSI:MS

proportional
type: Class
definition: OBSOLETE When resolution is proportional with respect to m/z.
has_obo_namespace: MS
id: MS:1000089
comment: This child of the former purgatory term resolution type was made obsolete.
deprecated: true

Axiom
annotated source: proportional
annotated property: definition
annotated target: OBSOLETE When resolution is proportional with respect to m/z.
database_cross_reference: PSI:MS

mass scan
type: Class
definition: OBSOLETE A variation of instrument where a selected mass is scanned.
has_obo_namespace: MS
id: MS:1000090
comment: This child of the former purgatory term Scan Function was made obsolete.
deprecated: true

Axiom
annotated source: mass scan
annotated property: definition
annotated target: OBSOLETE A variation of instrument where a selected mass is scanned.
database_cross_reference: PSI:MS

selected ion detection
type: Class
definition: OBSOLETE Please see Single Ion Monitoring.
has_obo_namespace: MS
id: MS:1000091
comment: This child of the former purgatory term Scan Function was made obsolete.
deprecated: true

Axiom
annotated source: selected ion detection
annotated property: definition
annotated target: OBSOLETE Please see Single Ion Monitoring.
database_cross_reference: PSI:MS

decreasing m/z scan
type: Class
subclass of: scan direction
definition: High to low direction in terms of m/z of the scan for scanning analyzers.
has_obo_namespace: MS
id: MS:1000092

Axiom
annotated source: decreasing m/z scan
annotated property: definition
annotated target: High to low direction in terms of m/z of the scan for scanning analyzers.
database_cross_reference: PSI:MS

increasing m/z scan
type: Class
subclass of: scan direction
definition: Low to high direction in terms of m/z of the scan for scanning analyzers.
has_obo_namespace: MS
id: MS:1000093

Axiom
annotated source: increasing m/z scan
annotated property: definition
annotated target: Low to high direction in terms of m/z of the scan for scanning analyzers.
database_cross_reference: PSI:MS

exponential
type: Class
subclass of: scan law
definition: The mass scan is done in exponential mode.
has_obo_namespace: MS
id: MS:1000094

Axiom
annotated source: exponential
annotated property: definition
annotated target: The mass scan is done in exponential mode.
database_cross_reference: PSI:MS

linear
type: Class
subclass of: scan law
definition: OBSOLETE The mass scan is done in linear mode.
has_obo_namespace: MS
id: MS:1000095
comment: This term was made obsolete because it was redundant with the Pato Ontology term linear (UO:0001199).
deprecated: true

Axiom
annotated source: linear
annotated property: definition
annotated target: OBSOLETE The mass scan is done in linear mode.
database_cross_reference: PSI:MS

quadratic
type: Class
subclass of: scan law
definition: The mass scan is done in quadratic mode.
has_obo_namespace: MS
id: MS:1000096

Axiom
annotated source: quadratic
annotated property: definition
annotated target: The mass scan is done in quadratic mode.
database_cross_reference: PSI:MS

constant neutral mass loss
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000097
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: constant neutral mass loss
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

multiple ion monitoring
type: Class
definition: OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring.
has_obo_namespace: MS
id: MS:1000098
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: multiple ion monitoring
annotated property: definition
annotated target: OBSOLETE Data acquired when monitoring the ion current of a few specific m/z values. Remap to MS:1000205 -Selected Ion Monitoring.
database_cross_reference: PSI:MS

multiple reaction monitoring
type: Class
definition: OBSOLETE This term is not recommended. See Selected Reaction Monitoring.
has_exact_synonym: MRM
has_obo_namespace: MS
id: MS:1000099
comment: This term was made obsolete because it was merged with selected reaction monitoring (MS:1000206).
deprecated: true

Axiom
annotated source: multiple reaction monitoring
annotated property: definition
annotated target: OBSOLETE This term is not recommended. See Selected Reaction Monitoring.
database_cross_reference: PSI:MS

precursor ion scan
type: Class
definition: OBSOLETE The specific scan function or process that will record a precursor ion spectrum.
has_obo_namespace: MS
id: MS:1000100
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: precursor ion scan
annotated property: definition
annotated target: OBSOLETE The specific scan function or process that will record a precursor ion spectrum.
database_cross_reference: PSI:MS

product ion scan
type: Class
definition: OBSOLETE The specific scan function or process that records product ion spectrum.
has_obo_namespace: MS
id: MS:1000101
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: product ion scan
annotated property: definition
annotated target: OBSOLETE The specific scan function or process that records product ion spectrum.
database_cross_reference: PSI:MS

single ion monitoring
type: Class
definition: OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum.
has_obo_namespace: MS
id: MS:1000102
comment: This term was made obsolete because it was replaced by single ion monitoring (MS:100205).
deprecated: true

Axiom
annotated source: single ion monitoring
annotated property: definition
annotated target: OBSOLETE The operation of a mass spectrometer to monitor a single ion rather than scanning entire mass spectrum.
database_cross_reference: PSI:MS

single reaction monitoring
type: Class
definition: OBSOLETE This term is not recommended. See Selected Reaction Monitoring.
has_obo_namespace: MS
id: MS:1000103
comment: This term was made obsolete because it was replaced by selected reaction monitoring (MS:1000206).
deprecated: true

Axiom
annotated source: single reaction monitoring
annotated property: definition
annotated target: OBSOLETE This term is not recommended. See Selected Reaction Monitoring.
database_cross_reference: PSI:MS

None ??
type: Class
definition: OBSOLETE None.
has_obo_namespace: MS
id: MS:1000104
comment: This term was made obsolete because .
deprecated: true

Axiom
annotated source: None ??
annotated property: definition
annotated target: OBSOLETE None.
database_cross_reference: PSI:MS

reflectron off
type: Class
subclass of: reflectron state
definition: Reflectron is off.
has_obo_namespace: MS
id: MS:1000105

Axiom
annotated source: reflectron off
annotated property: definition
annotated target: Reflectron is off.
database_cross_reference: PSI:MS

reflectron on
type: Class
subclass of: reflectron state
definition: Reflectron is on.
has_obo_namespace: MS
id: MS:1000106

Axiom
annotated source: reflectron on
annotated property: definition
annotated target: Reflectron is on.
database_cross_reference: PSI:MS

channeltron
type: Class
subclass of: detector type
definition: 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.
has_exact_synonym: Channeltron Detector
has_obo_namespace: MS
id: MS:1000107

Axiom
annotated source: channeltron
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

conversion dynode electron multiplier
type: Class
subclass of: conversion dynode
definition: A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected.
has_obo_namespace: MS
id: MS:1000108

Axiom
annotated source: conversion dynode electron multiplier
annotated property: definition
annotated target: A surface that is held at high potential so that ions striking the surface produce electrons that are subsequently detected.
database_cross_reference: PSI:MS

conversion dynode photomultiplier
type: Class
subclass of: conversion dynode
definition: 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.
has_obo_namespace: MS
has_related_synonym: ion-to-photon detector
id: MS:1000109

Axiom
annotated source: conversion dynode photomultiplier
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

daly detector
type: Class
subclass of: detector type
definition: 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.
has_exact_synonym: Daly
has_obo_namespace: MS
id: MS:1000110

Axiom
annotated source: daly detector
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

electron multiplier tube
type: Class
subclass of: electron multiplier
definition: 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.
has_exact_synonym: EMT
has_obo_namespace: MS
id: MS:1000111

Axiom
annotated source: electron multiplier tube
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

faraday cup
type: Class
subclass of: detector type
definition: A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device.
has_obo_namespace: MS
id: MS:1000112

Axiom
annotated source: faraday cup
annotated property: definition
annotated target: A conducting cup or chamber that intercepts a charged particle beam and is electrically connected to a current measuring device.
database_cross_reference: PSI:MS

focal plane array
type: Class
subclass of: focal plane collector
definition: An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
has_obo_namespace: MS
id: MS:1000113

Axiom
annotated source: focal plane array
annotated property: definition
annotated target: An array of detectors for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
database_cross_reference: PSI:MS

microchannel plate detector
type: Class
subclass of: array detector
definition: 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.
has_exact_synonym: multichannel plate
has_obo_namespace: MS
id: MS:1000114

Axiom
annotated source: microchannel plate detector
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

multi-collector
type: Class
subclass of: detector type
definition: A detector system commonly used in inductively coupled plasma mass spectrometers.
has_obo_namespace: MS
id: MS:1000115

Axiom
annotated source: multi-collector
annotated property: definition
annotated target: A detector system commonly used in inductively coupled plasma mass spectrometers.
database_cross_reference: PSI:MS

photomultiplier
type: Class
subclass of: detector type
definition: A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected.
has_exact_synonym: PMT
has_obo_namespace: MS
id: MS:1000116

Axiom
annotated source: photomultiplier
annotated property: definition
annotated target: A detector for conversion of the ion/electron signal into photon(s) which are then amplified and detected.
database_cross_reference: PSI:MS

analog-digital converter
type: Class
subclass of: detector acquisition mode
definition: 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.
has_exact_synonym: ADC
has_obo_namespace: MS
id: MS:1000117

Axiom
annotated source: analog-digital converter
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

pulse counting
type: Class
subclass of: detector acquisition mode
definition: Definition to do.
has_obo_namespace: MS
id: MS:1000118

Axiom
annotated source: pulse counting
annotated property: definition
annotated target: Definition to do.
database_cross_reference: PSI:MS

time-digital converter
type: Class
subclass of: detector acquisition mode
definition: A device for converting a signal of sporadic pluses into a digital representation of their time indices.
has_exact_synonym: TDC
has_obo_namespace: MS
id: MS:1000119

Axiom
annotated source: time-digital converter
annotated property: definition
annotated target: A device for converting a signal of sporadic pluses into a digital representation of their time indices.
database_cross_reference: PSI:MS

transient recorder
type: Class
subclass of: detector acquisition mode
definition: A detector acquisition mode used for detecting transient signals.
has_obo_namespace: MS
id: MS:1000120

Axiom
annotated source: transient recorder
annotated property: definition
annotated target: A detector acquisition mode used for detecting transient signals.
database_cross_reference: PSI:MS

SCIEX instrument model
type: Class
subclass of: instrument model
definition: SCIEX instrument model.
has_obo_namespace: MS
has_related_synonym: Applied Biosystems|MDS SCIEX
id: MS:1000121

Axiom
annotated source: SCIEX instrument model
annotated property: definition
annotated target: SCIEX instrument model.
database_cross_reference: PSI:MS

Bruker Daltonics instrument model
type: Class
subclass of: instrument model
definition: Bruker Daltonics' instrument model.
has_obo_namespace: MS
id: MS:1000122

Axiom
annotated source: Bruker Daltonics instrument model
annotated property: definition
annotated target: Bruker Daltonics' instrument model.
database_cross_reference: PSI:MS

IonSpec instrument model
type: Class
subclass of: Varian instrument model
definition: IonSpec corporation instrument model.
has_obo_namespace: MS
id: MS:1000123

Axiom
annotated source: IonSpec instrument model
annotated property: definition
annotated target: IonSpec corporation instrument model.
database_cross_reference: PSI:MS

Shimadzu instrument model
type: Class
subclass of: instrument model
definition: Shimadzu corporation instrument model.
has_obo_namespace: MS
id: MS:1000124

Axiom
annotated source: Shimadzu instrument model
annotated property: definition
annotated target: Shimadzu corporation instrument model.
database_cross_reference: PSI:MS

Thermo Finnigan instrument model
type: Class
subclass of: Thermo Fisher Scientific instrument model
definition: ThermoFinnigan from Thermo Electron Corporation instrument model.
has_obo_namespace: MS
id: MS:1000125

Axiom
annotated source: Thermo Finnigan instrument model
annotated property: definition
annotated target: ThermoFinnigan from Thermo Electron Corporation instrument model.
database_cross_reference: PSI:MS

Waters instrument model
type: Class
subclass of: instrument model
definition: Waters Corporation instrument model.
has_obo_namespace: MS
id: MS:1000126

Axiom
annotated source: Waters instrument model
annotated property: definition
annotated target: Waters Corporation instrument model.
database_cross_reference: PSI:MS

centroid spectrum
type: Class
subclass of: spectrum representation
definition: Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.
has_exact_synonym: Discrete Mass Spectrum
has_obo_namespace: MS
id: MS:1000127

Axiom
annotated source: centroid spectrum
annotated property: definition
annotated target: Processing of profile data to produce spectra that contains discrete peaks of zero width. Often used to reduce the size of dataset.
database_cross_reference: PSI:MS

profile spectrum
type: Class
subclass of: spectrum representation
definition: 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.
has_exact_synonym: Continuum Mass Spectrum
has_exact_synonym: continuous mass spectrum
has_obo_namespace: MS
id: MS:1000128

Axiom
annotated source: profile spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

negative scan
type: Class
subclass of: scan polarity
subclass of: chromatogram attribute
definition: Polarity of the scan is negative.
has_obo_namespace: MS
id: MS:1000129

Axiom
annotated source: negative scan
annotated property: definition
annotated target: Polarity of the scan is negative.
database_cross_reference: PSI:MS

positive scan
type: Class
subclass of: scan polarity
subclass of: chromatogram attribute
definition: Polarity of the scan is positive.
has_obo_namespace: MS
id: MS:1000130

Axiom
annotated source: positive scan
annotated property: definition
annotated target: Polarity of the scan is positive.
database_cross_reference: PSI:MS

number of detector counts
type: Class
subclass of: intensity unit
definition: The number of counted events observed in one or a group of elements of a detector.
has_obo_namespace: MS
id: MS:1000131

Axiom
annotated source: number of detector counts
annotated property: definition
annotated target: The number of counted events observed in one or a group of elements of a detector.
database_cross_reference: PSI:MS

percent of base peak
type: Class
subclass of: intensity unit
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity.
has_obo_namespace: MS
id: MS:1000132

Axiom
annotated source: percent of base peak
annotated property: definition
annotated target: The magnitude of a peak or measurement element expressed in terms of the percentage of the magnitude of the base peak intensity.
database_cross_reference: PSI:MS

collision-induced dissociation
type: Class
subclass of: dissociation method
definition: The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
has_exact_synonym: CAD
has_exact_synonym: CID
has_exact_synonym: collisionally activated dissociation
has_obo_namespace: MS
id: MS:1000133

Axiom
annotated source: collision-induced dissociation
annotated property: definition
annotated target: The dissociation of an ion after collisional excitation. The term collisional-activated dissociation is not recommended.
database_cross_reference: PSI:MS

plasma desorption
type: Class
subclass of: dissociation method
definition: 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.
has_exact_synonym: PD
has_obo_namespace: MS
id: MS:1000134

Axiom
annotated source: plasma desorption
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

post-source decay
type: Class
subclass of: dissociation method
definition: 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.
has_exact_synonym: PSD
has_obo_namespace: MS
id: MS:1000135

Axiom
annotated source: post-source decay
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

surface-induced dissociation
type: Class
subclass of: dissociation method
definition: Fragmentation that results from the collision of an ion with a surface.
has_exact_synonym: SID
has_obo_namespace: MS
id: MS:1000136

Axiom
annotated source: surface-induced dissociation
annotated property: definition
annotated target: Fragmentation that results from the collision of an ion with a surface.
database_cross_reference: PSI:MS

electron volt
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000137
comment: This term was made obsolete because it was redundant with the Unit Ontology term electron volt (UO:0000266).
deprecated: true

Axiom
annotated source: electron volt
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

normalized collision energy
type: Class
subclass of: precursor activation attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.
has_obo_namespace: MS
id: MS:1000138

Axiom
annotated source: normalized collision energy
annotated property: definition
annotated target: Instrument setting, expressed in percent, for adjusting collisional energies of ions in an effort to provide equivalent excitation of all ions.
database_cross_reference: PSI:PI

4000 QTRAP
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX Q 4000 TRAP MS.
has_obo_namespace: MS
id: MS:1000139

Axiom
annotated source: 4000 QTRAP
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX Q 4000 TRAP MS.
database_cross_reference: PSI:MS

4700 Proteomics Analyzer
type: Class
subclass of: Applied Biosystems instrument model
definition: Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS.
has_obo_namespace: MS
id: MS:1000140

Axiom
annotated source: 4700 Proteomics Analyzer
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX 4700 Proteomics Analyzer MS.
database_cross_reference: PSI:MS

apex IV
type: Class
subclass of: Bruker Daltonics apex series
definition: Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
has_obo_namespace: MS
id: MS:1000141

Axiom
annotated source: apex IV
annotated property: definition
annotated target: Bruker Daltonics' apex IV: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
database_cross_reference: PSI:MS

apex Q
type: Class
subclass of: Bruker Daltonics apex series
definition: Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
has_obo_namespace: MS
id: MS:1000142

Axiom
annotated source: apex Q
annotated property: definition
annotated target: Bruker Daltonics' apex Q: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
database_cross_reference: PSI:MS

API 150EX
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX API 150EX MS.
has_obo_namespace: MS
id: MS:1000143

Axiom
annotated source: API 150EX
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX API 150EX MS.
database_cross_reference: PSI:MS

API 150EX Prep
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX API 150EX Prep MS.
has_obo_namespace: MS
id: MS:1000144

Axiom
annotated source: API 150EX Prep
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX API 150EX Prep MS.
database_cross_reference: PSI:MS

API 2000
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX API 2000 MS.
has_obo_namespace: MS
id: MS:1000145

Axiom
annotated source: API 2000
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX API 2000 MS.
database_cross_reference: PSI:MS

API 3000
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX API 3000 MS.
has_obo_namespace: MS
id: MS:1000146

Axiom
annotated source: API 3000
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX API 3000 MS.
database_cross_reference: PSI:MS

API 4000
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX API 4000 MS.
has_obo_namespace: MS
id: MS:1000147

Axiom
annotated source: API 4000
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX API 4000 MS.
database_cross_reference: PSI:MS

autoflex II
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' autoflex II: MALDI TOF.
has_obo_namespace: MS
id: MS:1000148

Axiom
annotated source: autoflex II
annotated property: definition
annotated target: Bruker Daltonics' autoflex II: MALDI TOF.
database_cross_reference: PSI:MS

autoflex TOF/TOF
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF.
has_obo_namespace: MS
id: MS:1000149

Axiom
annotated source: autoflex TOF/TOF
annotated property: definition
annotated target: Bruker Daltonics' autoflex TOF/TOF MS: MALDI TOF.
database_cross_reference: PSI:MS

Auto Spec Ultima NT
type: Class
subclass of: Waters instrument model
definition: Waters magnetic sector based AutoSpec Ultima NT MS.
has_obo_namespace: MS
id: MS:1000150

Axiom
annotated source: Auto Spec Ultima NT
annotated property: definition
annotated target: Waters magnetic sector based AutoSpec Ultima NT MS.
database_cross_reference: PSI:MS

BioTOF II
type: Class
subclass of: Bruker Daltonics BioTOF series
definition: Bruker Daltonics' BioTOF II: ESI TOF.
has_obo_namespace: MS
id: MS:1000151

Axiom
annotated source: BioTOF II
annotated property: definition
annotated target: Bruker Daltonics' BioTOF II: ESI TOF.
database_cross_reference: PSI:MS

BioTOF-Q
type: Class
subclass of: Bruker Daltonics BioTOF series
definition: Bruker Daltonics' BioTOF-Q: ESI Q-TOF.
has_obo_namespace: MS
id: MS:1000152

Axiom
annotated source: BioTOF-Q
annotated property: definition
annotated target: Bruker Daltonics' BioTOF-Q: ESI Q-TOF.
database_cross_reference: PSI:MS

DELTA plusAdvantage
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan DELTA plusAdvantage MS.
has_obo_namespace: MS
id: MS:1000153

Axiom
annotated source: DELTA plusAdvantage
annotated property: definition
annotated target: ThermoFinnigan DELTA plusAdvantage MS.
database_cross_reference: PSI:MS

DELTAplusXP
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan DELTAplusXP MS.
has_obo_namespace: MS
id: MS:1000154

Axiom
annotated source: DELTAplusXP
annotated property: definition
annotated target: ThermoFinnigan DELTAplusXP MS.
database_cross_reference: PSI:MS

ELEMENT2
type: Class
definition: OBSOLETE ThermoFinnigan ELEMENT2 MS.
has_obo_namespace: MS
id: MS:1000155
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: ELEMENT2
annotated property: definition
annotated target: OBSOLETE ThermoFinnigan ELEMENT2 MS.
database_cross_reference: PSI:MS

esquire 4000
type: Class
subclass of: Bruker Daltonics esquire series
definition: Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000156

Axiom
annotated source: esquire 4000
annotated property: definition
annotated target: Bruker Daltonics' esquire 4000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

esquire 6000
type: Class
subclass of: Bruker Daltonics esquire series
definition: Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000157

Axiom
annotated source: esquire 6000
annotated property: definition
annotated target: Bruker Daltonics' esquire 6000: linear ion trap, ESI, MALDI, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

explorer
type: Class
subclass of: IonSpec instrument model
definition: IonSpec Explorer MS.
has_obo_namespace: MS
id: MS:1000158

Axiom
annotated source: explorer
annotated property: definition
annotated target: IonSpec Explorer MS.
database_cross_reference: PSI:MS

GCT
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based GCT.
has_obo_namespace: MS
id: MS:1000159

Axiom
annotated source: GCT
annotated property: definition
annotated target: Waters oa-ToF based GCT.
database_cross_reference: PSI:MS

HCT
type: Class
subclass of: Bruker Daltonics HCT Series
definition: Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000160

Axiom
annotated source: HCT
annotated property: definition
annotated target: Bruker Daltonics' HCT: ESI Q-TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

HCTplus
type: Class
subclass of: Bruker Daltonics HCT Series
definition: Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000161

Axiom
annotated source: HCTplus
annotated property: definition
annotated target: Bruker Daltonics' HCTplus: ESI Q-TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

HiRes ESI
type: Class
subclass of: IonSpec instrument model
definition: IonSpec HiResESI MS.
has_obo_namespace: MS
id: MS:1000162

Axiom
annotated source: HiRes ESI
annotated property: definition
annotated target: IonSpec HiResESI MS.
database_cross_reference: PSI:MS

HiRes MALDI
type: Class
subclass of: IonSpec instrument model
definition: IonSpec HiResMALDI MS.
has_obo_namespace: MS
id: MS:1000163

Axiom
annotated source: HiRes MALDI
annotated property: definition
annotated target: IonSpec HiResMALDI MS.
database_cross_reference: PSI:MS

IsoPrime
type: Class
subclass of: Waters instrument model
definition: Waters IsoPrime MS.
has_obo_namespace: MS
id: MS:1000164

Axiom
annotated source: IsoPrime
annotated property: definition
annotated target: Waters IsoPrime MS.
database_cross_reference: PSI:MS

IsoProbe
type: Class
subclass of: Waters instrument model
definition: Waters IsoProbe MS.
has_obo_namespace: MS
id: MS:1000165

Axiom
annotated source: IsoProbe
annotated property: definition
annotated target: Waters IsoProbe MS.
database_cross_reference: PSI:MS

IsoProbe T
type: Class
subclass of: Waters instrument model
definition: Waters IsoProbe T MS.
has_obo_namespace: MS
id: MS:1000166

Axiom
annotated source: IsoProbe T
annotated property: definition
annotated target: Waters IsoProbe T MS.
database_cross_reference: PSI:MS

LCQ Advantage
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan LCQ Advantage MS.
has_obo_namespace: MS
id: MS:1000167

Axiom
annotated source: LCQ Advantage
annotated property: definition
annotated target: ThermoFinnigan LCQ Advantage MS.
database_cross_reference: PSI:MS

LCQ Classic
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan LCQ Classic MS.
has_obo_namespace: MS
id: MS:1000168

Axiom
annotated source: LCQ Classic
annotated property: definition
annotated target: ThermoFinnigan LCQ Classic MS.
database_cross_reference: PSI:MS

LCQ Deca XP Plus
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan LCQ Deca XP Plus MS.
has_obo_namespace: MS
id: MS:1000169

Axiom
annotated source: LCQ Deca XP Plus
annotated property: definition
annotated target: ThermoFinnigan LCQ Deca XP Plus MS.
database_cross_reference: PSI:MS

M@LDI L
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI L.
has_obo_namespace: MS
id: MS:1000170

Axiom
annotated source: M@LDI L
annotated property: definition
annotated target: Waters oa-ToF based MALDI L.
database_cross_reference: PSI:MS

M@LDI LR
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI LR.
has_obo_namespace: MS
id: MS:1000171

Axiom
annotated source: M@LDI LR
annotated property: definition
annotated target: Waters oa-ToF based MALDI LR.
database_cross_reference: PSI:MS

MAT253
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan MAT253 MS.
has_obo_namespace: MS
id: MS:1000172

Axiom
annotated source: MAT253
annotated property: definition
annotated target: ThermoFinnigan MAT253 MS.
database_cross_reference: PSI:MS

MAT900XP
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan MAT900XP MS.
has_obo_namespace: MS
id: MS:1000173

Axiom
annotated source: MAT900XP
annotated property: definition
annotated target: ThermoFinnigan MAT900XP MS.
database_cross_reference: PSI:MS

MAT900XP Trap
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan MAT900XP Trap MS.
has_obo_namespace: MS
id: MS:1000174

Axiom
annotated source: MAT900XP Trap
annotated property: definition
annotated target: ThermoFinnigan MAT900XP Trap MS.
database_cross_reference: PSI:MS

MAT95XP
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan MAT95XP MS.
has_obo_namespace: MS
id: MS:1000175

Axiom
annotated source: MAT95XP
annotated property: definition
annotated target: ThermoFinnigan MAT95XP MS.
database_cross_reference: PSI:MS

MAT95XP Trap
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan MAT95XP Trap MS.
has_obo_namespace: MS
id: MS:1000176

Axiom
annotated source: MAT95XP Trap
annotated property: definition
annotated target: ThermoFinnigan MAT95XP Trap MS.
database_cross_reference: PSI:MS

microflex
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' microflex: MALDI TOF.
has_obo_namespace: MS
id: MS:1000177

Axiom
annotated source: microflex
annotated property: definition
annotated target: Bruker Daltonics' microflex: MALDI TOF.
database_cross_reference: PSI:MS

microTOF LC
type: Class
subclass of: Bruker Daltonics micrOTOF series
definition: Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000178

Axiom
annotated source: microTOF LC
annotated property: definition
annotated target: Bruker Daltonics' microTOF LC: ESI TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

neptune
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan NEPTUNE MS.
has_obo_namespace: MS
id: MS:1000179

Axiom
annotated source: neptune
annotated property: definition
annotated target: ThermoFinnigan NEPTUNE MS.
database_cross_reference: PSI:MS

NG-5400
type: Class
subclass of: Waters instrument model
definition: Waters NG-5400 MS.
has_obo_namespace: MS
id: MS:1000180

Axiom
annotated source: NG-5400
annotated property: definition
annotated target: Waters NG-5400 MS.
database_cross_reference: PSI:MS

OMEGA
type: Class
subclass of: IonSpec instrument model
definition: IonSpec OMEGA MS.
has_obo_namespace: MS
id: MS:1000181

Axiom
annotated source: OMEGA
annotated property: definition
annotated target: IonSpec OMEGA MS.
database_cross_reference: PSI:MS

OMEGA-2001
type: Class
subclass of: IonSpec instrument model
definition: IonSpec OMEGA-2001 MS.
has_obo_namespace: MS
id: MS:1000182

Axiom
annotated source: OMEGA-2001
annotated property: definition
annotated target: IonSpec OMEGA-2001 MS.
database_cross_reference: PSI:MS

OmniFlex
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' OmniFlex: MALDI TOF.
has_obo_namespace: MS
id: MS:1000183

Axiom
annotated source: OmniFlex
annotated property: definition
annotated target: Bruker Daltonics' OmniFlex: MALDI TOF.
database_cross_reference: PSI:MS

Platform ICP
type: Class
subclass of: Waters instrument model
definition: Waters Platform ICP MS.
has_obo_namespace: MS
id: MS:1000184

Axiom
annotated source: Platform ICP
annotated property: definition
annotated target: Waters Platform ICP MS.
database_cross_reference: PSI:MS

PolarisQ
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan PolarisQ MS.
has_obo_namespace: MS
id: MS:1000185

Axiom
annotated source: PolarisQ
annotated property: definition
annotated target: ThermoFinnigan PolarisQ MS.
database_cross_reference: PSI:MS

proteomics solution 1
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS.
has_obo_namespace: MS
id: MS:1000186

Axiom
annotated source: proteomics solution 1
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX Proteomics Solution 1 MS.
database_cross_reference: PSI:MS

Q TRAP
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX Q TRAP MS.
has_obo_namespace: MS
id: MS:1000187

Axiom
annotated source: Q TRAP
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX Q TRAP MS.
database_cross_reference: PSI:MS

Q-Tof micro
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Q-Tof micro.
has_obo_namespace: MS
id: MS:1000188

Axiom
annotated source: Q-Tof micro
annotated property: definition
annotated target: Waters oa-ToF based Q-Tof micro.
database_cross_reference: PSI:MS

Q-Tof Ultima
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Q-Tof Ultima.
has_obo_namespace: MS
id: MS:1000189

Axiom
annotated source: Q-Tof Ultima
annotated property: definition
annotated target: Waters oa-ToF based Q-Tof Ultima.
database_cross_reference: PSI:MS

QSTAR
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX QSTAR MS.
has_obo_namespace: MS
id: MS:1000190

Axiom
annotated source: QSTAR
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX QSTAR MS.
database_cross_reference: PSI:MS

quattro micro
type: Class
subclass of: Waters instrument model
definition: Waters (triple) quadrupole based micro.
has_obo_namespace: MS
id: MS:1000191

Axiom
annotated source: quattro micro
annotated property: definition
annotated target: Waters (triple) quadrupole based micro.
database_cross_reference: PSI:MS

Quattro Ultima
type: Class
subclass of: Waters instrument model
definition: Waters (triple) quadrupole based Ultima.
has_obo_namespace: MS
id: MS:1000192

Axiom
annotated source: Quattro Ultima
annotated property: definition
annotated target: Waters (triple) quadrupole based Ultima.
database_cross_reference: PSI:MS

Surveyor MSQ
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan Surveyor MSQ MS.
has_obo_namespace: MS
id: MS:1000193

Axiom
annotated source: Surveyor MSQ
annotated property: definition
annotated target: ThermoFinnigan Surveyor MSQ MS.
database_cross_reference: PSI:MS

SymBiot I
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX SymBiot I MS.
has_obo_namespace: MS
id: MS:1000194

Axiom
annotated source: SymBiot I
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX SymBiot I MS.
database_cross_reference: PSI:MS

SymBiot XVI
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems/MDS SCIEX SymBiot XVI MS.
has_obo_namespace: MS
id: MS:1000195

Axiom
annotated source: SymBiot XVI
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX SymBiot XVI MS.
database_cross_reference: PSI:MS

TEMPUS TOF
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan TEMPUS TOF MS.
has_obo_namespace: MS
id: MS:1000196

Axiom
annotated source: TEMPUS TOF
annotated property: definition
annotated target: ThermoFinnigan TEMPUS TOF MS.
database_cross_reference: PSI:MS

TRACE DSQ
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan TRACE DSQ MS.
has_obo_namespace: MS
id: MS:1000197

Axiom
annotated source: TRACE DSQ
annotated property: definition
annotated target: ThermoFinnigan TRACE DSQ MS.
database_cross_reference: PSI:MS

TRITON
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan TRITON MS.
has_obo_namespace: MS
id: MS:1000198

Axiom
annotated source: TRITON
annotated property: definition
annotated target: ThermoFinnigan TRITON MS.
database_cross_reference: PSI:MS

TSQ Quantum
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan TSQ Quantum MS.
has_obo_namespace: MS
id: MS:1000199

Axiom
annotated source: TSQ Quantum
annotated property: definition
annotated target: ThermoFinnigan TSQ Quantum MS.
database_cross_reference: PSI:MS

ultima
type: Class
subclass of: IonSpec instrument model
definition: IonSpec Ultima MS.
has_obo_namespace: MS
id: MS:1000200

Axiom
annotated source: ultima
annotated property: definition
annotated target: IonSpec Ultima MS.
database_cross_reference: PSI:MS

ultraflex
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' ultraflex: MALDI TOF.
has_obo_namespace: MS
id: MS:1000201

Axiom
annotated source: ultraflex
annotated property: definition
annotated target: Bruker Daltonics' ultraflex: MALDI TOF.
database_cross_reference: PSI:MS

ultraflex TOF/TOF
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF.
has_obo_namespace: MS
id: MS:1000202

Axiom
annotated source: ultraflex TOF/TOF
annotated property: definition
annotated target: Bruker Daltonics' ultraflex TOF/TOF: MALDI TOF.
database_cross_reference: PSI:MS

Voyager-DE PRO
type: Class
subclass of: Applied Biosystems instrument model
definition: Applied Biosystems/MDS SCIEX Voyager-DE PRO MS.
has_obo_namespace: MS
id: MS:1000203

Axiom
annotated source: Voyager-DE PRO
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX Voyager-DE PRO MS.
database_cross_reference: PSI:MS

Voyager-DE STR
type: Class
subclass of: Applied Biosystems instrument model
definition: Applied Biosystems/MDS SCIEX Voyager-DE STR MS.
has_obo_namespace: MS
id: MS:1000204

Axiom
annotated source: Voyager-DE STR
annotated property: definition
annotated target: Applied Biosystems/MDS SCIEX Voyager-DE STR MS.
database_cross_reference: PSI:MS

selected ion monitoring
type: Class
subclass of: MS_1003213
subclass of: MS_1003214
subclass of: Restriction
  on property: part_of
  some values from: MS_1003905
definition: The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
has_exact_synonym: SIM
has_obo_namespace: MS
has_related_synonym: MIM
has_related_synonym: Multiple Ion Monitoring
id: MS:1000205

Axiom
annotated source: selected ion monitoring
annotated property: definition
annotated target: The operation of a mass spectrometer in which the intensities of several specific m/z values are recorded rather than the entire mass spectrum.
database_cross_reference: PSI:MS

selected reaction monitoring
type: Class
subclass of: MS_1003213
subclass of: MS_1003214
subclass of: Restriction
  on property: part_of
  some values from: MS_1003905
definition: 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.
has_exact_synonym: SRM
has_obo_namespace: MS
has_related_synonym: MRM
has_related_synonym: Multiple Reaction Monitoring
id: MS:1000206

Axiom
annotated source: selected reaction monitoring
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

accurate mass
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000002
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000207
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: accurate mass
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

average mass
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000002
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance.
has_obo_namespace: MS
id: MS:1000208
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: average mass
annotated property: definition
annotated target: OBSOLETE The mass of an ion or molecule calculated using the average mass of each element weighted for its natural isotopic abundance.
database_cross_reference: PSI:MS

appearance energy
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000266
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_exact_synonym: AE
has_obo_namespace: MS
id: MS:1000209
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: appearance energy
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

base peak
type: Class
subclass of: peak
definition: The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.
has_exact_synonym: BP
has_obo_namespace: MS
id: MS:1000210

Axiom
annotated source: base peak
annotated property: definition
annotated target: The peak in a mass spectrum that has the greatest intensity. This term may be applied to the spectra of pure substances or mixtures.
database_cross_reference: PSI:MS

OBSOLETE charge number
type: Class
subclass of: Restriction
  on property: has value type
  some values from: int
definition: 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.
has_obo_namespace: MS
id: MS:1000211
deprecated: true

Axiom
annotated source: OBSOLETE charge number
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

dalton
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000212
comment: This term was made obsolete because it was redundant with the Unit Ontology term dalton (UO:0000221).
deprecated: true

Axiom
annotated source: dalton
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

electron affinity
type: Class
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_exact_synonym: EA
has_obo_namespace: MS
id: MS:1000213
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: electron affinity
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

electron energy obsolete
type: Class
definition: OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization.
has_obo_namespace: MS
id: MS:1000214
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: electron energy obsolete
annotated property: definition
annotated target: OBSOLETE The potential difference through which electrons are accelerated before they are used to bring about electron ionization.
database_cross_reference: PSI:MS

exact mass
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000002
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom.
has_obo_namespace: MS
id: MS:1000215
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: exact mass
annotated property: definition
annotated target: OBSOLETE The calculated mass of an ion or molecule containing a single isotope of each atom.
database_cross_reference: PSI:MS

field-free region
type: Class
subclass of: ion optics attribute
definition: A section of a mass spectrometer in which there are no electric or magnetic fields.
has_exact_synonym: FFR
has_obo_namespace: MS
id: MS:1000216

Axiom
annotated source: field-free region
annotated property: definition
annotated target: A section of a mass spectrometer in which there are no electric or magnetic fields.
database_cross_reference: PSI:MS

ionization cross section
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000217
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ionization cross section
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ionization efficiency
type: Class
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used.
has_obo_namespace: MS
id: MS:1000218
comment: This term was made obsolete because it was replaced by ionization efficiency (MS:1000392).
deprecated: true

Axiom
annotated source: ionization efficiency
annotated property: definition
annotated target: OBSOLETE The ratio of the number of ions formed to the number of electrons, molecules or photons used.
database_cross_reference: PSI:MS

ionization energy
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000266
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion.
has_exact_synonym: IE
has_obo_namespace: MS
id: MS:1000219
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: ionization energy
annotated property: definition
annotated target: OBSOLETE The minimum energy required to remove an electron from an atom or molecule to produce a positive ion.
database_cross_reference: PSI:MS

isotope dilution mass spectrometry
type: Class
definition: OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard.
has_exact_synonym: IDMS
has_obo_namespace: MS
id: MS:1000220
comment: This child of the former purgatory term mass spectrometry was made obsolete.
deprecated: true

Axiom
annotated source: isotope dilution mass spectrometry
annotated property: definition
annotated target: OBSOLETE A quantitative mass spectrometry technique in which an isotopically enriched compound is used as an internal standard.
database_cross_reference: PSI:MS

magnetic deflection
type: Class
subclass of: ion optics type
definition: 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.
has_obo_namespace: MS
id: MS:1000221

Axiom
annotated source: magnetic deflection
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mass defect
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000002
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom.
has_obo_namespace: MS
id: MS:1000222
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: mass defect
annotated property: definition
annotated target: OBSOLETE The difference between the monoisotopic and nominal mass of a molecule or atom.
database_cross_reference: PSI:MS

mass number
type: Class
subclass of: Restriction
  on property: has value type
  some values from: int
definition: OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion.
has_obo_namespace: MS
id: MS:1000223
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: mass number
annotated property: definition
annotated target: OBSOLETE The sum of the protons and neutrons in an atom, molecule or ion.
database_cross_reference: PSI:MS

molecular mass
type: Class
subclass of: molecular entity property
subclass of: Restriction
  on property: has_units
  some values from: UO_0000002
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Mass of a molecule measured in unified atomic mass units (u or Da).
has_obo_namespace: MS
id: MS:1000224

Axiom
annotated source: molecular mass
annotated property: definition
annotated target: Mass of a molecule measured in unified atomic mass units (u or Da).
database_cross_reference: https://en.wikipedia.org/wiki/Molecular_mass

monoisotopic mass
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000002
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element.
has_obo_namespace: MS
id: MS:1000225
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: monoisotopic mass
annotated property: definition
annotated target: OBSOLETE The mass of an ion or molecule calculated using the mass of the most abundant isotope of each element.
database_cross_reference: PSI:MS

molecular beam mass spectrometry
type: Class
definition: OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.
has_exact_synonym: MBMS
has_obo_namespace: MS
id: MS:1000226
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: molecular beam mass spectrometry
annotated property: definition
annotated target: OBSOLETE A mass spectrometry technique in which the sample is introduced into the mass spectrometer as a molecular beam.
database_cross_reference: PSI:MS

multiphoton ionization
type: Class
subclass of: ionization type
definition: Photoionization of an atom or molecule in which in two or more photons are absorbed.
has_exact_synonym: MPI
has_obo_namespace: MS
id: MS:1000227

Axiom
annotated source: multiphoton ionization
annotated property: definition
annotated target: Photoionization of an atom or molecule in which in two or more photons are absorbed.
database_cross_reference: PSI:MS

nitrogen rule
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000228
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: nitrogen rule
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

nominal mass
type: Class
subclass of: Restriction
  on property: has_units
  some values from: UO_0000002
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000229
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: nominal mass
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

odd-electron rule
type: Class
definition: OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions.
has_obo_namespace: MS
id: MS:1000230
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: odd-electron rule
annotated property: definition
annotated target: OBSOLETE Odd-electron ions may dissociate to form either odd or even-electron ions, whereas even-electron ions generally form even-electron fragment ions.
database_cross_reference: PSI:MS

peak
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
definition: 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.
has_obo_namespace: MS
id: MS:1000231

Axiom
annotated source: peak
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

peak intensity
type: Class
definition: OBSOLETE The height or area of a peak in a mass spectrum.
has_obo_namespace: MS
id: MS:1000232
comment: This term was made obsolete because it was replaced by base peak intensity (MS:1000505).
deprecated: true

Axiom
annotated source: peak intensity
annotated property: definition
annotated target: OBSOLETE The height or area of a peak in a mass spectrum.
database_cross_reference: PSI:MS

proton affinity
type: Class
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_exact_synonym: PA
has_obo_namespace: MS
id: MS:1000233
comment: This child of the former purgatory term ion attribute was made obsolete.
deprecated: true

Axiom
annotated source: proton affinity
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Axiom
annotated source: proton affinity
annotated property: has_exact_synonym
annotated target: PA
database_cross_reference: PSI:MS

mass resolving power
type: Class
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000234
comment: This term was made obsolete because it was replaced by mass resolving power (MS:1000800).
deprecated: true

Axiom
annotated source: mass resolving power
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

total ion current chromatogram
type: Class
subclass of: ion current chromatogram
definition: Representation of the total ion current detected in each of a series of mass spectra versus time.
has_exact_synonym: TIC chromatogram
has_obo_namespace: MS
id: MS:1000235

Axiom
annotated source: total ion current chromatogram
annotated property: definition
annotated target: Representation of the total ion current detected in each of a series of mass spectra versus time.
database_cross_reference: PSI:MS

transmission
type: Class
subclass of: instrument attribute
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region.
has_obo_namespace: MS
id: MS:1000236

Axiom
annotated source: transmission
annotated property: definition
annotated target: The ratio of the number of ions leaving a region of a mass spectrometer to the number entering that region.
database_cross_reference: PSI:MS

unified atomic mass unit
type: Class
definition: 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.
has_exact_synonym: u
has_obo_namespace: MS
id: MS:1000237
comment: This term was made obsolete because it was redundant with Unit Ontology dalton (UO:0000221).
deprecated: true

Axiom
annotated source: unified atomic mass unit
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

accelerator mass spectrometry
type: Class
definition: 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.
has_exact_synonym: AMS
has_obo_namespace: MS
id: MS:1000238
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: accelerator mass spectrometry
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

atmospheric pressure matrix-assisted laser desorption ionization
type: Class
subclass of: atmospheric pressure ionization
definition: 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.
has_exact_synonym: AP MALDI
has_obo_namespace: MS
id: MS:1000239

Axiom
annotated source: atmospheric pressure matrix-assisted laser desorption ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

atmospheric pressure ionization
type: Class
subclass of: ionization type
definition: Any ionization process in which ions are formed in the gas phase at atmospheric pressure.
has_exact_synonym: API
has_obo_namespace: MS
id: MS:1000240

Axiom
annotated source: atmospheric pressure ionization
annotated property: definition
annotated target: Any ionization process in which ions are formed in the gas phase at atmospheric pressure.
database_cross_reference: PSI:MS

Atmostpheric Pressure Photoionization
type: Class
definition: OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
has_exact_synonym: APPI
has_obo_namespace: MS
id: MS:1000241
comment: This term was made obsolete because it was replaced by atmospheric pressure photoionization (MS:1000382).
deprecated: true

Axiom
annotated source: Atmostpheric Pressure Photoionization
annotated property: definition
annotated target: OBSOLETE Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
database_cross_reference: PSI:MS

blackbody infrared radiative dissociation
type: Class
subclass of: dissociation method
definition: 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.
has_exact_synonym: BIRD
has_obo_namespace: MS
id: MS:1000242

Axiom
annotated source: blackbody infrared radiative dissociation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge-remote fragmentation
type: Class
definition: OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site.
has_exact_synonym: CRF
has_obo_namespace: MS
id: MS:1000243
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: charge-remote fragmentation
annotated property: definition
annotated target: OBSOLETE A fragmentation of an even-electron ion in which the cleaved bond is not adjacent to the apparent charge site.
database_cross_reference: PSI:MS

consecutive reaction monitoring
type: Class
definition: OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
has_exact_synonym: CRM
has_obo_namespace: MS
id: MS:1000244
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: consecutive reaction monitoring
annotated property: definition
annotated target: OBSOLETE MSn experiment with three or more stages of m/z separation and in which a particular multi-step reaction path is monitored.
database_cross_reference: PSI:MS

charge stripping
type: Class
subclass of: precursor activation attribute
definition: The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion.
has_exact_synonym: CS
has_obo_namespace: MS
id: MS:1000245

Axiom
annotated source: charge stripping
annotated property: definition
annotated target: The reaction of a positive ion with an atom or molecule that results in the removal of one or more electrons from the ion.
database_cross_reference: PSI:MS

delayed extraction
type: Class
subclass of: ion optics type
definition: 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.
has_exact_synonym: DE
has_obo_namespace: MS
id: MS:1000246

Axiom
annotated source: delayed extraction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

desorption ionization
type: Class
subclass of: ionization type
definition: The formation of ions from a solid or liquid material after the rapid vaporization of that sample.
has_exact_synonym: DI
has_obo_namespace: MS
id: MS:1000247

Axiom
annotated source: desorption ionization
annotated property: definition
annotated target: The formation of ions from a solid or liquid material after the rapid vaporization of that sample.
database_cross_reference: PSI:MS

direct insertion probe
type: Class
subclass of: inlet type
definition: A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization.
has_exact_synonym: DIP
has_obo_namespace: MS
id: MS:1000248

Axiom
annotated source: direct insertion probe
annotated property: definition
annotated target: A device for introducing a solid or liquid sample into a mass spectrometer ion source for desorption ionization.
database_cross_reference: PSI:MS

direct liquid introduction
type: Class
subclass of: inlet type
definition: A legacy liquid chromatography-mass spectrometry interface in which a minor fraction of the eluate flow is split and introduced through a narrow orifice or diaphragm directly into the ion source, with solvent-mediated chemical ionization. This interface was largely superseded by atmospheric pressure ionization methods.
has_exact_synonym: DLI
has_obo_namespace: MS
id: MS:1000249

Axiom
annotated source: direct liquid introduction
annotated property: definition
annotated target: A legacy liquid chromatography-mass spectrometry interface in which a minor fraction of the eluate flow is split and introduced through a narrow orifice or diaphragm directly into the ion source, with solvent-mediated chemical ionization. This interface was largely superseded by atmospheric pressure ionization methods.
database_cross_reference: PSI:MS

electron capture dissociation
type: Class
subclass of: dissociation method
definition: 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.
has_exact_synonym: ECD
has_obo_namespace: MS
id: MS:1000250

Axiom
annotated source: electron capture dissociation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

even-electron ion
type: Class
definition: OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state.
has_exact_synonym: EE
has_obo_namespace: MS
id: MS:1000251
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: even-electron ion
annotated property: definition
annotated target: OBSOLETE An ion containing no unpaired electrons in its ground electronic state, e.g. CH3+ in its ground state.
database_cross_reference: PSI:MS

electron-induced excitation in organics
type: Class
definition: 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.
has_exact_synonym: EIEIO
has_obo_namespace: MS
id: MS:1000252
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: electron-induced excitation in organics
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

electron multiplier
type: Class
subclass of: detector type
definition: 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.
has_exact_synonym: EM
has_obo_namespace: MS
id: MS:1000253

Axiom
annotated source: electron multiplier
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

electrostatic energy analyzer
type: Class
subclass of: mass analyzer type
definition: 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.
has_exact_synonym: ESA
has_obo_namespace: MS
id: MS:1000254

Axiom
annotated source: electrostatic energy analyzer
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

flowing afterglow
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: FA
has_obo_namespace: MS
id: MS:1000255

Axiom
annotated source: flowing afterglow
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

high-field asymmetric waveform ion mobility spectrometry
type: Class
definition: 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.
has_exact_synonym: FAIMS
has_obo_namespace: MS
id: MS:1000256
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: high-field asymmetric waveform ion mobility spectrometry
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

field desorption
type: Class
subclass of: desorption ionization
definition: 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.
has_exact_synonym: FD
has_obo_namespace: MS
id: MS:1000257

Axiom
annotated source: field desorption
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

field ionization
type: Class
subclass of: ionization type
definition: The removal of electrons from any species by interaction with a high electric field.
has_exact_synonym: FI
has_obo_namespace: MS
id: MS:1000258

Axiom
annotated source: field ionization
annotated property: definition
annotated target: The removal of electrons from any species by interaction with a high electric field.
database_cross_reference: PSI:MS

glow discharge ionization
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: GD-MS
has_obo_namespace: MS
id: MS:1000259

Axiom
annotated source: glow discharge ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ion kinetic energy spectrometry
type: Class
definition: OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge.
has_exact_synonym: IKES
has_obo_namespace: MS
id: MS:1000260
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: ion kinetic energy spectrometry
annotated property: definition
annotated target: OBSOLETE A method of analysis in which a beam of ions is separated according to the ratio of its translational energy to charge.
database_cross_reference: PSI:MS

ion mobility spectrometry
type: Class
definition: OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field.
has_exact_synonym: IMS
has_obo_namespace: MS
id: MS:1000261
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: ion mobility spectrometry
annotated property: definition
annotated target: OBSOLETE The separation of ions according to their velocity through a buffer gas under the influence of an electric field.
database_cross_reference: PSI:MS

infrared multiphoton dissociation
type: Class
subclass of: photodissociation
definition: Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons.
has_exact_synonym: IRMPD
has_obo_namespace: MS
id: MS:1000262

Axiom
annotated source: infrared multiphoton dissociation
annotated property: definition
annotated target: Multiphoton ionization where the reactant ion dissociates as a result of the absorption of multiple infrared photons.
database_cross_reference: PSI:MS

isotope ratio mass spectrometry
type: Class
definition: OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer.
has_exact_synonym: IRMS
has_obo_namespace: MS
id: MS:1000263
comment: This child of the former purgatory term mass spectrometry was made obsolete.
deprecated: true

Axiom
annotated source: isotope ratio mass spectrometry
annotated property: definition
annotated target: OBSOLETE The measurement of the relative quantity of the different isotopes of an element in a material with a mass spectrometer.
database_cross_reference: PSI:MS

ion trap
type: Class
subclass of: mass analyzer type
subclass of: MS_1003761
definition: A device for spatially confining ions using electric and magnetic fields alone or in combination.
has_exact_synonym: IT
has_obo_namespace: MS
id: MS:1000264

Axiom
annotated source: ion trap
annotated property: definition
annotated target: A device for spatially confining ions using electric and magnetic fields alone or in combination.
database_cross_reference: PSI:MS

kinetic energy release distribution
type: Class
definition: OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction.
has_exact_synonym: KERD
has_obo_namespace: MS
id: MS:1000265
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: kinetic energy release distribution
annotated property: definition
annotated target: OBSOLETE Distribution of values of translational kinetic energy release for an ensemble of metastable ions undergoing a specific dissociation reaction.
database_cross_reference: PSI:MS

Laser Desorption
type: Class
definition: OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules.
term replaced by: MS:1000393
has_exact_synonym: LD
has_exact_synonym: Laser Ionization MERGE
has_obo_namespace: MS
id: MS:1000266
comment: This term was made obsolete because it was replaced by laser desorption ionization (MS:1000393).
deprecated: true

Axiom
annotated source: Laser Desorption
annotated property: definition
annotated target: OBSOLETE The formation of ions through the interaction of a laser with a material or with gas-phase ions or molecules.
database_cross_reference: PSI:MS

mass analyzed ion kinetic energy spectrometry
type: Class
definition: 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.
has_exact_synonym: MIKES
has_obo_namespace: MS
id: MS:1000267
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: mass analyzed ion kinetic energy spectrometry
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mass spectrometry
type: Class
definition: OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments.
has_exact_synonym: MS
has_obo_namespace: MS
id: MS:1000268
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: mass spectrometry
annotated property: definition
annotated target: OBSOLETE The branch of science that deals with all aspects of mass spectrometers and the results obtained with these instruments.
database_cross_reference: PSI:MS

mass spectrometry/mass spectrometry
type: Class
definition: OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions.
has_exact_synonym: MS/MS
has_obo_namespace: MS
id: MS:1000269
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: mass spectrometry/mass spectrometry
annotated property: definition
annotated target: OBSOLETE The acquisition, study and spectra of the electrically charged products or precursors of a m/z selected ion or ions.
database_cross_reference: PSI:MS

multiple stage mass spectrometry
type: Class
definition: OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions.
has_exact_synonym: MSn
has_obo_namespace: MS
id: MS:1000270
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: multiple stage mass spectrometry
annotated property: definition
annotated target: OBSOLETE Multiple stages of precursor ion m/z selection followed by product ion detection for successive progeny ions.
database_cross_reference: PSI:MS

Negative Ion chemical ionization
type: Class
subclass of: ionization type
definition: Chemical ionization that results in the formation of negative ions.
has_exact_synonym: NICI
has_obo_namespace: MS
id: MS:1000271

Axiom
annotated source: Negative Ion chemical ionization
annotated property: definition
annotated target: Chemical ionization that results in the formation of negative ions.
database_cross_reference: PSI:MS

neutralization reionization mass spectrometry
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: NRMS
has_obo_namespace: MS
id: MS:1000272

Axiom
annotated source: neutralization reionization mass spectrometry
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

photoionization
type: Class
subclass of: ionization type
definition: The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended.
has_exact_synonym: PI
has_obo_namespace: MS
id: MS:1000273

Axiom
annotated source: photoionization
annotated property: definition
annotated target: The ionization of an atom or molecule by a photon, written M + h? ? M^+ + e. The term photon impact is not recommended.
database_cross_reference: PSI:MS

pyrolysis mass spectrometry
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: PyMS
has_obo_namespace: MS
id: MS:1000274

Axiom
annotated source: pyrolysis mass spectrometry
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

collision quadrupole
type: Class
subclass of: ion optics type
definition: 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.
has_exact_synonym: q
has_obo_namespace: MS
id: MS:1000275

Axiom
annotated source: collision quadrupole
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

resonance enhanced multiphoton ionization
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: REMPI
has_obo_namespace: MS
id: MS:1000276

Axiom
annotated source: resonance enhanced multiphoton ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

residual gas analyzer
type: Class
definition: OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber.
has_exact_synonym: RGA
has_obo_namespace: MS
id: MS:1000277
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: residual gas analyzer
annotated property: definition
annotated target: OBSOLETE A mass spectrometer used to measure the composition and pressure of gasses in an evacuated chamber.
database_cross_reference: PSI:MS

surface enhanced laser desorption ionization
type: Class
subclass of: surface ionization
definition: 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.
has_exact_synonym: SELDI
has_obo_namespace: MS
id: MS:1000278

Axiom
annotated source: surface enhanced laser desorption ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

surface enhanced neat desorption
type: Class
subclass of: surface ionization
definition: Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface.
has_exact_synonym: SEND
has_obo_namespace: MS
id: MS:1000279

Axiom
annotated source: surface enhanced neat desorption
annotated property: definition
annotated target: Matrix-assisted laser desorption ionization in which the matrix is covalently linked to the target surface.
database_cross_reference: PSI:MS

surface ionization
type: Class
definition: OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
has_exact_synonym: SI
has_obo_namespace: MS
id: MS:1000280
comment: This term was made obsolete because it was replaced by surface ionization (MS:1000406).
deprecated: true

Axiom
annotated source: surface ionization
annotated property: definition
annotated target: OBSOLETE The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
database_cross_reference: PSI:MS

selected ion flow tube
type: Class
subclass of: ion optics type
definition: A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions.
has_exact_synonym: SIFT
has_obo_namespace: MS
id: MS:1000281

Axiom
annotated source: selected ion flow tube
annotated property: definition
annotated target: A device in which m/z selected ions are entrained in an inert carrier gas and undergo ion-molecule reactions.
database_cross_reference: PSI:MS

sustained off-resonance irradiation
type: Class
subclass of: dissociation method
definition: 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.
has_exact_synonym: SORI
has_obo_namespace: MS
id: MS:1000282

Axiom
annotated source: sustained off-resonance irradiation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Spark Source Mass Spectrometry
type: Class
definition: OBSOLETE Mass spectrometry using spark ionization.
has_exact_synonym: SSMS
has_obo_namespace: MS
id: MS:1000283
comment: This term was made obsolete because it was replaced by spark ionization (MS:1000404).
deprecated: true

Axiom
annotated source: Spark Source Mass Spectrometry
annotated property: definition
annotated target: OBSOLETE Mass spectrometry using spark ionization.
database_cross_reference: PSI:MS

stored waveform inverse fourier transform
type: Class
subclass of: MS_1003213
definition: 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.
has_exact_synonym: SWIFT
has_obo_namespace: MS
id: MS:1000284

Axiom
annotated source: stored waveform inverse fourier transform
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

total ion current
type: Class
subclass of: MS_1003058
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_exact_synonym: TIC
has_obo_namespace: MS
id: MS:1000285

Axiom
annotated source: total ion current
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

time lag focusing
type: Class
subclass of: ion optics type
definition: 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.
has_exact_synonym: TLF
has_obo_namespace: MS
id: MS:1000286

Axiom
annotated source: time lag focusing
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

time-of-flight mass spectrometer
type: Class
definition: OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy.
has_exact_synonym: TOF-MS
has_obo_namespace: MS
id: MS:1000287
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: time-of-flight mass spectrometer
annotated property: definition
annotated target: OBSOLETE An instrument that separates ions by m/z in a field-free region after acceleration to a fixed kinetic energy.
database_cross_reference: PSI:MS

cyclotron
type: Class
subclass of: ion optics type
definition: A device that uses an oscillating electric field and magnetic field to accelerate charged particles.
has_obo_namespace: MS
id: MS:1000288

Axiom
annotated source: cyclotron
annotated property: definition
annotated target: A device that uses an oscillating electric field and magnetic field to accelerate charged particles.
database_cross_reference: PSI:MS

double-focusing mass spectrometer
type: Class
definition: OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam.
has_obo_namespace: MS
id: MS:1000289
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: double-focusing mass spectrometer
annotated property: definition
annotated target: OBSOLETE A mass spectrometer that uses a magnetic sector for m/z focusing and an electric sector for energy focusing of an ion beam.
database_cross_reference: PSI:MS

hybrid mass spectrometer
type: Class
definition: OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry.
has_obo_namespace: MS
id: MS:1000290
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: hybrid mass spectrometer
annotated property: definition
annotated target: OBSOLETE A mass spectrometer that combines m/z analyzers of different types to perform tandem mass spectrometry.
database_cross_reference: PSI:MS

linear ion trap
type: Class
subclass of: ion trap
definition: 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.
has_obo_namespace: MS
id: MS:1000291

Axiom
annotated source: linear ion trap
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mass spectrograph obsolete
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000292
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: mass spectrograph obsolete
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mass spectrometer
type: Class
definition: OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions.
has_obo_namespace: MS
id: MS:1000293
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: mass spectrometer
annotated property: definition
annotated target: OBSOLETE An instrument that measures the mass-to-charge ratio and relative abundances of ions.
database_cross_reference: PSI:MS

mass spectrum
type: Class
subclass of: data file content
subclass of: spectrum type
definition: 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).
has_obo_namespace: MS
id: MS:1000294

Axiom
annotated source: mass spectrum
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:MS

mattauch-herzog geometry
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000295
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: mattauch-herzog geometry
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

nier-johnson geometry
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000296
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: nier-johnson geometry
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

paul ion trap
type: Class
definition: 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.
has_obo_namespace: MS
has_related_synonym: quadrupole ion trap
id: MS:1000297
comment: This term was made obsolete because it is redundant to quadrupole ion trap.
deprecated: true

Axiom
annotated source: paul ion trap
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

prolate traochoidal mass spectrometer
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000298
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: prolate traochoidal mass spectrometer
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

quistor
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000299
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: quistor
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

reflectron
type: Class
subclass of: ion optics type
definition: 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.
has_obo_namespace: MS
id: MS:1000300

Axiom
annotated source: reflectron
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

sector mass spectrometer
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000301
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: sector mass spectrometer
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

tandem mass spectrometer
type: Class
definition: OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry.
has_obo_namespace: MS
id: MS:1000302
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: tandem mass spectrometer
annotated property: definition
annotated target: OBSOLETE A mass spectrometer designed for mass spectrometry/mass spectrometry.
database_cross_reference: PSI:MS

transmission quadrupole mass spectrometer
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000303
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: transmission quadrupole mass spectrometer
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

accelerating voltage
type: Class
subclass of: ion optics attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The electrical potential used to impart kinetic energy to ions in a mass spectrometer.
has_obo_namespace: MS
id: MS:1000304

Axiom
annotated source: accelerating voltage
annotated property: definition
annotated target: The electrical potential used to impart kinetic energy to ions in a mass spectrometer.
database_cross_reference: PSI:MS

cyclotron motion
type: Class
definition: OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB.
has_obo_namespace: MS
id: MS:1000305
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: cyclotron motion
annotated property: definition
annotated target: OBSOLETE The circular motion of a charged particle moving at velocity v in a magnetic field B that results from the force qvB.
database_cross_reference: PSI:MS

dynamic mass spectrometry
type: Class
definition: OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time.
has_obo_namespace: MS
id: MS:1000306
comment: This child of the former purgatory term mass spectrometer was made obsolete.
deprecated: true

Axiom
annotated source: dynamic mass spectrometry
annotated property: definition
annotated target: OBSOLETE A mass spectrometer in which m/z separation using one or more electric fields that vary with time.
database_cross_reference: PSI:MS

einzel lens
type: Class
subclass of: ion optics type
definition: 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.
has_obo_namespace: MS
id: MS:1000307

Axiom
annotated source: einzel lens
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

electric field strength
type: Class
subclass of: ion optics attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000268
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The magnitude of the force per unit charge at a given point in space.
has_obo_namespace: MS
id: MS:1000308

Axiom
annotated source: electric field strength
annotated property: definition
annotated target: The magnitude of the force per unit charge at a given point in space.
database_cross_reference: PSI:MS

first stability region
type: Class
subclass of: ion optics type
definition: The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole.
has_obo_namespace: MS
id: MS:1000309

Axiom
annotated source: first stability region
annotated property: definition
annotated target: The region of a Mathieu stability diagram closest to the origin. Ions within this region can traverse the full length of a transmission quadrupole.
database_cross_reference: PSI:MS

fringing field
type: Class
subclass of: ion optics type
definition: The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element.
has_obo_namespace: MS
id: MS:1000310

Axiom
annotated source: fringing field
annotated property: definition
annotated target: The electric or magnetic field that extends from the edge of a sector, lens or other ion optics element.
database_cross_reference: PSI:MS

kinetic energy analyzer
type: Class
subclass of: ion optics type
definition: 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.
has_obo_namespace: MS
id: MS:1000311

Axiom
annotated source: kinetic energy analyzer
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mass limit
type: Class
definition: OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer.
has_obo_namespace: MS
id: MS:1000312
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: mass limit
annotated property: definition
annotated target: OBSOLETE The m/z value above which ions cannot be detected in a mass spectrometer.
database_cross_reference: PSI:MS

scan m/z range?
type: Class
definition: OBSOLETE The limit of m/z over which a mass spectrometer can detect ions.
has_obo_namespace: MS
id: MS:1000313
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: scan m/z range?
annotated property: definition
annotated target: OBSOLETE The limit of m/z over which a mass spectrometer can detect ions.
database_cross_reference: PSI:MS

mass selective axial ejection
type: Class
definition: OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap.
has_obo_namespace: MS
id: MS:1000314
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: mass selective axial ejection
annotated property: definition
annotated target: OBSOLETE The use of mass selective instability to eject ions of selected m/z values from an ion trap.
database_cross_reference: PSI:MS

mass selective instability
type: Class
definition: OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap.
has_obo_namespace: MS
id: MS:1000315
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: mass selective instability
annotated property: definition
annotated target: OBSOLETE A method for selective ejection of ions according to their m/z value in an ion trap.
database_cross_reference: PSI:MS

mathieu stability diagram
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000316
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: mathieu stability diagram
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

orthogonal extraction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000317
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: orthogonal extraction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

resonance ion ejection
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000318
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: resonance ion ejection
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

space charge effect
type: Class
subclass of: ion optics attribute
definition: 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.
has_obo_namespace: MS
id: MS:1000319

Axiom
annotated source: space charge effect
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

static field
type: Class
subclass of: ion optics type
definition: An electric or magnetic field that does not change in time.
has_obo_namespace: MS
id: MS:1000320

Axiom
annotated source: static field
annotated property: definition
annotated target: An electric or magnetic field that does not change in time.
database_cross_reference: PSI:MS

2E Mass Spectrum
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000321
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: 2E Mass Spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge inversion mass spectrum
type: Class
subclass of: mass spectrum
definition: The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z.
has_obo_namespace: MS
id: MS:1000322

Axiom
annotated source: charge inversion mass spectrum
annotated property: definition
annotated target: The measurement of the relative abundance of ions that result from a charge inversion reaction as a function of m/z.
database_cross_reference: PSI:MS

constant neutral loss scan
type: Class
definition: OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement.
has_obo_namespace: MS
has_related_synonym: constant neutral mass loss scan
has_related_synonym: fixed neutral fragment scan
id: MS:1000323
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: constant neutral loss scan
annotated property: definition
annotated target: OBSOLETE Spectrum of all precursor ions that undergo a selected m/z decrement.
database_cross_reference: PSI:MS

constant neutral gain scan
type: Class
definition: OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment.
has_exact_synonym: Constant Neutral Mass Gain Scan
has_obo_namespace: MS
id: MS:1000324
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: constant neutral gain scan
annotated property: definition
annotated target: OBSOLETE Spectrum of all precursor ions that undergo a selected m/z increment.
database_cross_reference: PSI:MS

constant neutral gain spectrum
type: Class
subclass of: mass spectrum
definition: 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.
has_exact_synonym: constant neutral mass gain spectrum
has_obo_namespace: MS
id: MS:1000325

Axiom
annotated source: constant neutral gain spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

constant neutral loss spectrum
type: Class
subclass of: mass spectrum
definition: 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.
has_exact_synonym: constant neutral mass loss spectrum
has_obo_namespace: MS
id: MS:1000326

Axiom
annotated source: constant neutral loss spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

consecutive reaction monitoring
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000327
comment: This term was made obsolete because it was replaced by consecutive reaction monitoring (MS:1000244).
deprecated: true

Axiom
annotated source: consecutive reaction monitoring
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

e/2 mass spectrum
type: Class
subclass of: mass spectrum
definition: 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.
has_obo_namespace: MS
id: MS:1000328

Axiom
annotated source: e/2 mass spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

linked scan
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000329
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: linked scan
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

linked scan at constant b/e
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000330
comment: This child of the former purgatory term linked scan was made obsolete.
deprecated: true

Axiom
annotated source: linked scan at constant b/e
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Linked Scan at Constant E2/V
type: Class
definition: 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 records a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors.
has_obo_namespace: MS
id: MS:1000331
comment: This child of the former purgatory term linked scan was made obsolete.
deprecated: true

Axiom
annotated source: Linked Scan at Constant E2/V
annotated property: definition
annotated target: 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 records a product ion spectrum of dissociation or other reactions occurring in a field free region (FFR) preceding the two sectors.
database_cross_reference: PSI:MS

Linked Scan at Constant B2/E
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000332
comment: This child of the former purgatory term linked scan was made obsolete.
deprecated: true

Axiom
annotated source: Linked Scan at Constant B2/E
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Linked Scan at Constant B[1-(E/E0)]^1/2 / E
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000333
comment: This child of the former purgatory term linked scan was made obsolete.
deprecated: true

Axiom
annotated source: Linked Scan at Constant B[1-(E/E0)]^1/2 / E
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

MS/MS in Time
type: Class
definition: 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 discrete steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time.
has_obo_namespace: MS
id: MS:1000334
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: MS/MS in Time
annotated property: definition
annotated target: 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 discrete steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time.
database_cross_reference: PSI:MS

MS/MS in Space
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000335
comment: This child of the former purgatory term m/z Separation Method was made obsolete.
deprecated: true

Axiom
annotated source: MS/MS in Space
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

neutral loss
type: Class
subclass of: modification parameters
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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).
has_obo_namespace: MS
id: MS:1000336

Axiom
annotated source: neutral loss
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:MS

nth generation product ion
type: Class
definition: 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.
has_obo_namespace: MS
has_related_synonym: granddaughter ion
id: MS:1000337
comment: This child of the former purgatory term product ion was made obsolete.
deprecated: true

Axiom
annotated source: nth generation product ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

nth generation product ion scan
type: Class
definition: OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions.
has_obo_namespace: MS
id: MS:1000338
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: nth generation product ion scan
annotated property: definition
annotated target: OBSOLETE The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions.
database_cross_reference: PSI:MS

nth generation product ion spectrum
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000339
comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580).
deprecated: true

Axiom
annotated source: nth generation product ion spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

precursor ion
type: Class
definition: 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.
has_obo_namespace: MS
has_related_synonym: parent ion
id: MS:1000340
comment: This child of the former purgatory term ion role was made obsolete.
deprecated: true

Axiom
annotated source: precursor ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

precursor ion spectrum
type: Class
subclass of: mass spectrum
definition: Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z.
has_obo_namespace: MS
id: MS:1000341

Axiom
annotated source: precursor ion spectrum
annotated property: definition
annotated target: Spectrum generated by scanning precursor m/z while monitoring a fixed product m/z.
database_cross_reference: PSI:MS

product ion
type: Class
definition: 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.
has_obo_namespace: MS
has_related_synonym: daughter ion
id: MS:1000342
comment: This child of the former purgatory term ion role was made obsolete.
deprecated: true

Axiom
annotated source: product ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

product ion spectrum
type: Class
subclass of: mass spectrum
definition: 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.
has_obo_namespace: MS
id: MS:1000343
comment: This term was made obsolete because it was merged with MSn spectrum (MS:1000580).
deprecated: true

Axiom
annotated source: product ion spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

progeny ion
type: Class
definition: 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+.
has_exact_synonym: Progeny Fragment Ion
has_obo_namespace: MS
id: MS:1000344
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: progeny ion
annotated property: definition
annotated target: 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+.
database_cross_reference: PSI:MS

array detector
type: Class
subclass of: detector type
definition: Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector.
has_obo_namespace: MS
id: MS:1000345

Axiom
annotated source: array detector
annotated property: definition
annotated target: Detector comprising several ion collection elements, arranged in a line or grid where each element is an individual detector.
database_cross_reference: PSI:MS

conversion dynode
type: Class
subclass of: detector type
definition: A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected.
has_obo_namespace: MS
id: MS:1000346

Axiom
annotated source: conversion dynode
annotated property: definition
annotated target: A surface that is held at high potential such that ions striking the surface produce electrons that are subsequently detected.
database_cross_reference: PSI:MS

dynode
type: Class
subclass of: detector type
definition: One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode.
has_obo_namespace: MS
id: MS:1000347

Axiom
annotated source: dynode
annotated property: definition
annotated target: One of a series of electrodes in a photomultiplier tube. Such an arrangement is able to amplify the current emitted by the photocathode.
database_cross_reference: PSI:MS

focal plane collector
type: Class
subclass of: detector type
definition: A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
has_obo_namespace: MS
id: MS:1000348

Axiom
annotated source: focal plane collector
annotated property: definition
annotated target: A detector for spatially disperse ion beams in which all ions simultaneously impinge on the detector plane.
database_cross_reference: PSI:MS

ion-to-photon detector
type: Class
subclass of: detector type
definition: 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.
has_obo_namespace: MS
id: MS:1000349

Axiom
annotated source: ion-to-photon detector
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

point collector
type: Class
subclass of: detector type
definition: A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially.
has_obo_namespace: MS
id: MS:1000350

Axiom
annotated source: point collector
annotated property: definition
annotated target: A detector in which the ion beam is focused onto a point and the individual ions arrive sequentially.
database_cross_reference: PSI:MS

postacceleration detector
type: Class
subclass of: detector type
definition: 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.
has_obo_namespace: MS
id: MS:1000351

Axiom
annotated source: postacceleration detector
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

secondary electron
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000352
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: secondary electron
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

adduct ion
type: Class
subclass of: MS_1003055
definition: 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.
has_obo_namespace: MS
id: MS:1000353

Axiom
annotated source: adduct ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

aromatic ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000354
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: aromatic ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

analog ion
type: Class
definition: OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+.
has_obo_namespace: MS
id: MS:1000355
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: analog ion
annotated property: definition
annotated target: OBSOLETE Ions that have similar chemical valence, for example the acetyl cation CH3-CO+ and the thioacetyl cation CH3-CS+.
database_cross_reference: PSI:MS

anti-aromatic ion
type: Class
definition: OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic.
has_obo_namespace: MS
id: MS:1000356
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: anti-aromatic ion
annotated property: definition
annotated target: OBSOLETE A planar cyclic ion with 4n ? electrons and is therefore not aromatic.
database_cross_reference: PSI:MS

cationized molecule
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000357
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: cationized molecule
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

cluster ion
type: Class
definition: 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]-.
has_obo_namespace: MS
id: MS:1000358
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: cluster ion
annotated property: definition
annotated target: 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]-.
database_cross_reference: PSI:MS

Conventional ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000359
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: Conventional ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

diagnostic ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000360
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: diagnostic ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

dimeric ion
type: Class
definition: 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]+.
has_obo_namespace: MS
id: MS:1000361
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: dimeric ion
annotated property: definition
annotated target: 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]+.
database_cross_reference: PSI:MS

distonic ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000362
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: distonic ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

enium ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000363
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: enium ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

fragment ion
type: Class
definition: OBSOLETE A product ion that results from the dissociation of a precursor ion.
has_obo_namespace: MS
id: MS:1000364
comment: This term was made obsolete because it was replaced by product ion (MS:1000342).
deprecated: true

Axiom
annotated source: fragment ion
annotated property: definition
annotated target: OBSOLETE A product ion that results from the dissociation of a precursor ion.
database_cross_reference: PSI:MS

ion?
type: Class
definition: OBSOLETE An atomic or molecular species having a net positive or negative electric charge.
has_obo_namespace: MS
id: MS:1000365
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: ion?
annotated property: definition
annotated target: OBSOLETE An atomic or molecular species having a net positive or negative electric charge.
database_cross_reference: PSI:MS

Isotopologue ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000366
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: Isotopologue ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Isotopomeric ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000367
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: Isotopomeric ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

metastable ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000368
comment: This child of the former purgatory term ion stability type was made obsolete.
deprecated: true

Axiom
annotated source: metastable ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

molecular ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000369
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: molecular ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

negative ion
type: Class
definition: OBSOLETE An atomic or molecular species having a net negative electric charge.
has_obo_namespace: MS
id: MS:1000370
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: negative ion
annotated property: definition
annotated target: OBSOLETE An atomic or molecular species having a net negative electric charge.
database_cross_reference: PSI:MS

non-classical ion
type: Class
definition: OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions.
has_obo_namespace: MS
id: MS:1000371
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: non-classical ion
annotated property: definition
annotated target: OBSOLETE Hyper-coordinated carbonium ion such as the penta-coordinated norbornyl cation. Note: Tri-coordinated carbenium ions are termed classical ions.
database_cross_reference: PSI:MS

onium ion
type: Class
definition: 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+.
has_obo_namespace: MS
id: MS:1000372
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: onium ion
annotated property: definition
annotated target: 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+.
database_cross_reference: PSI:MS

principal ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000373
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: principal ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

positive ion
type: Class
definition: OBSOLETE An atomic or molecular species having a net positive electric charge.
has_obo_namespace: MS
id: MS:1000374
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: positive ion
annotated property: definition
annotated target: OBSOLETE An atomic or molecular species having a net positive electric charge.
database_cross_reference: PSI:MS

protonated molecule
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000375
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: protonated molecule
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

radical ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000376
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: radical ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

reference ion
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000377
comment: This child of the former purgatory term ion chemical type was made obsolete.
deprecated: true

Axiom
annotated source: reference ion
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

stable ion
type: Class
definition: OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer.
has_obo_namespace: MS
id: MS:1000378
comment: This child of the former purgatory term ion stability type was made obsolete.
deprecated: true

Axiom
annotated source: stable ion
annotated property: definition
annotated target: OBSOLETE An ion with internal energy sufficiently low that it does not rearrange or dissociate prior to detection in a mass spectrometer.
database_cross_reference: PSI:MS

unstable ion
type: Class
definition: OBSOLETE An ion with sufficient energy to dissociate within the ion source.
has_obo_namespace: MS
id: MS:1000379
comment: This child of the former purgatory term ion stability type was made obsolete.
deprecated: true

Axiom
annotated source: unstable ion
annotated property: definition
annotated target: OBSOLETE An ion with sufficient energy to dissociate within the ion source.
database_cross_reference: PSI:MS

adiabatic ionization
type: Class
subclass of: ionization type
definition: A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state.
has_obo_namespace: MS
id: MS:1000380

Axiom
annotated source: adiabatic ionization
annotated property: definition
annotated target: A process whereby an electron is removed from an atom, ion, or molecule to produce an ion in its lowest energy state.
database_cross_reference: PSI:MS

associative ionization
type: Class
subclass of: ionization type
definition: An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron.
has_obo_namespace: MS
id: MS:1000381

Axiom
annotated source: associative ionization
annotated property: definition
annotated target: An ionization process in which two excited atoms or molecules react to form a single positive ion and an electron.
database_cross_reference: PSI:MS

atmospheric pressure photoionization
type: Class
subclass of: atmospheric pressure ionization
definition: Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
has_obo_namespace: MS
id: MS:1000382

Axiom
annotated source: atmospheric pressure photoionization
annotated property: definition
annotated target: Atmospheric pressure chemical ionization in which the reactant ions are generated by photo-ionization.
database_cross_reference: PSI:MS

autodetachment
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000383

Axiom
annotated source: autodetachment
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

autoionization
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000384

Axiom
annotated source: autoionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge exchange ionization
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000385

Axiom
annotated source: charge exchange ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

chemi-ionization
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000386

Axiom
annotated source: chemi-ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

desorption/ionization on silicon
type: Class
subclass of: desorption ionization
definition: The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface.
has_obo_namespace: MS
id: MS:1000387

Axiom
annotated source: desorption/ionization on silicon
annotated property: definition
annotated target: The formation of ions by laser desorption ionization of a sample deposited on a porous silicon surface.
database_cross_reference: PSI:MS

dissociative ionization
type: Class
subclass of: ionization type
definition: The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion.
has_obo_namespace: MS
id: MS:1000388

Axiom
annotated source: dissociative ionization
annotated property: definition
annotated target: The reaction of a gas-phase molecule that results in its decomposition to form products, one of which is an ion.
database_cross_reference: PSI:MS

electron ionization
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000389

Axiom
annotated source: electron ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ion desolvation
type: Class
definition: OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules.
has_obo_namespace: MS
id: MS:1000390
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ion desolvation
annotated property: definition
annotated target: OBSOLETE The removal of solvent molecules clustered around a gas-phase ion by means of heating and/or collisions with gas molecules.
database_cross_reference: PSI:MS

ion-pair formation
type: Class
definition: OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products.
has_obo_namespace: MS
id: MS:1000391
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ion-pair formation
annotated property: definition
annotated target: OBSOLETE The reaction of a molecule to form both a positive ion and negative ion fragment among the products.
database_cross_reference: PSI:MS

ionization efficiency
type: Class
subclass of: source attribute
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The ratio of the number of ions formed to the number of electrons, molecules or photons used.
has_obo_namespace: MS
id: MS:1000392

Axiom
annotated source: ionization efficiency
annotated property: definition
annotated target: The ratio of the number of ions formed to the number of electrons, molecules or photons used.
database_cross_reference: PSI:MS

laser desorption ionization
type: Class
subclass of: desorption ionization
definition: The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.
has_obo_namespace: MS
id: MS:1000393

Axiom
annotated source: laser desorption ionization
annotated property: definition
annotated target: The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.
database_cross_reference: PSI:MS

no sequence database
type: Class
subclass of: database file formats
definition: No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing.
has_obo_namespace: MS
id: MS:1000394

Axiom
annotated source: no sequence database
annotated property: definition
annotated target: No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing.
database_cross_reference: PSI:PI

liquid secondary ionization
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000395

Axiom
annotated source: liquid secondary ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

membrane inlet
type: Class
subclass of: inlet type
definition: A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source.
has_obo_namespace: MS
id: MS:1000396

Axiom
annotated source: membrane inlet
annotated property: definition
annotated target: A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source.
database_cross_reference: PSI:MS

microelectrospray
type: Class
subclass of: electrospray ionization
definition: Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray.
has_obo_namespace: MS
id: MS:1000397

Axiom
annotated source: microelectrospray
annotated property: definition
annotated target: Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray.
database_cross_reference: PSI:MS

nanoelectrospray
type: Class
subclass of: electrospray ionization
definition: Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potential on the tip of the electrospray needle and/or a gas pressure to push the sample through the needle. See also electrospray ionization and microelectrospray.
has_exact_synonym: nanospray
has_obo_namespace: MS
id: MS:1000398

Axiom
annotated source: nanoelectrospray
annotated property: definition
annotated target: Electrospray ionization at a flow rate less than ~25 nL/min. Nanoelectrospray is synonymous with nanospray. The flow is dependent on the potential on the tip of the electrospray needle and/or a gas pressure to push the sample through the needle. See also electrospray ionization and microelectrospray.
database_cross_reference: PSI:MS

penning ionization
type: Class
subclass of: ionization type
definition: Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited.
has_obo_namespace: MS
id: MS:1000399

Axiom
annotated source: penning ionization
annotated property: definition
annotated target: Ionization that occurs through the interaction of two or more neutral gaseous species, at least one of which is internally excited.
database_cross_reference: PSI:MS

plasma desorption ionization
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000400

Axiom
annotated source: plasma desorption ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

pre-ionization state
type: Class
definition: OBSOLETE An electronic state capable of undergoing auto-Ionization.
has_obo_namespace: MS
id: MS:1000401
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: pre-ionization state
annotated property: definition
annotated target: OBSOLETE An electronic state capable of undergoing auto-Ionization.
database_cross_reference: PSI:MS

secondary ionization
type: Class
subclass of: ionization type
definition: The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions.
has_obo_namespace: MS
id: MS:1000402

Axiom
annotated source: secondary ionization
annotated property: definition
annotated target: The process in which ions are ejected from a sample surface as a result of bombardment by a primary beam of atoms or ions.
database_cross_reference: PSI:MS

soft ionization
type: Class
subclass of: ionization type
definition: The formation of gas-phase ions without extensive fragmentation.
has_obo_namespace: MS
id: MS:1000403

Axiom
annotated source: soft ionization
annotated property: definition
annotated target: The formation of gas-phase ions without extensive fragmentation.
database_cross_reference: PSI:MS

spark ionization
type: Class
subclass of: ionization type
definition: The formation of ions from a solid material by an intermittent electrical discharge.
has_obo_namespace: MS
id: MS:1000404

Axiom
annotated source: spark ionization
annotated property: definition
annotated target: The formation of ions from a solid material by an intermittent electrical discharge.
database_cross_reference: PSI:MS

surface-assisted laser desorption ionization
type: Class
subclass of: desorption ionization
definition: 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.
has_obo_namespace: MS
id: MS:1000405

Axiom
annotated source: surface-assisted laser desorption ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

surface ionization
type: Class
subclass of: ionization type
definition: The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
has_obo_namespace: MS
id: MS:1000406

Axiom
annotated source: surface ionization
annotated property: definition
annotated target: The ionization of a neutral species when it interacts with a solid surface with an appropriate work function and temperature.
database_cross_reference: PSI:MS

thermal ionization
type: Class
subclass of: ionization type
definition: The ionization of a neutral species through contact with a high temperature surface.
has_obo_namespace: MS
id: MS:1000407

Axiom
annotated source: thermal ionization
annotated property: definition
annotated target: The ionization of a neutral species through contact with a high temperature surface.
database_cross_reference: PSI:MS

vertical ionization
type: Class
subclass of: ionization type
definition: 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.
has_obo_namespace: MS
id: MS:1000408

Axiom
annotated source: vertical ionization
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

association reaction
type: Class
definition: OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion.
has_obo_namespace: MS
id: MS:1000409
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: association reaction
annotated property: definition
annotated target: OBSOLETE The reaction of an ion with a neutral species in which the reactants combine to form a single ion.
database_cross_reference: PSI:MS

alpha-cleavage
type: Class
definition: OBSOLETE A homolytic cleavage where the bond fission occurs between the atom adjacent to the atom at the apparent charge site and an atom removed from the apparent charge site by two bonds.
has_obo_namespace: MS
id: MS:1000410
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: alpha-cleavage
annotated property: definition
annotated target: OBSOLETE A homolytic cleavage where the bond fission occurs between the atom adjacent to the atom at the apparent charge site and an atom removed from the apparent charge site by two bonds.
database_cross_reference: PSI:MS

beta-cleavage
type: Class
definition: OBSOLETE A homolytic cleavage where the bond fission occurs between an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the apparent charge site by three bonds.
has_obo_namespace: MS
id: MS:1000411
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: beta-cleavage
annotated property: definition
annotated target: OBSOLETE A homolytic cleavage where the bond fission occurs between an atom removed from the apparent charge site atom by two bonds and an atom adjacent to that atom and removed from the apparent charge site by three bonds.
database_cross_reference: PSI:MS

buffer gas
type: Class
subclass of: precursor activation attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: An inert gas used for collisional deactivation of internally excited ions.
has_obo_namespace: MS
id: MS:1000412

Axiom
annotated source: buffer gas
annotated property: definition
annotated target: An inert gas used for collisional deactivation of internally excited ions.
database_cross_reference: PSI:MS

charge-induced fragmentation
type: Class
definition: OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation.
has_obo_namespace: MS
id: MS:1000413
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: charge-induced fragmentation
annotated property: definition
annotated target: OBSOLETE Fragmentation of an odd electron ion in which the cleaved bond is adjacent to the apparent charge site. Synonymous with charge mediated fragmentation.
database_cross_reference: PSI:MS

charge inversion reaction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000414
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: charge inversion reaction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge permutation reaction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000415
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: charge permutation reaction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge stripping reaction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000416
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: charge stripping reaction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

charge transfer reaction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000417
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: charge transfer reaction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

collisional excitation
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000418
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: collisional excitation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

collision gas
type: Class
subclass of: precursor activation attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: An inert gas used for collisional excitation. The term target gas is not recommended.
has_obo_namespace: MS
id: MS:1000419

Axiom
annotated source: collision gas
annotated property: definition
annotated target: An inert gas used for collisional excitation. The term target gas is not recommended.
database_cross_reference: PSI:MS

heterolytic cleavage
type: Class
definition: 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.
has_obo_namespace: MS
has_related_synonym: heterolysis
id: MS:1000420
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: heterolytic cleavage
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

high energy collision
type: Class
definition: OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV.
has_obo_namespace: MS
id: MS:1000421
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: high energy collision
annotated property: definition
annotated target: OBSOLETE Collision-induced dissociation process wherein the projectile ion has laboratory-frame translational energy higher than 1 keV.
database_cross_reference: PSI:MS

beam-type collision-induced dissociation
type: Class
subclass of: collision-induced dissociation
definition: A collision-induced dissociation process that occurs in a beam-type collision cell.
has_exact_synonym: HCD
has_obo_namespace: MS
id: MS:1000422

Axiom
annotated source: beam-type collision-induced dissociation
annotated property: definition
annotated target: A collision-induced dissociation process that occurs in a beam-type collision cell.
database_cross_reference: PSI:MS

homolytic cleavage
type: Class
definition: 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.
has_obo_namespace: MS
has_related_synonym: homolysis
id: MS:1000423
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: homolytic cleavage
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

hydrogen/deuterium exchange
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000424
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: hydrogen/deuterium exchange
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ion energy loss spectrum
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000425
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: ion energy loss spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ionizing collision
type: Class
definition: OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral.
has_obo_namespace: MS
id: MS:1000426
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ionizing collision
annotated property: definition
annotated target: OBSOLETE The reaction of an ion with a neutral species in which one or more electrons are removed from either the ion or neutral.
database_cross_reference: PSI:MS

ion/molecule reaction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000427
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ion/molecule reaction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ion/neutral complex
type: Class
definition: OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions.
has_obo_namespace: MS
id: MS:1000428
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ion/neutral complex
annotated property: definition
annotated target: OBSOLETE A particular type of transition state that lies between precursor and product ions on the reaction coordinate of some ion reactions.
database_cross_reference: PSI:MS

ion/neutral species reaction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000429
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ion/neutral species reaction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ion/neutral species exchange reaction
type: Class
definition: OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product.
has_obo_namespace: MS
id: MS:1000430
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: ion/neutral species exchange reaction
annotated property: definition
annotated target: OBSOLETE In this reaction an association reaction is accompanied by the subsequent or simultaneous liberation of a different neutral species as a product.
database_cross_reference: PSI:MS

kinetic method
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000431
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: kinetic method
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

low energy collisions
type: Class
definition: OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower.
has_obo_namespace: MS
id: MS:1000432
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: low energy collisions
annotated property: definition
annotated target: OBSOLETE A collision between an ion and neutral species with translational energy approximately 1000 eV or lower.
database_cross_reference: PSI:MS

low-energy collision-induced dissociation
type: Class
subclass of: dissociation method
definition: 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.
has_obo_namespace: MS
id: MS:1000433

Axiom
annotated source: low-energy collision-induced dissociation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

McLafferty Rearrangement
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000434
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: McLafferty Rearrangement
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

photodissociation
type: Class
subclass of: dissociation method
definition: A process wherein the reactant ion is dissociated as a result of absorption of one or more photons.
has_exact_synonym: MPD
has_exact_synonym: multiphoton dissociation
has_obo_namespace: MS
id: MS:1000435

Axiom
annotated source: photodissociation
annotated property: definition
annotated target: A process wherein the reactant ion is dissociated as a result of absorption of one or more photons.
database_cross_reference: PSI:MS

partial charge transfer reaction
type: Class
definition: OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral.
has_obo_namespace: MS
id: MS:1000436
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: partial charge transfer reaction
annotated property: definition
annotated target: OBSOLETE Reaction of an ion with a neutral species in which some but not all of the ion charge is transferred to the neutral.
database_cross_reference: PSI:MS

ion reaction
type: Class
definition: OBSOLETE Chemical transformation involving an ion.
has_obo_namespace: MS
id: MS:1000437
comment: This child of the former purgatory term ion was made obsolete.
deprecated: true

Axiom
annotated source: ion reaction
annotated property: definition
annotated target: OBSOLETE Chemical transformation involving an ion.
database_cross_reference: PSI:MS

superelastic collision
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000438
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: superelastic collision
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

surface-induced reaction
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000439
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: surface-induced reaction
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

unimolecular dissociation
type: Class
definition: 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.
has_obo_namespace: MS
id: MS:1000440
comment: This child of the former purgatory term ion reaction was made obsolete.
deprecated: true

Axiom
annotated source: unimolecular dissociation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

scan
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Function or process of the mass spectrometer where it records a spectrum.
has_obo_namespace: MS
id: MS:1000441

Axiom
annotated source: scan
annotated property: definition
annotated target: Function or process of the mass spectrometer where it records a spectrum.
database_cross_reference: PSI:MS

spectrum
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Representation of intensity values corresponding to a range of measurement space.
has_obo_namespace: MS
id: MS:1000442

Axiom
annotated source: spectrum
annotated property: definition
annotated target: Representation of intensity values corresponding to a range of measurement space.
database_cross_reference: PSI:MS

mass analyzer type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: mass analyzer
definition: Mass analyzer separates the ions according to their mass-to-charge ratio.
has_obo_namespace: MS
id: MS:1000443

Axiom
annotated source: mass analyzer type
annotated property: definition
annotated target: Mass analyzer separates the ions according to their mass-to-charge ratio.
database_cross_reference: PSI:MS

m/z Separation Method
type: Class
definition: OBSOLETE Mass/charge separation Method.
has_obo_namespace: MS
id: MS:1000444
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: m/z Separation Method
annotated property: definition
annotated target: OBSOLETE Mass/charge separation Method.
database_cross_reference: PSI:MS

sequential m/z separation method
type: Class
definition: OBSOLETE Sequential m/z separation method.
has_obo_namespace: MS
id: MS:1000445
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: sequential m/z separation method
annotated property: definition
annotated target: OBSOLETE Sequential m/z separation method.
database_cross_reference: PSI:MS

fast ion bombardment
type: Class
subclass of: ionization type
definition: 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.
has_exact_synonym: FIB
has_obo_namespace: MS
id: MS:1000446

Axiom
annotated source: fast ion bombardment
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

LTQ
type: Class
subclass of: Thermo Scientific instrument model
definition: Finnigan LTQ MS.
has_obo_namespace: MS
id: MS:1000447

Axiom
annotated source: LTQ
annotated property: definition
annotated target: Finnigan LTQ MS.
database_cross_reference: PSI:MS

LTQ FT
type: Class
subclass of: Thermo Scientific instrument model
definition: Finnigan LTQ FT MS.
has_obo_namespace: MS
id: MS:1000448

Axiom
annotated source: LTQ FT
annotated property: definition
annotated target: Finnigan LTQ FT MS.
database_cross_reference: PSI:MS

LTQ Orbitrap
type: Class
subclass of: Thermo Scientific instrument model
definition: Finnigan LTQ Orbitrap MS.
has_obo_namespace: MS
id: MS:1000449

Axiom
annotated source: LTQ Orbitrap
annotated property: definition
annotated target: Finnigan LTQ Orbitrap MS.
database_cross_reference: PSI:MS

LXQ
type: Class
subclass of: Thermo Scientific instrument model
definition: Finnigan LXQ MS.
has_obo_namespace: MS
id: MS:1000450

Axiom
annotated source: LXQ
annotated property: definition
annotated target: Finnigan LXQ MS.
database_cross_reference: PSI:MS

mass analyzer
type: Class
subclass of: Restriction
  on property: part_of
  some values from: instrument
definition: Terms used to describe the Analyzer.
has_exact_synonym: analyzer
has_obo_namespace: MS
id: MS:1000451

Axiom
annotated source: mass analyzer
annotated property: definition
annotated target: Terms used to describe the Analyzer.
database_cross_reference: PSI:MS

data transformation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Terms used to describe types of data processing.
has_exact_synonym: data processing
has_obo_namespace: MS
id: MS:1000452

Axiom
annotated source: data transformation
annotated property: definition
annotated target: Terms used to describe types of data processing.
database_cross_reference: PSI:MS

detector
type: Class
subclass of: Restriction
  on property: part_of
  some values from: instrument
definition: The device that detects ions.
has_obo_namespace: MS
id: MS:1000453

Axiom
annotated source: detector
annotated property: definition
annotated target: The device that detects ions.
database_cross_reference: PSI:MS

instrument additional description
type: Class
definition: OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5.
has_obo_namespace: MS
id: MS:1000454
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: instrument additional description
annotated property: definition
annotated target: OBSOLETE Additional terms to describe the instrument as outlined in the mass spec doc, Appendix 1, section 1.5.
database_cross_reference: PSI:MS

ion selection attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: spectrum
definition: Ion selection properties that are associated with a value.
has_obo_namespace: MS
id: MS:1000455

Axiom
annotated source: ion selection attribute
annotated property: definition
annotated target: Ion selection properties that are associated with a value.
database_cross_reference: PSI:MS

precursor activation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
definition: Terms to describe the precursor activation.
has_exact_synonym: activation
has_obo_namespace: MS
id: MS:1000456

Axiom
annotated source: precursor activation
annotated property: definition
annotated target: Terms to describe the precursor activation.
database_cross_reference: PSI:MS

sample
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Terms to describe the sample.
has_obo_namespace: MS
id: MS:1000457

Axiom
annotated source: sample
annotated property: definition
annotated target: Terms to describe the sample.
database_cross_reference: PSI:MS

source
type: Class
subclass of: Restriction
  on property: part_of
  some values from: instrument
definition: Terms to describe the source.
has_obo_namespace: MS
id: MS:1000458

Axiom
annotated source: source
annotated property: definition
annotated target: Terms to describe the source.
database_cross_reference: PSI:MS

spectrum instrument description
type: Class
definition: OBSOLETE Terms used to describe the spectrum.
has_obo_namespace: MS
id: MS:1000459
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: spectrum instrument description
annotated property: definition
annotated target: OBSOLETE Terms used to describe the spectrum.
database_cross_reference: PSI:MS

unit
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: OBSOLETE Terms to describe units.
has_obo_namespace: MS
id: MS:1000460
comment: This term was made obsolete because it was redundant with the Unit Ontology term unit (UO:0000000).
deprecated: true

Axiom
annotated source: unit
annotated property: definition
annotated target: OBSOLETE Terms to describe units.
database_cross_reference: PSI:MS

additional description
type: Class
definition: OBSOLETE Terms to describe Additional.
has_obo_namespace: MS
id: MS:1000461
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: additional description
annotated property: definition
annotated target: OBSOLETE Terms to describe Additional.
database_cross_reference: PSI:MS

ion optics
type: Class
subclass of: Restriction
  on property: part_of
  some values from: instrument
definition: Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions.
has_obo_namespace: MS
id: MS:1000462

Axiom
annotated source: ion optics
annotated property: definition
annotated target: Device used in the construction of a mass spectrometer to focus, contain or otherwise manipulate ions.
database_cross_reference: PSI:MS

instrument
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Description of the instrument or the mass spectrometer.
has_exact_synonym: instrument configuration
has_obo_namespace: MS
id: MS:1000463

Axiom
annotated source: instrument
annotated property: definition
annotated target: Description of the instrument or the mass spectrometer.
database_cross_reference: PSI:MS

mass unit
type: Class
definition: OBSOLETE A unit of measurement for mass.
has_obo_namespace: MS
id: MS:1000464
comment: This term was made obsolete because it was redundant with Unit Ontology mass unit (UO:0000002).
deprecated: true

Axiom
annotated source: mass unit
annotated property: definition
annotated target: OBSOLETE A unit of measurement for mass.
database_cross_reference: PSI:MS

scan polarity
type: Class
subclass of: Restriction
  on property: part_of
  some values from: scan
definition: Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer.
has_obo_namespace: MS
id: MS:1000465

Axiom
annotated source: scan polarity
annotated property: definition
annotated target: Relative orientation of the electromagnetic field during the selection and detection of ions in the mass spectrometer.
database_cross_reference: PSI:MS

alternating
type: Class
definition: OBSOLETE Alternating.
has_obo_namespace: MS
id: MS:1000466
comment: This term was made obsolete because .
deprecated: true

Axiom
annotated source: alternating
annotated property: definition
annotated target: OBSOLETE Alternating.
database_cross_reference: PSI:MS

1200 series LC/MSD SL
type: Class
subclass of: ion trap
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000467

Axiom
annotated source: 1200 series LC/MSD SL
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6110 Quadrupole LC/MS
type: Class
subclass of: quadrupole
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000468

Axiom
annotated source: 6110 Quadrupole LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6120A Quadrupole LC/MS
type: Class
subclass of: quadrupole
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000469

Axiom
annotated source: 6120A Quadrupole LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6130 Quadrupole LC/MS
type: Class
subclass of: quadrupole
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000470

Axiom
annotated source: 6130 Quadrupole LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6140 Quadrupole LC/MS
type: Class
subclass of: quadrupole
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000471

Axiom
annotated source: 6140 Quadrupole LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6210 Time-of-Flight LC/MS
type: Class
subclass of: time-of-flight
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000472

Axiom
annotated source: 6210 Time-of-Flight LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6310 Ion Trap LC/MS
type: Class
subclass of: ion trap
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000473

Axiom
annotated source: 6310 Ion Trap LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6320 Ion Trap LC/MS
type: Class
subclass of: ion trap
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000474

Axiom
annotated source: 6320 Ion Trap LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6330 Ion Trap LC/MS
type: Class
subclass of: ion trap
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000475

Axiom
annotated source: 6330 Ion Trap LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6340 Ion Trap LC/MS
type: Class
subclass of: ion trap
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000476

Axiom
annotated source: 6340 Ion Trap LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6410 Triple Quadrupole LC/MS
type: Class
subclass of: Agilent instrument model
subclass of: MS_1003762
definition: 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.
has_exact_synonym: 6410 Triple Quad LC/MS
has_obo_namespace: MS
id: MS:1000477

Axiom
annotated source: 6410 Triple Quadrupole LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

1200 series LC/MSD VL
type: Class
subclass of: ion trap
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000478

Axiom
annotated source: 1200 series LC/MSD VL
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

purgatory
type: Class
definition: OBSOLETE Terms that will likely become obsolete unless there are wails of dissent.
has_obo_namespace: MS
id: MS:1000479
comment: The whole branch purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: purgatory
annotated property: definition
annotated target: OBSOLETE Terms that will likely become obsolete unless there are wails of dissent.
database_cross_reference: PSI:MS

mass analyzer attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: mass analyzer
definition: Analyzer properties that are associated with a value.
has_obo_namespace: MS
id: MS:1000480

Axiom
annotated source: mass analyzer attribute
annotated property: definition
annotated target: Analyzer properties that are associated with a value.
database_cross_reference: PSI:MS

detector attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: detector
definition: Detector attribute recognized as a value.
has_obo_namespace: MS
id: MS:1000481

Axiom
annotated source: detector attribute
annotated property: definition
annotated target: Detector attribute recognized as a value.
database_cross_reference: PSI:MS

source attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source
definition: Property of a source device that need a value.
has_obo_namespace: MS
id: MS:1000482

Axiom
annotated source: source attribute
annotated property: definition
annotated target: Property of a source device that need a value.
database_cross_reference: PSI:MS

Thermo Fisher Scientific instrument model
type: Class
subclass of: instrument model
definition: Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific.
has_obo_namespace: MS
has_related_synonym: Thermo Scientific
id: MS:1000483

Axiom
annotated source: Thermo Fisher Scientific instrument model
annotated property: definition
annotated target: Thermo Fisher Scientific instrument model. The company has gone through several names including Thermo Finnigan, Thermo Scientific.
database_cross_reference: PSI:MS

orbitrap
type: Class
subclass of: mass analyzer type
subclass of: MS_1003761
definition: 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.
has_obo_namespace: MS
id: MS:1000484

Axiom
annotated source: orbitrap
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

nanospray inlet
type: Class
subclass of: electrospray inlet
definition: Nanospray Inlet.
has_obo_namespace: MS
id: MS:1000485

Axiom
annotated source: nanospray inlet
annotated property: definition
annotated target: Nanospray Inlet.
database_cross_reference: PSI:MS

source potential
type: Class
subclass of: source attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Potential difference at the MS source in volts.
has_obo_namespace: MS
id: MS:1000486

Axiom
annotated source: source potential
annotated property: definition
annotated target: Potential difference at the MS source in volts.
database_cross_reference: PSI:MS

ion optics attribute
type: Class
subclass of: ion optics
definition: Ion optics involves components that help focus ion streams in mass spectrometry.
has_obo_namespace: MS
id: MS:1000487

Axiom
annotated source: ion optics attribute
annotated property: definition
annotated target: Ion optics involves components that help focus ion streams in mass spectrometry.
database_cross_reference: PSI:MS

Hitachi instrument model
type: Class
subclass of: instrument model
definition: Hitachi instrument model.
has_obo_namespace: MS
id: MS:1000488

Axiom
annotated source: Hitachi instrument model
annotated property: definition
annotated target: Hitachi instrument model.
database_cross_reference: PSI:MS

Varian instrument model
type: Class
subclass of: instrument model
definition: Varian instrument model.
has_obo_namespace: MS
id: MS:1000489

Axiom
annotated source: Varian instrument model
annotated property: definition
annotated target: Varian instrument model.
database_cross_reference: PSI:MS

Agilent instrument model
type: Class
subclass of: instrument model
definition: Agilent instrument model.
has_obo_namespace: MS
id: MS:1000490

Axiom
annotated source: Agilent instrument model
annotated property: definition
annotated target: Agilent instrument model.
database_cross_reference: PSI:MS

Dionex instrument model
type: Class
subclass of: instrument model
definition: Dionex instrument model.
has_obo_namespace: MS
id: MS:1000491

Axiom
annotated source: Dionex instrument model
annotated property: definition
annotated target: Dionex instrument model.
database_cross_reference: PSI:MS

Thermo Electron instrument model
type: Class
subclass of: Thermo Fisher Scientific instrument model
definition: Thermo Electron Corporation instrument model.
has_obo_namespace: MS
id: MS:1000492

Axiom
annotated source: Thermo Electron instrument model
annotated property: definition
annotated target: Thermo Electron Corporation instrument model.
database_cross_reference: PSI:MS

Finnigan MAT instrument model
type: Class
subclass of: Thermo Fisher Scientific instrument model
definition: Finnigan MAT instrument model.
has_obo_namespace: MS
id: MS:1000493

Axiom
annotated source: Finnigan MAT instrument model
annotated property: definition
annotated target: Finnigan MAT instrument model.
database_cross_reference: PSI:MS

Thermo Scientific instrument model
type: Class
subclass of: Thermo Fisher Scientific instrument model
definition: Thermo Scientific instrument model.
has_obo_namespace: MS
id: MS:1000494

Axiom
annotated source: Thermo Scientific instrument model
annotated property: definition
annotated target: Thermo Scientific instrument model.
database_cross_reference: PSI:MS

Applied Biosystems instrument model
type: Class
subclass of: instrument model
definition: Applied Biosystems instrument model.
has_exact_synonym: ABI
has_obo_namespace: MS
id: MS:1000495

Axiom
annotated source: Applied Biosystems instrument model
annotated property: definition
annotated target: Applied Biosystems instrument model.
database_cross_reference: PSI:MS

instrument attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: instrument
definition: Instrument properties that are associated with a value.
has_obo_namespace: MS
id: MS:1000496

Axiom
annotated source: instrument attribute
annotated property: definition
annotated target: Instrument properties that are associated with a value.
database_cross_reference: PSI:MS

zoom scan
type: Class
subclass of: scan attribute
definition: 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.
has_exact_synonym: enhanced resolution scan
has_obo_namespace: MS
id: MS:1000497

Axiom
annotated source: zoom scan
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

full scan
type: Class
definition: OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range.
has_obo_namespace: MS
id: MS:1000498
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: full scan
annotated property: definition
annotated target: OBSOLETE Feature of the ion trap mass spectrometer where MS data is acquired over a mass range.
database_cross_reference: PSI:MS

spectrum attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
definition: Nonphysical characteristic attributed to a spectrum.
has_obo_namespace: MS
id: MS:1000499

Axiom
annotated source: spectrum attribute
annotated property: definition
annotated target: Nonphysical characteristic attributed to a spectrum.
database_cross_reference: PSI:MS

scan window upper limit
type: Class
subclass of: selection window attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The upper m/z bound of a mass spectrometer scan window.
has_obo_namespace: MS
has_related_synonym: mzRangeStop
id: MS:1000500

Axiom
annotated source: scan window upper limit
annotated property: definition
annotated target: The upper m/z bound of a mass spectrometer scan window.
database_cross_reference: PSI:MS

scan window lower limit
type: Class
subclass of: selection window attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The lower m/z bound of a mass spectrometer scan window.
has_obo_namespace: MS
has_related_synonym: mzRangeStart
id: MS:1000501

Axiom
annotated source: scan window lower limit
annotated property: definition
annotated target: The lower m/z bound of a mass spectrometer scan window.
database_cross_reference: PSI:MS

dwell time
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The time spent gathering data across a peak.
has_obo_namespace: MS
has_related_synonym: Scan Duration
id: MS:1000502

Axiom
annotated source: dwell time
annotated property: definition
annotated target: The time spent gathering data across a peak.
database_cross_reference: PSI:MS

scan attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: scan
definition: Nonphysical characteristic attributed to a spectrum acquisition scan.
has_obo_namespace: MS
id: MS:1000503

Axiom
annotated source: scan attribute
annotated property: definition
annotated target: Nonphysical characteristic attributed to a spectrum acquisition scan.
database_cross_reference: PSI:MS

base peak m/z
type: Class
subclass of: MS_1003058
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: M/z value of the signal of highest intensity in the mass spectrum.
has_obo_namespace: MS
id: MS:1000504

Axiom
annotated source: base peak m/z
annotated property: definition
annotated target: M/z value of the signal of highest intensity in the mass spectrum.
database_cross_reference: PSI:MS

base peak intensity
type: Class
subclass of: MS_1003058
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
subclass of: Restriction
  on property: has_units
  some values from: UO_0000269
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The intensity of the greatest peak in the mass spectrum.
has_obo_namespace: MS
id: MS:1000505

Axiom
annotated source: base peak intensity
annotated property: definition
annotated target: The intensity of the greatest peak in the mass spectrum.
database_cross_reference: PSI:MS

ion role
type: Class
definition: OBSOLETE Ion Role.
has_obo_namespace: MS
id: MS:1000506
comment: This child of the former purgatory term ion was made obsolete.
deprecated: true

Axiom
annotated source: ion role
annotated property: definition
annotated target: OBSOLETE Ion Role.
database_cross_reference: PSI:MS

ion property
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MS_1002806
definition: Nonphysical characteristic attributed to an ion.
has_obo_namespace: MS
id: MS:1000507

Axiom
annotated source: ion property
annotated property: definition
annotated target: Nonphysical characteristic attributed to an ion.
database_cross_reference: PSI:MS

ion chemical type
type: Class
definition: OBSOLETE Ion Type.
has_obo_namespace: MS
id: MS:1000508
comment: This child of the former purgatory term ion was made obsolete.
deprecated: true

Axiom
annotated source: ion chemical type
annotated property: definition
annotated target: OBSOLETE Ion Type.
database_cross_reference: PSI:MS

activation energy
type: Class
subclass of: precursor activation attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000266
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Activation Energy.
has_obo_namespace: MS
id: MS:1000509

Axiom
annotated source: activation energy
annotated property: definition
annotated target: Activation Energy.
database_cross_reference: PSI:MS

precursor activation attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: precursor activation
definition: Precursor Activation Attribute.
has_obo_namespace: MS
id: MS:1000510

Axiom
annotated source: precursor activation attribute
annotated property: definition
annotated target: Precursor Activation Attribute.
database_cross_reference: PSI:MS

ms level
type: Class
subclass of: spectrum attribute
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Stage number achieved in a multi stage mass spectrometry acquisition.
has_obo_namespace: MS
id: MS:1000511

Axiom
annotated source: ms level
annotated property: definition
annotated target: Stage number achieved in a multi stage mass spectrometry acquisition.
database_cross_reference: PSI:MS

filter string
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A string unique to Thermo instrument describing instrument settings for the scan.
has_obo_namespace: MS
id: MS:1000512

Axiom
annotated source: filter string
annotated property: definition
annotated target: A string unique to Thermo instrument describing instrument settings for the scan.
database_cross_reference: PSI:MS

binary data array
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
subclass of: Restriction
  on property: part_of
  some values from: chromatogram
definition: A data array of values.
has_obo_namespace: MS
id: MS:1000513

Axiom
annotated source: binary data array
annotated property: definition
annotated target: A data array of values.
database_cross_reference: PSI:MS

m/z array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has_units
  some values from: m/z
definition: A data array of m/z values.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000514

Axiom
annotated source: m/z array
annotated property: definition
annotated target: A data array of m/z values.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: m/z array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: m/z array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

intensity array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
subclass of: Restriction
  on property: has_units
  some values from: UO_0000269
definition: A data array of intensity values.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000515

Axiom
annotated source: intensity array
annotated property: definition
annotated target: A data array of intensity values.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: intensity array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: intensity array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

charge array
type: Class
subclass of: binary data array
definition: A data array of charge values.
database_cross_reference: binary-data-type:MS:1000519
has_obo_namespace: MS
id: MS:1000516

Axiom
annotated source: charge array
annotated property: definition
annotated target: A data array of charge values.
database_cross_reference: PSI:MS

32-bit integer
type: Axiom
annotated source: charge array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000519

signal to noise array
type: Class
subclass of: binary data array
definition: A data array of signal-to-noise values.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000517

Axiom
annotated source: signal to noise array
annotated property: definition
annotated target: A data array of signal-to-noise values.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: signal to noise array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: signal to noise array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

binary data type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
subclass of: Restriction
  on property: part_of
  some values from: chromatogram
definition: Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float.
has_obo_namespace: MS
id: MS:1000518

Axiom
annotated source: binary data type
annotated property: definition
annotated target: Encoding type of binary data specifying the binary representation and precision, e.g. 64-bit float.
database_cross_reference: PSI:MS

32-bit integer
type: Class
subclass of: binary data type
definition: Signed 32-bit little-endian integer.
has_obo_namespace: MS
id: MS:1000519

Axiom
annotated source: 32-bit integer
annotated property: definition
annotated target: Signed 32-bit little-endian integer.
database_cross_reference: PSI:MS

16-bit float
type: Class
subclass of: binary data type
definition: OBSOLETE Signed 16-bit float.
has_obo_namespace: MS
id: MS:1000520
deprecated: true

Axiom
annotated source: 16-bit float
annotated property: definition
annotated target: OBSOLETE Signed 16-bit float.
database_cross_reference: PSI:MS

32-bit float
type: Class
subclass of: binary data type
definition: 32-bit precision little-endian floating point conforming to IEEE-754.
has_obo_namespace: MS
id: MS:1000521

Axiom
annotated source: 32-bit float
annotated property: definition
annotated target: 32-bit precision little-endian floating point conforming to IEEE-754.
database_cross_reference: PSI:MS

64-bit integer
type: Class
subclass of: binary data type
definition: Signed 64-bit little-endian integer.
has_obo_namespace: MS
id: MS:1000522

Axiom
annotated source: 64-bit integer
annotated property: definition
annotated target: Signed 64-bit little-endian integer.
database_cross_reference: PSI:MS

64-bit float
type: Class
subclass of: binary data type
definition: 64-bit precision little-endian floating point conforming to IEEE-754.
has_obo_namespace: MS
id: MS:1000523

Axiom
annotated source: 64-bit float
annotated property: definition
annotated target: 64-bit precision little-endian floating point conforming to IEEE-754.
database_cross_reference: PSI:MS

data file content
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source data file
definition: Describes the data content on the file.
has_obo_namespace: MS
id: MS:1000524

Axiom
annotated source: data file content
annotated property: definition
annotated target: Describes the data content on the file.
database_cross_reference: PSI:MS

spectrum representation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
definition: Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks.
has_obo_namespace: MS
id: MS:1000525

Axiom
annotated source: spectrum representation
annotated property: definition
annotated target: Way in which the spectrum is represented, either with regularly spaced data points or with a list of centroided peaks.
database_cross_reference: PSI:MS

Waters raw format
type: Class
subclass of: mass spectrometer file format
definition: Waters data file format found in a Waters RAW directory, generated from an MS acquisition.
has_obo_namespace: MS
id: MS:1000526

Axiom
annotated source: Waters raw format
annotated property: definition
annotated target: Waters data file format found in a Waters RAW directory, generated from an MS acquisition.
database_cross_reference: PSI:MS

highest observed m/z
type: Class
subclass of: chromatogram attribute
subclass of: MS_1003058
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Highest m/z value observed in the m/z array.
has_obo_namespace: MS
id: MS:1000527

Axiom
annotated source: highest observed m/z
annotated property: definition
annotated target: Highest m/z value observed in the m/z array.
database_cross_reference: PSI:MS

lowest observed m/z
type: Class
subclass of: chromatogram attribute
subclass of: MS_1003058
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Lowest m/z value observed in the m/z array.
has_obo_namespace: MS
id: MS:1000528

Axiom
annotated source: lowest observed m/z
annotated property: definition
annotated target: Lowest m/z value observed in the m/z array.
database_cross_reference: PSI:MS

instrument serial number
type: Class
subclass of: instrument attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Serial Number of the instrument.
has_obo_namespace: MS
id: MS:1000529

Axiom
annotated source: instrument serial number
annotated property: definition
annotated target: Serial Number of the instrument.
database_cross_reference: PSI:MS

file format conversion
type: Class
subclass of: data transformation
definition: Conversion of one file format to another.
has_obo_namespace: MS
id: MS:1000530

Axiom
annotated source: file format conversion
annotated property: definition
annotated target: Conversion of one file format to another.
database_cross_reference: PSI:MS

software
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Proteomics Standards Initiative Mass Spectrometry Vocabularies
definition: Software related to the recording or transformation of spectra.
has_obo_namespace: MS
id: MS:1000531

Axiom
annotated source: software
annotated property: definition
annotated target: Software related to the recording or transformation of spectra.
database_cross_reference: PSI:MS

Xcalibur
type: Class
subclass of: Thermo Finnigan software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: Thermo Finnigan software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000532

Axiom
annotated source: Xcalibur
annotated property: definition
annotated target: Thermo Finnigan software for data acquisition and analysis.
database_cross_reference: PSI:MS

Bioworks
type: Class
subclass of: Thermo Finnigan software
subclass of: analysis software
subclass of: data processing software
definition: Thermo Finnigan software for data analysis of peptides and proteins.
has_obo_namespace: MS
has_related_synonym: Bioworks Browser
id: MS:1000533

Axiom
annotated source: Bioworks
annotated property: definition
annotated target: Thermo Finnigan software for data analysis of peptides and proteins.
database_cross_reference: PSI:MS

MassLynx
type: Class
subclass of: Waters software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: Micromass software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000534

Axiom
annotated source: MassLynx
annotated property: definition
annotated target: Micromass software for data acquisition and analysis.
database_cross_reference: PSI:MS

FlexAnalysis
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker software for data analysis.
has_obo_namespace: MS
id: MS:1000535

Axiom
annotated source: FlexAnalysis
annotated property: definition
annotated target: Bruker software for data analysis.
database_cross_reference: PSI:MS

Data Explorer
type: Class
subclass of: Applied Biosystems software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000536

Axiom
annotated source: Data Explorer
annotated property: definition
annotated target: Applied Biosystems software for data acquisition and analysis.
database_cross_reference: PSI:MS

4700 Explorer
type: Class
subclass of: Applied Biosystems software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000537

Axiom
annotated source: 4700 Explorer
annotated property: definition
annotated target: Applied Biosystems software for data acquisition and analysis.
database_cross_reference: PSI:MS

massWolf
type: Class
subclass of: data processing software
definition: A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology.
has_exact_synonym: wolf
has_obo_namespace: MS
id: MS:1000538

Axiom
annotated source: massWolf
annotated property: definition
annotated target: A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology.
database_cross_reference: PSI:MS

Voyager Biospectrometry Workstation System
type: Class
subclass of: Applied Biosystems software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems MALDI-TOF data acquisition and analysis system.
has_obo_namespace: MS
id: MS:1000539

Axiom
annotated source: Voyager Biospectrometry Workstation System
annotated property: definition
annotated target: Applied Biosystems MALDI-TOF data acquisition and analysis system.
database_cross_reference: PSI:MS

FlexControl
type: Class
subclass of: Bruker software
subclass of: acquisition software
definition: Bruker software for data acquisition.
has_obo_namespace: MS
id: MS:1000540

Axiom
annotated source: FlexControl
annotated property: definition
annotated target: Bruker software for data acquisition.
database_cross_reference: PSI:MS

ReAdW
type: Class
subclass of: data processing software
definition: 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".
has_obo_namespace: MS
id: MS:1000541

Axiom
annotated source: ReAdW
annotated property: definition
annotated target: 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".
database_cross_reference: PSI:MS

MzStar
type: Class
subclass of: data processing software
definition: 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.
has_obo_namespace: MS
id: MS:1000542

Axiom
annotated source: MzStar
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

data processing action
type: Class
subclass of: data transformation
definition: Data processing attribute used to describe the type of data processing performed on the data file.
has_obo_namespace: MS
id: MS:1000543

Axiom
annotated source: data processing action
annotated property: definition
annotated target: Data processing attribute used to describe the type of data processing performed on the data file.
database_cross_reference: PSI:MS

Conversion to mzML
type: Class
subclass of: file format conversion
definition: Conversion of a file format to Proteomics Standards Initiative mzML file format.
has_obo_namespace: MS
id: MS:1000544

Axiom
annotated source: Conversion to mzML
annotated property: definition
annotated target: Conversion of a file format to Proteomics Standards Initiative mzML file format.
database_cross_reference: PSI:MS

Conversion to mzXML
type: Class
subclass of: file format conversion
definition: Conversion of a file format to Institute of Systems Biology mzXML file format.
has_obo_namespace: MS
id: MS:1000545

Axiom
annotated source: Conversion to mzXML
annotated property: definition
annotated target: Conversion of a file format to Institute of Systems Biology mzXML file format.
database_cross_reference: PSI:MS

Conversion to mzData
type: Class
subclass of: file format conversion
definition: Conversion of a file format to Proteomics Standards Initiative mzData file format.
has_obo_namespace: MS
id: MS:1000546

Axiom
annotated source: Conversion to mzData
annotated property: definition
annotated target: Conversion of a file format to Proteomics Standards Initiative mzData file format.
database_cross_reference: PSI:MS

object attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Object Attribute.
has_obo_namespace: MS
id: MS:1000547

Axiom
annotated source: object attribute
annotated property: definition
annotated target: Object Attribute.
database_cross_reference: PSI:MS

sample attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: sample
definition: Sample properties that are associated with a value.
has_obo_namespace: MS
id: MS:1000548

Axiom
annotated source: sample attribute
annotated property: definition
annotated target: Sample properties that are associated with a value.
database_cross_reference: PSI:MS

selection window attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: scan
definition: Selection window properties that are associated with a value.
has_obo_namespace: MS
id: MS:1000549

Axiom
annotated source: selection window attribute
annotated property: definition
annotated target: Selection window properties that are associated with a value.
database_cross_reference: PSI:MS

time unit
type: Class
definition: OBSOLETE Time Unit.
has_obo_namespace: MS
id: MS:1000550
comment: This term was made obsolete because it was redundant with the Unit Ontology term time unit (UO:0000003).
deprecated: true

Axiom
annotated source: time unit
annotated property: definition
annotated target: OBSOLETE Time Unit.
database_cross_reference: PSI:MS

Analyst
type: Class
subclass of: SCIEX software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition.
has_obo_namespace: MS
id: MS:1000551

Axiom
annotated source: Analyst
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition.
database_cross_reference: PSI:MS

maldi spot identifier
type: Class
definition: OBSOLETE Maldi Spot Identifier.
has_obo_namespace: MS
id: MS:1000552
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: maldi spot identifier
annotated property: definition
annotated target: OBSOLETE Maldi Spot Identifier.
database_cross_reference: PSI:MS

Trapper
type: Class
subclass of: data processing software
definition: A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology.
has_obo_namespace: MS
id: MS:1000553

Axiom
annotated source: Trapper
annotated property: definition
annotated target: A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology.
database_cross_reference: PSI:MS

LCQ Deca
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan LCQ Deca.
has_obo_namespace: MS
id: MS:1000554

Axiom
annotated source: LCQ Deca
annotated property: definition
annotated target: ThermoFinnigan LCQ Deca.
database_cross_reference: PSI:MS

LTQ Orbitrap Discovery
type: Class
subclass of: Thermo Scientific instrument model
definition: LTQ Orbitrap Discovery.
has_obo_namespace: MS
id: MS:1000555

Axiom
annotated source: LTQ Orbitrap Discovery
annotated property: definition
annotated target: LTQ Orbitrap Discovery.
database_cross_reference: PSI:MS

LTQ Orbitrap XL
type: Class
subclass of: Thermo Scientific instrument model
definition: LTQ Orbitrap XL.
has_obo_namespace: MS
id: MS:1000556

Axiom
annotated source: LTQ Orbitrap XL
annotated property: definition
annotated target: LTQ Orbitrap XL.
database_cross_reference: PSI:MS

LTQ FT Ultra
type: Class
subclass of: Thermo Scientific instrument model
definition: LTQ FT Ultra.
has_obo_namespace: MS
id: MS:1000557

Axiom
annotated source: LTQ FT Ultra
annotated property: definition
annotated target: LTQ FT Ultra.
database_cross_reference: PSI:MS

GC Quantum
type: Class
subclass of: Thermo Finnigan instrument model
definition: GC Quantum.
has_obo_namespace: MS
id: MS:1000558

Axiom
annotated source: GC Quantum
annotated property: definition
annotated target: GC Quantum.
database_cross_reference: PSI:MS

spectrum type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
definition: Spectrum type.
has_obo_namespace: MS
id: MS:1000559

Axiom
annotated source: spectrum type
annotated property: definition
annotated target: Spectrum type.
database_cross_reference: PSI:MS

mass spectrometer file format
type: Class
subclass of: file format
definition: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
has_obo_namespace: MS
id: MS:1000560

Axiom
annotated source: mass spectrometer file format
annotated property: definition
annotated target: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
database_cross_reference: PSI:MS

data file checksum type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source data file
definition: Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
has_obo_namespace: MS
id: MS:1000561

Axiom
annotated source: data file checksum type
annotated property: definition
annotated target: Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
database_cross_reference: PSI:MS

ABI WIFF format
type: Class
subclass of: mass spectrometer file format
definition: Applied Biosystems WIFF file format.
has_obo_namespace: MS
id: MS:1000562

Axiom
annotated source: ABI WIFF format
annotated property: definition
annotated target: Applied Biosystems WIFF file format.
database_cross_reference: PSI:MS

Thermo RAW format
type: Class
subclass of: mass spectrometer file format
definition: Thermo Scientific RAW file format.
has_obo_namespace: MS
id: MS:1000563

Axiom
annotated source: Thermo RAW format
annotated property: definition
annotated target: Thermo Scientific RAW file format.
database_cross_reference: PSI:MS

PSI mzData format
type: Class
subclass of: mass spectrometer file format
definition: Proteomics Standards Initiative mzData file format.
has_obo_namespace: MS
id: MS:1000564

Axiom
annotated source: PSI mzData format
annotated property: definition
annotated target: Proteomics Standards Initiative mzData file format.
database_cross_reference: PSI:MS

Micromass PKL format
type: Class
subclass of: mass spectrometer file format
definition: Micromass PKL file format.
has_obo_namespace: MS
id: MS:1000565

Axiom
annotated source: Micromass PKL format
annotated property: definition
annotated target: Micromass PKL file format.
database_cross_reference: PSI:MS

ISB mzXML format
type: Class
subclass of: mass spectrometer file format
definition: Institute of Systems Biology mzXML file format.
has_obo_namespace: MS
id: MS:1000566

Axiom
annotated source: ISB mzXML format
annotated property: definition
annotated target: Institute of Systems Biology mzXML file format.
database_cross_reference: PSI:MS

Bruker/Agilent YEP format
type: Class
subclass of: mass spectrometer file format
definition: Bruker/Agilent YEP file format.
has_obo_namespace: MS
id: MS:1000567

Axiom
annotated source: Bruker/Agilent YEP format
annotated property: definition
annotated target: Bruker/Agilent YEP file format.
database_cross_reference: PSI:MS

MD5
type: Class
subclass of: data file checksum type
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000568

Axiom
annotated source: MD5
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

SHA-1
type: Class
subclass of: data file checksum type
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000569

Axiom
annotated source: SHA-1
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

spectra combination
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
definition: Method used to combine the mass spectra.
has_obo_namespace: MS
id: MS:1000570

Axiom
annotated source: spectra combination
annotated property: definition
annotated target: Method used to combine the mass spectra.
database_cross_reference: PSI:MS

sum of spectra
type: Class
subclass of: spectra combination
definition: Spectra Sum.
has_obo_namespace: MS
id: MS:1000571

Axiom
annotated source: sum of spectra
annotated property: definition
annotated target: Spectra Sum.
database_cross_reference: PSI:MS

binary data compression type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum
subclass of: Restriction
  on property: part_of
  some values from: chromatogram
definition: Compression Type.
has_obo_namespace: MS
id: MS:1000572

Axiom
annotated source: binary data compression type
annotated property: definition
annotated target: Compression Type.
database_cross_reference: PSI:MS

median of spectra
type: Class
subclass of: spectra combination
definition: Spectra is combined by calculating the median of the spectra.
has_obo_namespace: MS
id: MS:1000573

Axiom
annotated source: median of spectra
annotated property: definition
annotated target: Spectra is combined by calculating the median of the spectra.
database_cross_reference: PSI:MS

zlib compression
type: Class
subclass of: binary data compression type
definition: Zlib.
has_obo_namespace: MS
id: MS:1000574

Axiom
annotated source: zlib compression
annotated property: definition
annotated target: Zlib.
database_cross_reference: PSI:MS

mean of spectra
type: Class
subclass of: spectra combination
definition: Spectra is combined by calculating the mean of the spectra.
has_obo_namespace: MS
id: MS:1000575

Axiom
annotated source: mean of spectra
annotated property: definition
annotated target: Spectra is combined by calculating the mean of the spectra.
database_cross_reference: PSI:MS

no compression
type: Class
subclass of: binary data compression type
definition: No Compression.
has_obo_namespace: MS
id: MS:1000576

Axiom
annotated source: no compression
annotated property: definition
annotated target: No Compression.
database_cross_reference: PSI:MS

source data file
type: Class
subclass of: spectrum attribute
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Data file from which an entity is sourced.
has_exact_synonym: source file
has_obo_namespace: MS
id: MS:1000577

Axiom
annotated source: source data file
annotated property: definition
annotated target: Data file from which an entity is sourced.
database_cross_reference: PSI:MS

LCQ Fleet
type: Class
subclass of: Thermo Finnigan instrument model
definition: LCQ Fleet.
has_obo_namespace: MS
id: MS:1000578

Axiom
annotated source: LCQ Fleet
annotated property: definition
annotated target: LCQ Fleet.
database_cross_reference: PSI:MS

MS1 spectrum
type: Class
subclass of: mass spectrum
definition: Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
has_exact_synonym: Q1 spectrum
has_exact_synonym: Q3 spectrum
has_exact_synonym: Single-Stage Mass Spectrometry
has_exact_synonym: full spectrum
has_obo_namespace: MS
id: MS:1000579

Axiom
annotated source: MS1 spectrum
annotated property: definition
annotated target: Mass spectrum created by a single-stage MS experiment or the first stage of a multi-stage experiment.
database_cross_reference: PSI:MS

MSn spectrum
type: Class
subclass of: mass spectrum
definition: 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.
has_exact_synonym: multiple-stage mass spectrometry spectrum
has_exact_synonym: nth generation product ion spectrum
has_exact_synonym: product ion spectrum
has_obo_namespace: MS
id: MS:1000580

Axiom
annotated source: MSn spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

CRM spectrum
type: Class
subclass of: mass spectrum
definition: 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.
has_obo_namespace: MS
id: MS:1000581

Axiom
annotated source: CRM spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

SIM spectrum
type: Class
subclass of: mass spectrum
definition: 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).
has_exact_synonym: MIM spectrum
has_exact_synonym: multiple ion monitoring spectrum
has_exact_synonym: selected ion monitoring spectrum
has_obo_namespace: MS
id: MS:1000582

Axiom
annotated source: SIM spectrum
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:MS

SRM spectrum
type: Class
subclass of: mass spectrum
definition: 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.
has_exact_synonym: MRM spectrum
has_exact_synonym: multiple reaction monitoring spectrum
has_exact_synonym: selected reaction monitoring spectrum
has_obo_namespace: MS
id: MS:1000583

Axiom
annotated source: SRM spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mzML format
type: Class
subclass of: mass spectrometer file format
definition: Proteomics Standards Initiative mzML file format.
has_obo_namespace: MS
id: MS:1000584

Axiom
annotated source: mzML format
annotated property: definition
annotated target: Proteomics Standards Initiative mzML file format.
database_cross_reference: PSI:MS

contact attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: Proteomics Standards Initiative Mass Spectrometry Vocabularies
definition: Details about a person or organization to contact in case of concern or discussion about the file.
has_obo_namespace: MS
id: MS:1000585

Axiom
annotated source: contact attribute
annotated property: definition
annotated target: Details about a person or organization to contact in case of concern or discussion about the file.
database_cross_reference: PSI:MS

contact name
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Name of the contact person or organization.
has_obo_namespace: MS
id: MS:1000586

Axiom
annotated source: contact name
annotated property: definition
annotated target: Name of the contact person or organization.
database_cross_reference: PSI:MS

contact address
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Postal address of the contact person or organization.
has_obo_namespace: MS
id: MS:1000587

Axiom
annotated source: contact address
annotated property: definition
annotated target: Postal address of the contact person or organization.
database_cross_reference: PSI:MS

contact URL
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Uniform Resource Locator related to the contact person or organization.
has_obo_namespace: MS
id: MS:1000588

Axiom
annotated source: contact URL
annotated property: definition
annotated target: Uniform Resource Locator related to the contact person or organization.
database_cross_reference: PSI:MS

contact email
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Email address of the contact person or organization.
has_obo_namespace: MS
id: MS:1000589

Axiom
annotated source: contact email
annotated property: definition
annotated target: Email address of the contact person or organization.
database_cross_reference: PSI:MS

contact affiliation
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Home institution of the contact person.
has_obo_namespace: MS
id: MS:1000590

Axiom
annotated source: contact affiliation
annotated property: definition
annotated target: Home institution of the contact person.
database_cross_reference: PSI:MS

MzWiff
type: Class
subclass of: data processing software
definition: 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.
has_obo_namespace: MS
id: MS:1000591

Axiom
annotated source: MzWiff
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

smoothing
type: Class
subclass of: data processing action
definition: 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.
has_obo_namespace: MS
id: MS:1000592

Axiom
annotated source: smoothing
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

baseline reduction
type: Class
subclass of: data processing action
definition: A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparison between intensities of m/z values.
has_obo_namespace: MS
id: MS:1000593

Axiom
annotated source: baseline reduction
annotated property: definition
annotated target: A process of removal of varying intensities generated due to variable energy absorption before further processing can take place. Baseline reduction facilitates meaningful comparison between intensities of m/z values.
database_cross_reference: PSI:MS

low intensity data point removal
type: Class
subclass of: data filtering
definition: The removal of very low intensity data points that are likely to be spurious noise rather than real signal.
has_exact_synonym: thresholding
has_obo_namespace: MS
id: MS:1000594

Axiom
annotated source: low intensity data point removal
annotated property: definition
annotated target: The removal of very low intensity data points that are likely to be spurious noise rather than real signal.
database_cross_reference: PSI:MS

time array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
definition: A data array of relative time offset values from a reference time.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000595

Axiom
annotated source: time array
annotated property: definition
annotated target: A data array of relative time offset values from a reference time.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: time array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: time array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

measurement method
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: An attribute of resolution when recording the detector response in absence of the analyte.
has_obo_namespace: MS
id: MS:1000596

Axiom
annotated source: measurement method
annotated property: definition
annotated target: An attribute of resolution when recording the detector response in absence of the analyte.
database_cross_reference: PSI:MS

ion optics type
type: Class
subclass of: ion optics
definition: The electrical potential used to impart kinetic energy to ions in a mass spectrometer.
has_obo_namespace: MS
id: MS:1000597

Axiom
annotated source: ion optics type
annotated property: definition
annotated target: The electrical potential used to impart kinetic energy to ions in a mass spectrometer.
database_cross_reference: PSI:MS

electron transfer dissociation
type: Class
subclass of: dissociation method
definition: 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.
has_exact_synonym: ETD
has_obo_namespace: MS
id: MS:1000598

Axiom
annotated source: electron transfer dissociation
annotated property: definition
annotated target: 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.
database_cross_reference: DOI:10.1073/pnas.0402700101
database_cross_reference: PMID:15210983
database_cross_reference: PSI:MS

pulsed q dissociation
type: Class
subclass of: dissociation method
definition: 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.
has_exact_synonym: PQD
has_obo_namespace: MS
id: MS:1000599

Axiom
annotated source: pulsed q dissociation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Proteios
type: Class
subclass of: analysis software
subclass of: data processing software
definition: Database application and analysis platform for proteomics.
has_obo_namespace: MS
id: MS:1000600

Axiom
annotated source: Proteios
annotated property: definition
annotated target: Database application and analysis platform for proteomics.
database_cross_reference: PSI:MS
database_cross_reference: source:http://www.proteios.org

ProteinLynx Global Server
type: Class
subclass of: Waters software
subclass of: analysis software
subclass of: data processing software
definition: Waters software for data analysis.
has_obo_namespace: MS
id: MS:1000601

Axiom
annotated source: ProteinLynx Global Server
annotated property: definition
annotated target: Waters software for data analysis.
database_cross_reference: PSI:MS

Shimadzu MALDI-TOF instrument model
type: Class
subclass of: Shimadzu instrument model
definition: Shimadzu MALDI-TOF instrument model.
has_obo_namespace: MS
id: MS:1000602

Axiom
annotated source: Shimadzu MALDI-TOF instrument model
annotated property: definition
annotated target: Shimadzu MALDI-TOF instrument model.
database_cross_reference: PSI:MS

Shimadzu Scientific Instruments instrument model
type: Class
subclass of: Shimadzu instrument model
definition: Shimadzu Scientific Instruments instrument model.
has_obo_namespace: MS
id: MS:1000603

Axiom
annotated source: Shimadzu Scientific Instruments instrument model
annotated property: definition
annotated target: Shimadzu Scientific Instruments instrument model.
database_cross_reference: PSI:MS

LCMS-IT-TOF
type: Class
subclass of: Shimadzu Scientific Instruments instrument model
definition: Shimadzu Scientific Instruments LCMS-IT-TOF MS.
has_obo_namespace: MS
id: MS:1000604

Axiom
annotated source: LCMS-IT-TOF
annotated property: definition
annotated target: Shimadzu Scientific Instruments LCMS-IT-TOF MS.
database_cross_reference: PSI:MS

LCMS-2010EV
type: Class
subclass of: Shimadzu Scientific Instruments instrument model
definition: Shimadzu Scientific Instruments LCMS-2010EV MS.
has_obo_namespace: MS
id: MS:1000605

Axiom
annotated source: LCMS-2010EV
annotated property: definition
annotated target: Shimadzu Scientific Instruments LCMS-2010EV MS.
database_cross_reference: PSI:MS

LCMS-2010A
type: Class
subclass of: Shimadzu Scientific Instruments instrument model
definition: Shimadzu Scientific Instruments LCMS-2010A MS.
has_obo_namespace: MS
id: MS:1000606

Axiom
annotated source: LCMS-2010A
annotated property: definition
annotated target: Shimadzu Scientific Instruments LCMS-2010A MS.
database_cross_reference: PSI:MS

AXIMA CFR MALDI-TOF
type: Class
subclass of: Shimadzu MALDI-TOF instrument model
definition: Shimadzu Biotech AXIMA CFR MALDI-TOF MS.
has_obo_namespace: MS
id: MS:1000607

Axiom
annotated source: AXIMA CFR MALDI-TOF
annotated property: definition
annotated target: Shimadzu Biotech AXIMA CFR MALDI-TOF MS.
database_cross_reference: PSI:MS

AXIMA-QIT
type: Class
subclass of: Shimadzu MALDI-TOF instrument model
definition: Shimadzu Biotech AXIMA-QIT MS.
has_obo_namespace: MS
id: MS:1000608

Axiom
annotated source: AXIMA-QIT
annotated property: definition
annotated target: Shimadzu Biotech AXIMA-QIT MS.
database_cross_reference: PSI:MS

AXIMA-CFR plus
type: Class
subclass of: Shimadzu MALDI-TOF instrument model
definition: Shimadzu Biotech AXIMA-CFR plus MS.
has_obo_namespace: MS
id: MS:1000609

Axiom
annotated source: AXIMA-CFR plus
annotated property: definition
annotated target: Shimadzu Biotech AXIMA-CFR plus MS.
database_cross_reference: PSI:MS

AXIMA Performance MALDI-TOF/TOF
type: Class
subclass of: Shimadzu MALDI-TOF instrument model
definition: Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS.
has_obo_namespace: MS
id: MS:1000610

Axiom
annotated source: AXIMA Performance MALDI-TOF/TOF
annotated property: definition
annotated target: Shimadzu Biotech AXIMA Performance MALDI-TOF/TOF MS.
database_cross_reference: PSI:MS

AXIMA Confidence MALDI-TOF
type: Class
subclass of: Shimadzu MALDI-TOF instrument model
definition: Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS.
has_obo_namespace: MS
id: MS:1000611

Axiom
annotated source: AXIMA Confidence MALDI-TOF
annotated property: definition
annotated target: Shimadzu Biotech AXIMA Confidence MALDI-TOF (curved field reflectron) MS.
database_cross_reference: PSI:MS

AXIMA Assurance Linear MALDI-TOF
type: Class
subclass of: Shimadzu MALDI-TOF instrument model
definition: Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS.
has_obo_namespace: MS
id: MS:1000612

Axiom
annotated source: AXIMA Assurance Linear MALDI-TOF
annotated property: definition
annotated target: Shimadzu Biotech AXIMA Assurance Linear MALDI-TOF MS.
database_cross_reference: PSI:MS

DTA format
type: Class
subclass of: mass spectrometer file format
definition: SEQUEST DTA file format.
has_obo_namespace: MS
id: MS:1000613

Axiom
annotated source: DTA format
annotated property: definition
annotated target: SEQUEST DTA file format.
database_cross_reference: PSI:MS

ProteinLynx Global Server mass spectrum XML format
type: Class
subclass of: mass spectrometer file format
definition: Peak list file format used by ProteinLynx Global Server.
has_obo_namespace: MS
id: MS:1000614

Axiom
annotated source: ProteinLynx Global Server mass spectrum XML format
annotated property: definition
annotated target: Peak list file format used by ProteinLynx Global Server.
database_cross_reference: PSI:MS

ProteoWizard software
type: Class
subclass of: analysis software
subclass of: data processing software
definition: ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb.
has_exact_synonym: pwiz
has_obo_namespace: MS
id: MS:1000615

Axiom
annotated source: ProteoWizard software
annotated property: definition
annotated target: ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb.
database_cross_reference: PSI:MS

preset scan configuration
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000616

Axiom
annotated source: preset scan configuration
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

wavelength array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has_units
  some values from: UO_0000018
definition: A data array of electromagnetic radiation wavelength values.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000617

Axiom
annotated source: wavelength array
annotated property: definition
annotated target: A data array of electromagnetic radiation wavelength values.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: wavelength array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: wavelength array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

highest observed wavelength
type: Class
subclass of: chromatogram attribute
subclass of: MS_1003058
subclass of: Restriction
  on property: has_units
  some values from: UO_0000018
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Highest wavelength observed in an EMR spectrum.
has_obo_namespace: MS
id: MS:1000618

Axiom
annotated source: highest observed wavelength
annotated property: definition
annotated target: Highest wavelength observed in an EMR spectrum.
database_cross_reference: PSI:MS

lowest observed wavelength
type: Class
subclass of: chromatogram attribute
subclass of: MS_1003058
subclass of: Restriction
  on property: has_units
  some values from: UO_0000018
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Lowest wavelength observed in an EMR spectrum.
has_obo_namespace: MS
id: MS:1000619

Axiom
annotated source: lowest observed wavelength
annotated property: definition
annotated target: Lowest wavelength observed in an EMR spectrum.
database_cross_reference: PSI:MS

PDA spectrum
type: Class
subclass of: data file content
subclass of: spectrum type
definition: OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum).
has_obo_namespace: MS
id: MS:1000620
comment: This term was made obsolete because it was replaced by absorption spectrum (MS:1000806).
deprecated: true

Axiom
annotated source: PDA spectrum
annotated property: definition
annotated target: OBSOLETE Spectrum generated from a photodiode array detector (ultraviolet/visible spectrum).
database_cross_reference: PSI:MS

photodiode array detector
type: Class
subclass of: array detector
definition: An array detector used to record spectra in the ultraviolet and visible region of light.
has_exact_synonym: PDA
has_obo_namespace: MS
id: MS:1000621

Axiom
annotated source: photodiode array detector
annotated property: definition
annotated target: An array detector used to record spectra in the ultraviolet and visible region of light.
database_cross_reference: PSI:MS

Surveyor PDA
type: Class
subclass of: Thermo Scientific instrument model
definition: Surveyor PDA.
has_obo_namespace: MS
id: MS:1000622

Axiom
annotated source: Surveyor PDA
annotated property: definition
annotated target: Surveyor PDA.
database_cross_reference: PSI:MS

Accela PDA
type: Class
subclass of: Thermo Scientific instrument model
definition: Accela PDA.
has_obo_namespace: MS
id: MS:1000623

Axiom
annotated source: Accela PDA
annotated property: definition
annotated target: Accela PDA.
database_cross_reference: PSI:MS

inductive detector
type: Class
subclass of: detector type
definition: Inductive detector.
has_exact_synonym: image current detector
has_obo_namespace: MS
id: MS:1000624

Axiom
annotated source: inductive detector
annotated property: definition
annotated target: Inductive detector.
database_cross_reference: PSI:MS

chromatogram
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Representation of a chromatographic separation attribute measurement versus time.
has_obo_namespace: MS
id: MS:1000625

Axiom
annotated source: chromatogram
annotated property: definition
annotated target: Representation of a chromatographic separation attribute measurement versus time.
database_cross_reference: PSI:MS

chromatogram type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: chromatogram
definition: Type of chromatogram measurement being represented.
has_obo_namespace: MS
id: MS:1000626

Axiom
annotated source: chromatogram type
annotated property: definition
annotated target: Type of chromatogram measurement being represented.
database_cross_reference: PSI:MS

selected ion current chromatogram
type: Class
subclass of: ion current chromatogram
definition: Representation of an array of the measurements of a specific single ion current versus time.
has_exact_synonym: SIC chromatogram
has_obo_namespace: MS
id: MS:1000627

Axiom
annotated source: selected ion current chromatogram
annotated property: definition
annotated target: Representation of an array of the measurements of a specific single ion current versus time.
database_cross_reference: PSI:MS

basepeak chromatogram
type: Class
subclass of: ion current chromatogram
definition: Representation of an array of the most intense peaks versus time.
has_obo_namespace: MS
id: MS:1000628

Axiom
annotated source: basepeak chromatogram
annotated property: definition
annotated target: Representation of an array of the most intense peaks versus time.
database_cross_reference: PSI:MS

low intensity threshold
type: Class
subclass of: data processing parameter
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
subclass of: Restriction
  on property: has_units
  some values from: UO_0000269
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Threshold below which some action is taken.
has_obo_namespace: MS
id: MS:1000629

Axiom
annotated source: low intensity threshold
annotated property: definition
annotated target: Threshold below which some action is taken.
database_cross_reference: PSI:MS

data processing parameter
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: Data processing parameter used in the data processing performed on the data file.
has_obo_namespace: MS
id: MS:1000630

Axiom
annotated source: data processing parameter
annotated property: definition
annotated target: Data processing parameter used in the data processing performed on the data file.
database_cross_reference: PSI:MS

high intensity threshold
type: Class
subclass of: data processing parameter
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
subclass of: Restriction
  on property: has_units
  some values from: UO_0000269
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Threshold above which some action is taken.
has_obo_namespace: MS
id: MS:1000631

Axiom
annotated source: high intensity threshold
annotated property: definition
annotated target: Threshold above which some action is taken.
database_cross_reference: PSI:MS

Q-Tof Premier
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Q-Tof Premier.
has_obo_namespace: MS
id: MS:1000632

Axiom
annotated source: Q-Tof Premier
annotated property: definition
annotated target: Waters oa-ToF based Q-Tof Premier.
database_cross_reference: PSI:MS

possible charge state
type: Class
subclass of: ion selection attribute
subclass of: Restriction
  on property: has value type
  some values from: int
definition: 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.
has_obo_namespace: MS
id: MS:1000633

Axiom
annotated source: possible charge state
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

DSQ
type: Class
subclass of: Thermo Finnigan instrument model
definition: ThermoFinnigan DSQ GC-MS.
has_obo_namespace: MS
id: MS:1000634

Axiom
annotated source: DSQ
annotated property: definition
annotated target: ThermoFinnigan DSQ GC-MS.
database_cross_reference: PSI:MS

ITQ 700
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific ITQ 700 GC-MS.
has_obo_namespace: MS
id: MS:1000635

Axiom
annotated source: ITQ 700
annotated property: definition
annotated target: Thermo Scientific ITQ 700 GC-MS.
database_cross_reference: PSI:MS

ITQ 900
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific ITQ 900 GC-MS.
has_obo_namespace: MS
id: MS:1000636

Axiom
annotated source: ITQ 900
annotated property: definition
annotated target: Thermo Scientific ITQ 900 GC-MS.
database_cross_reference: PSI:MS

ITQ 1100
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific ITQ 1100 GC-MS.
has_obo_namespace: MS
id: MS:1000637

Axiom
annotated source: ITQ 1100
annotated property: definition
annotated target: Thermo Scientific ITQ 1100 GC-MS.
database_cross_reference: PSI:MS

LTQ XL ETD
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific LTQ XL MS with ETD.
has_obo_namespace: MS
id: MS:1000638

Axiom
annotated source: LTQ XL ETD
annotated property: definition
annotated target: Thermo Scientific LTQ XL MS with ETD.
database_cross_reference: PSI:MS

LTQ Orbitrap XL ETD
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific LTQ Orbitrap XL MS with ETD.
has_obo_namespace: MS
id: MS:1000639

Axiom
annotated source: LTQ Orbitrap XL ETD
annotated property: definition
annotated target: Thermo Scientific LTQ Orbitrap XL MS with ETD.
database_cross_reference: PSI:MS

DFS
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific DFS HR GC-MS.
has_obo_namespace: MS
id: MS:1000640

Axiom
annotated source: DFS
annotated property: definition
annotated target: Thermo Scientific DFS HR GC-MS.
database_cross_reference: PSI:MS

DSQ II
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific DSQ II GC-MS.
has_obo_namespace: MS
id: MS:1000641

Axiom
annotated source: DSQ II
annotated property: definition
annotated target: Thermo Scientific DSQ II GC-MS.
database_cross_reference: PSI:MS

MALDI LTQ XL
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific MALDI LTQ XL MS.
has_obo_namespace: MS
id: MS:1000642

Axiom
annotated source: MALDI LTQ XL
annotated property: definition
annotated target: Thermo Scientific MALDI LTQ XL MS.
database_cross_reference: PSI:MS

MALDI LTQ Orbitrap
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific MALDI LTQ Orbitrap MS.
has_obo_namespace: MS
id: MS:1000643

Axiom
annotated source: MALDI LTQ Orbitrap
annotated property: definition
annotated target: Thermo Scientific MALDI LTQ Orbitrap MS.
database_cross_reference: PSI:MS

TSQ Quantum Access
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific TSQ Quantum Access MS.
has_obo_namespace: MS
id: MS:1000644

Axiom
annotated source: TSQ Quantum Access
annotated property: definition
annotated target: Thermo Scientific TSQ Quantum Access MS.
database_cross_reference: PSI:MS

Element XR
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific Element XR HR-ICP-MS.
has_obo_namespace: MS
id: MS:1000645

Axiom
annotated source: Element XR
annotated property: definition
annotated target: Thermo Scientific Element XR HR-ICP-MS.
database_cross_reference: PSI:MS

Element 2
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific Element 2 HR-ICP-MS.
has_obo_namespace: MS
id: MS:1000646

Axiom
annotated source: Element 2
annotated property: definition
annotated target: Thermo Scientific Element 2 HR-ICP-MS.
database_cross_reference: PSI:MS

Element GD
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific Element GD Glow Discharge MS.
has_obo_namespace: MS
id: MS:1000647

Axiom
annotated source: Element GD
annotated property: definition
annotated target: Thermo Scientific Element GD Glow Discharge MS.
database_cross_reference: PSI:MS

GC IsoLink
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific GC IsoLink Isotope Ratio MS.
has_obo_namespace: MS
id: MS:1000648

Axiom
annotated source: GC IsoLink
annotated property: definition
annotated target: Thermo Scientific GC IsoLink Isotope Ratio MS.
database_cross_reference: PSI:MS

Exactive
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific Exactive MS.
has_obo_namespace: MS
id: MS:1000649

Axiom
annotated source: Exactive
annotated property: definition
annotated target: Thermo Scientific Exactive MS.
database_cross_reference: PSI:MS

Proteome Discoverer
type: Class
subclass of: Thermo Finnigan software
subclass of: analysis software
subclass of: data processing software
definition: Thermo Scientific software for data analysis of peptides and proteins.
has_obo_namespace: MS
id: MS:1000650

Axiom
annotated source: Proteome Discoverer
annotated property: definition
annotated target: Thermo Scientific software for data analysis of peptides and proteins.
database_cross_reference: PSI:MS

3200 QTRAP
type: Class
subclass of: SCIEX instrument model
definition: SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200.
has_obo_namespace: MS
id: MS:1000651

Axiom
annotated source: 3200 QTRAP
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX QTRAP 3200.
database_cross_reference: PSI:MS

4800 Plus MALDI TOF/TOF
type: Class
subclass of: SCIEX instrument model
definition: SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer.
has_obo_namespace: MS
id: MS:1000652

Axiom
annotated source: 4800 Plus MALDI TOF/TOF
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX 4800 Plus MALDI TOF-TOF Analyzer.
database_cross_reference: PSI:MS

API 3200
type: Class
subclass of: SCIEX instrument model
definition: SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS.
has_obo_namespace: MS
id: MS:1000653

Axiom
annotated source: API 3200
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX API 3200 MS.
database_cross_reference: PSI:MS

API 5000
type: Class
subclass of: SCIEX instrument model
definition: SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS.
has_obo_namespace: MS
id: MS:1000654

Axiom
annotated source: API 5000
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX API 5000 MS.
database_cross_reference: PSI:MS

QSTAR Elite
type: Class
subclass of: SCIEX instrument model
definition: SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite.
has_obo_namespace: MS
id: MS:1000655

Axiom
annotated source: QSTAR Elite
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX QSTAR Elite.
database_cross_reference: PSI:MS

QSTAR Pulsar
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems|MDS SCIEX QSTAR Pulsar.
has_obo_namespace: MS
id: MS:1000656

Axiom
annotated source: QSTAR Pulsar
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX QSTAR Pulsar.
database_cross_reference: PSI:MS

QSTAR XL
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems|MDS SCIEX QSTAR XL.
has_obo_namespace: MS
id: MS:1000657

Axiom
annotated source: QSTAR XL
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX QSTAR XL.
database_cross_reference: PSI:MS

4800 Proteomics Analyzer
type: Class
subclass of: Applied Biosystems instrument model
definition: Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer.
has_obo_namespace: MS
id: MS:1000658

Axiom
annotated source: 4800 Proteomics Analyzer
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer.
database_cross_reference: PSI:MS

4000 Series Explorer Software
type: Class
subclass of: SCIEX software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: SCIEX or Applied Biosystems software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000659

Axiom
annotated source: 4000 Series Explorer Software
annotated property: definition
annotated target: SCIEX or Applied Biosystems software for data acquisition and analysis.
database_cross_reference: PSI:MS

Xevo MRT MS
type: Class
subclass of: Waters instrument model
definition: Waters Corporation Xevo MRT Mass Spectrometer.
has_obo_namespace: MS
id: MS:1000660

Axiom
annotated source: Xevo MRT MS
annotated property: definition
annotated target: Waters Corporation Xevo MRT Mass Spectrometer.
database_cross_reference: PSI:MS

GPS Explorer
type: Class
subclass of: SCIEX software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: SCIEX or Applied Biosystems software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000661

Axiom
annotated source: GPS Explorer
annotated property: definition
annotated target: SCIEX or Applied Biosystems software for data acquisition and analysis.
database_cross_reference: PSI:MS

LightSight Software
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification.
has_obo_namespace: MS
id: MS:1000662

Axiom
annotated source: LightSight Software
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification.
database_cross_reference: PSI:MS

ProteinPilot Software
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant.
has_obo_namespace: MS
id: MS:1000663

Axiom
annotated source: ProteinPilot Software
annotated property: definition
annotated target: SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant.
database_cross_reference: PSI:MS

TissueView Software
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for tissue imaging.
has_obo_namespace: MS
id: MS:1000664

Axiom
annotated source: TissueView Software
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for tissue imaging.
database_cross_reference: PSI:MS

MarkerView Software
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling.
has_obo_namespace: MS
id: MS:1000665

Axiom
annotated source: MarkerView Software
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling.
database_cross_reference: PSI:MS

MRMPilot Software
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for MRM assay development.
has_obo_namespace: MS
id: MS:1000666

Axiom
annotated source: MRMPilot Software
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for MRM assay development.
database_cross_reference: PSI:MS

BioAnalyst
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for bio-related data exploration.
has_obo_namespace: MS
id: MS:1000667

Axiom
annotated source: BioAnalyst
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for bio-related data exploration.
database_cross_reference: PSI:MS

Pro ID
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for protein identification.
has_obo_namespace: MS
id: MS:1000668

Axiom
annotated source: Pro ID
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for protein identification.
database_cross_reference: PSI:MS

Pro ICAT
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT.
has_obo_namespace: MS
id: MS:1000669

Axiom
annotated source: Pro ICAT
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT.
database_cross_reference: PSI:MS

Pro Quant
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ.
has_obo_namespace: MS
id: MS:1000670

Axiom
annotated source: Pro Quant
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ.
database_cross_reference: PSI:MS

Pro BLAST
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for MS-BLAST identification.
has_obo_namespace: MS
id: MS:1000671

Axiom
annotated source: Pro BLAST
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for MS-BLAST identification.
database_cross_reference: PSI:MS

Cliquid
type: Class
subclass of: SCIEX software
definition: SCIEX Cliquid software for data analysis and quantitation.
has_obo_namespace: MS
id: MS:1000672

Axiom
annotated source: Cliquid
annotated property: definition
annotated target: SCIEX Cliquid software for data analysis and quantitation.
database_cross_reference: PSI:MS

MIDAS Workflow Designer
type: Class
subclass of: SCIEX software
definition: Applied Biosystems|MDS SCIEX software for MRM assay development.
has_obo_namespace: MS
id: MS:1000673

Axiom
annotated source: MIDAS Workflow Designer
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for MRM assay development.
database_cross_reference: PSI:MS

MultiQuant
type: Class
subclass of: SCIEX software
subclass of: analysis software
subclass of: data processing software
definition: Applied Biosystems|MDS SCIEX software for MRM-based quantitation.
has_obo_namespace: MS
id: MS:1000674

Axiom
annotated source: MultiQuant
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for MRM-based quantitation.
database_cross_reference: PSI:MS

6220 Time-of-Flight LC/MS
type: Class
subclass of: time-of-flight
subclass of: Agilent instrument model
definition: 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.
has_obo_namespace: MS
id: MS:1000675

Axiom
annotated source: 6220 Time-of-Flight LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6510 Quadrupole Time-of-Flight LC/MS
type: Class
subclass of: Agilent instrument model
subclass of: MS_1003763
definition: 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.
has_obo_namespace: MS
id: MS:1000676

Axiom
annotated source: 6510 Quadrupole Time-of-Flight LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

6520A Quadrupole Time-of-Flight LC/MS
type: Class
subclass of: Agilent instrument model
subclass of: MS_1003763
definition: 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.
has_obo_namespace: MS
id: MS:1000677

Axiom
annotated source: 6520A Quadrupole Time-of-Flight LC/MS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

MassHunter Data Acquisition
type: Class
subclass of: Agilent software
subclass of: acquisition software
definition: Software for data acquisition of 6000 series instruments.
has_obo_namespace: MS
id: MS:1000678

Axiom
annotated source: MassHunter Data Acquisition
annotated property: definition
annotated target: Software for data acquisition of 6000 series instruments.
database_cross_reference: PSI:MS

MassHunter Easy Access
type: Class
subclass of: Agilent software
subclass of: acquisition software
definition: Software for open access data acquisition.
has_obo_namespace: MS
id: MS:1000679

Axiom
annotated source: MassHunter Easy Access
annotated property: definition
annotated target: Software for open access data acquisition.
database_cross_reference: PSI:MS

MassHunter Qualitative Analysis
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Software for data analysis of data from 6000 series instruments.
has_obo_namespace: MS
id: MS:1000680

Axiom
annotated source: MassHunter Qualitative Analysis
annotated property: definition
annotated target: Software for data analysis of data from 6000 series instruments.
database_cross_reference: PSI:MS

MassHunter Quantitative Analysis
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data.
has_obo_namespace: MS
id: MS:1000681

Axiom
annotated source: MassHunter Quantitative Analysis
annotated property: definition
annotated target: Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data.
database_cross_reference: PSI:MS

MassHunter Metabolite ID
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Software for identification of metabolites.
has_obo_namespace: MS
id: MS:1000682

Axiom
annotated source: MassHunter Metabolite ID
annotated property: definition
annotated target: Software for identification of metabolites.
database_cross_reference: PSI:MS

MassHunter BioConfirm
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Software for protein characterization.
has_obo_namespace: MS
id: MS:1000683

Axiom
annotated source: MassHunter BioConfirm
annotated property: definition
annotated target: Software for protein characterization.
database_cross_reference: PSI:MS

Genespring MS
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.
has_obo_namespace: MS
id: MS:1000684

Axiom
annotated source: Genespring MS
annotated property: definition
annotated target: Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.
database_cross_reference: PSI:MS

MassHunter Mass Profiler
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.
has_obo_namespace: MS
id: MS:1000685

Axiom
annotated source: MassHunter Mass Profiler
annotated property: definition
annotated target: Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.
database_cross_reference: PSI:MS

METLIN
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites.
has_obo_namespace: MS
id: MS:1000686

Axiom
annotated source: METLIN
annotated property: definition
annotated target: Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites.
database_cross_reference: PSI:MS

Spectrum Mill for MassHunter Workstation
type: Class
subclass of: Agilent software
subclass of: analysis software
subclass of: data processing software
definition: Software for protein identification and characterization of complex protein digest mixtures.
has_obo_namespace: MS
id: MS:1000687

Axiom
annotated source: Spectrum Mill for MassHunter Workstation
annotated property: definition
annotated target: Software for protein identification and characterization of complex protein digest mixtures.
database_cross_reference: PSI:MS

6300 Series Ion Trap Data Analysis Software
type: Class
subclass of: Agilent software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: Software for data analysis of 6300 series ion trap mass spectrometers.
has_obo_namespace: MS
id: MS:1000688

Axiom
annotated source: 6300 Series Ion Trap Data Analysis Software
annotated property: definition
annotated target: Software for data analysis of 6300 series ion trap mass spectrometers.
database_cross_reference: PSI:MS

Agilent software
type: Class
subclass of: software
definition: Agilent software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000689

Axiom
annotated source: Agilent software
annotated property: definition
annotated target: Agilent software for data acquisition and analysis.
database_cross_reference: PSI:MS

SCIEX software
type: Class
subclass of: software
definition: SCIEX or Applied Biosystems software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000690

Axiom
annotated source: SCIEX software
annotated property: definition
annotated target: SCIEX or Applied Biosystems software for data acquisition and analysis.
database_cross_reference: PSI:MS

Applied Biosystems software
type: Class
subclass of: software
definition: Applied Biosystems|MDS SCIEX software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000691

Axiom
annotated source: Applied Biosystems software
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX software for data acquisition and analysis.
database_cross_reference: PSI:MS

Bruker software
type: Class
subclass of: software
definition: Bruker software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000692

Axiom
annotated source: Bruker software
annotated property: definition
annotated target: Bruker software for data acquisition and analysis.
database_cross_reference: PSI:MS

Thermo Finnigan software
type: Class
subclass of: software
definition: Thermo Finnigan software for data acquisition and analysis.
has_obo_namespace: MS
has_related_synonym: Bioworks Browser
id: MS:1000693

Axiom
annotated source: Thermo Finnigan software
annotated property: definition
annotated target: Thermo Finnigan software for data acquisition and analysis.
database_cross_reference: PSI:MS

Waters software
type: Class
subclass of: software
definition: Waters software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1000694

Axiom
annotated source: Waters software
annotated property: definition
annotated target: Waters software for data acquisition and analysis.
database_cross_reference: PSI:MS

apex ultra
type: Class
subclass of: Bruker Daltonics apex series
definition: Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
has_obo_namespace: MS
id: MS:1000695

Axiom
annotated source: apex ultra
annotated property: definition
annotated target: Bruker Daltonics' apex ultra: ESI, MALDI, Nanospray, APCI, APPI, Qh-FT_ICR.
database_cross_reference: PSI:MS

autoflex III smartbeam
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' autoflex III smartbeam: MALDI TOF.
has_obo_namespace: MS
id: MS:1000696

Axiom
annotated source: autoflex III smartbeam
annotated property: definition
annotated target: Bruker Daltonics' autoflex III smartbeam: MALDI TOF.
database_cross_reference: PSI:MS

Bruker Daltonics HCT Series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' HCT Series.
has_obo_namespace: MS
id: MS:1000697

Axiom
annotated source: Bruker Daltonics HCT Series
annotated property: definition
annotated target: Bruker Daltonics' HCT Series.
database_cross_reference: PSI:MS

HCTultra
type: Class
subclass of: Bruker Daltonics HCT Series
definition: Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000698

Axiom
annotated source: HCTultra
annotated property: definition
annotated target: Bruker Daltonics' HCTultra: ESI TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

HCTultra PTM
type: Class
subclass of: Bruker Daltonics HCT Series
definition: Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR.
has_obo_namespace: MS
id: MS:1000699

Axiom
annotated source: HCTultra PTM
annotated property: definition
annotated target: Bruker Daltonics' HCTultra PTM: ESI TOF, Nanospray, APCI, APPI, PTR.
database_cross_reference: PSI:MS

HCTultra ETD II
type: Class
subclass of: Bruker Daltonics HCT Series
definition: Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD.
has_obo_namespace: MS
id: MS:1000700

Axiom
annotated source: HCTultra ETD II
annotated property: definition
annotated target: Bruker Daltonics' HCTultra ETD II: ESI Q-TOF, Nanospray, APCI, APPI, ETD.
database_cross_reference: PSI:MS

microflex LT
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' microflex LT: MALDI TOF.
has_obo_namespace: MS
id: MS:1000701

Axiom
annotated source: microflex LT
annotated property: definition
annotated target: Bruker Daltonics' microflex LT: MALDI TOF.
database_cross_reference: PSI:MS

micrOTOF
type: Class
subclass of: Bruker Daltonics micrOTOF series
definition: Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI.
has_obo_namespace: MS
id: MS:1000702

Axiom
annotated source: micrOTOF
annotated property: definition
annotated target: Bruker Daltonics' micrOTOF: ESI TOF, APCI, APPI.
database_cross_reference: PSI:MS

micrOTOF-Q
type: Class
subclass of: Bruker Daltonics micrOTOF series
definition: Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000703

Axiom
annotated source: micrOTOF-Q
annotated property: definition
annotated target: Bruker Daltonics' micrOTOF-Q: ESI Q-TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

micrOTOF-Q II
type: Class
subclass of: Bruker Daltonics micrOTOF series
definition: Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1000704

Axiom
annotated source: micrOTOF-Q II
annotated property: definition
annotated target: Bruker Daltonics' micrOTOF-Q II: ESI Q-TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

ultraflex III TOF/TOF
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF.
has_obo_namespace: MS
id: MS:1000705

Axiom
annotated source: ultraflex III TOF/TOF
annotated property: definition
annotated target: Bruker Daltonics' ultraflex III TOF/TOF: MALDI TOF.
database_cross_reference: PSI:MS

apexControl
type: Class
subclass of: Bruker software
subclass of: acquisition software
definition: Bruker software for data acquisition.
has_obo_namespace: MS
id: MS:1000706

Axiom
annotated source: apexControl
annotated property: definition
annotated target: Bruker software for data acquisition.
database_cross_reference: PSI:MS

BioTools
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker software for data analysis.
has_obo_namespace: MS
id: MS:1000707

Axiom
annotated source: BioTools
annotated property: definition
annotated target: Bruker software for data analysis.
database_cross_reference: PSI:MS

CLINPROT
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker CLINPROT software.
has_obo_namespace: MS
id: MS:1000708

Axiom
annotated source: CLINPROT
annotated property: definition
annotated target: Bruker CLINPROT software.
database_cross_reference: PSI:MS

CLINPROT micro
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker CLINPROT micro software.
has_obo_namespace: MS
id: MS:1000709

Axiom
annotated source: CLINPROT micro
annotated property: definition
annotated target: Bruker CLINPROT micro software.
database_cross_reference: PSI:MS

CLINPROT robot
type: Class
subclass of: Bruker software
definition: Bruker CLINPROT robot software.
has_obo_namespace: MS
id: MS:1000710

Axiom
annotated source: CLINPROT robot
annotated property: definition
annotated target: Bruker CLINPROT robot software.
database_cross_reference: PSI:MS

ClinProTools
type: Class
subclass of: Bruker software
definition: Bruker ClinProTools software.
has_obo_namespace: MS
id: MS:1000711

Axiom
annotated source: ClinProTools
annotated property: definition
annotated target: Bruker ClinProTools software.
database_cross_reference: PSI:MS

Compass
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker Compass software.
has_obo_namespace: MS
id: MS:1000712

Axiom
annotated source: Compass
annotated property: definition
annotated target: Bruker Compass software.
database_cross_reference: PSI:MS

Compass for HCT/esquire
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker Compass for HCT/esquire software.
has_obo_namespace: MS
id: MS:1000713

Axiom
annotated source: Compass for HCT/esquire
annotated property: definition
annotated target: Bruker Compass for HCT/esquire software.
database_cross_reference: PSI:MS

Compass for micrOTOF
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker Compass for micrOTOF software.
has_obo_namespace: MS
id: MS:1000714

Axiom
annotated source: Compass for micrOTOF
annotated property: definition
annotated target: Bruker Compass for micrOTOF software.
database_cross_reference: PSI:MS

Compass OpenAccess
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker compass OpenAccess software.
has_obo_namespace: MS
id: MS:1000715

Axiom
annotated source: Compass OpenAccess
annotated property: definition
annotated target: Bruker compass OpenAccess software.
database_cross_reference: PSI:MS

Compass Security Pack
type: Class
subclass of: Bruker software
definition: Bruker compass Security Pack software.
has_obo_namespace: MS
id: MS:1000716

Axiom
annotated source: Compass Security Pack
annotated property: definition
annotated target: Bruker compass Security Pack software.
database_cross_reference: PSI:MS

CompassXport
type: Class
subclass of: Bruker software
subclass of: data processing software
definition: Bruker stand-alone software for data conversion.
has_obo_namespace: MS
id: MS:1000717

Axiom
annotated source: CompassXport
annotated property: definition
annotated target: Bruker stand-alone software for data conversion.
database_cross_reference: PSI:MS

CompassXtract
type: Class
subclass of: Bruker software
subclass of: data processing software
definition: Bruker software library for data access.
has_obo_namespace: MS
id: MS:1000718

Axiom
annotated source: CompassXtract
annotated property: definition
annotated target: Bruker software library for data access.
database_cross_reference: PSI:MS

DataAnalysis
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker software for data analysis.
has_obo_namespace: MS
id: MS:1000719

Axiom
annotated source: DataAnalysis
annotated property: definition
annotated target: Bruker software for data analysis.
database_cross_reference: PSI:MS

dpControl
type: Class
subclass of: Bruker software
subclass of: acquisition software
definition: Bruker software for data acquisition.
has_obo_namespace: MS
id: MS:1000720

Axiom
annotated source: dpControl
annotated property: definition
annotated target: Bruker software for data acquisition.
database_cross_reference: PSI:MS

esquireControl
type: Class
subclass of: Bruker software
subclass of: acquisition software
definition: Bruker software for data acquisition.
has_obo_namespace: MS
id: MS:1000721

Axiom
annotated source: esquireControl
annotated property: definition
annotated target: Bruker software for data acquisition.
database_cross_reference: PSI:MS

flexImaging
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker software for data analysis.
has_obo_namespace: MS
id: MS:1000722

Axiom
annotated source: flexImaging
annotated property: definition
annotated target: Bruker software for data analysis.
database_cross_reference: PSI:MS

GENOLINK
type: Class
subclass of: Bruker software
definition: Bruker GENOLINK software.
has_obo_namespace: MS
id: MS:1000723

Axiom
annotated source: GENOLINK
annotated property: definition
annotated target: Bruker GENOLINK software.
database_cross_reference: PSI:MS

GenoTools
type: Class
subclass of: Bruker software
definition: Bruker GenoTools software.
has_obo_namespace: MS
id: MS:1000724

Axiom
annotated source: GenoTools
annotated property: definition
annotated target: Bruker GenoTools software.
database_cross_reference: PSI:MS

HCTcontrol
type: Class
subclass of: Bruker software
subclass of: acquisition software
definition: Bruker software for data acquisition.
has_obo_namespace: MS
id: MS:1000725

Axiom
annotated source: HCTcontrol
annotated property: definition
annotated target: Bruker software for data acquisition.
database_cross_reference: PSI:MS

micrOTOFcontrol
type: Class
subclass of: Bruker software
subclass of: acquisition software
definition: Bruker software for data acquisition.
has_obo_namespace: MS
id: MS:1000726

Axiom
annotated source: micrOTOFcontrol
annotated property: definition
annotated target: Bruker software for data acquisition.
database_cross_reference: PSI:MS

PolyTools
type: Class
subclass of: Bruker software
definition: Bruker PolyTools software.
has_obo_namespace: MS
id: MS:1000727

Axiom
annotated source: PolyTools
annotated property: definition
annotated target: Bruker PolyTools software.
database_cross_reference: PSI:MS

ProfileAnalysis
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker software for data analysis.
has_obo_namespace: MS
id: MS:1000728

Axiom
annotated source: ProfileAnalysis
annotated property: definition
annotated target: Bruker software for data analysis.
database_cross_reference: PSI:MS

PROTEINEER
type: Class
subclass of: Bruker software
definition: Bruker PROTEINEER software.
has_obo_namespace: MS
id: MS:1000729

Axiom
annotated source: PROTEINEER
annotated property: definition
annotated target: Bruker PROTEINEER software.
database_cross_reference: PSI:PI

PROTEINEER dp
type: Class
subclass of: Bruker software
definition: Bruker PROTEINEER dp software.
has_obo_namespace: MS
id: MS:1000730

Axiom
annotated source: PROTEINEER dp
annotated property: definition
annotated target: Bruker PROTEINEER dp software.
database_cross_reference: PSI:PI

PROTEINEER fc
type: Class
subclass of: Bruker software
definition: Bruker PROTEINEER fc software.
has_obo_namespace: MS
id: MS:1000731

Axiom
annotated source: PROTEINEER fc
annotated property: definition
annotated target: Bruker PROTEINEER fc software.
database_cross_reference: PSI:PI

PROTEINEER spII
type: Class
subclass of: Bruker software
definition: Bruker PROTEINEER spII software.
has_obo_namespace: MS
id: MS:1000732

Axiom
annotated source: PROTEINEER spII
annotated property: definition
annotated target: Bruker PROTEINEER spII software.
database_cross_reference: PSI:PI

PROTEINEER-LC
type: Class
subclass of: Bruker software
definition: Bruker PROTEINEER-LC software.
has_obo_namespace: MS
id: MS:1000733

Axiom
annotated source: PROTEINEER-LC
annotated property: definition
annotated target: Bruker PROTEINEER-LC software.
database_cross_reference: PSI:PI

ProteinScape
type: Class
subclass of: Bruker software
subclass of: analysis software
definition: Bruker ProteinScape software.
has_obo_namespace: MS
id: MS:1000734

Axiom
annotated source: ProteinScape
annotated property: definition
annotated target: Bruker ProteinScape software.
database_cross_reference: PSI:PI

PureDisk
type: Class
subclass of: Bruker software
definition: BrukerPureDisk software.
has_obo_namespace: MS
id: MS:1000735

Axiom
annotated source: PureDisk
annotated property: definition
annotated target: BrukerPureDisk software.
database_cross_reference: PSI:MS

QuantAnalysis
type: Class
subclass of: Bruker software
subclass of: analysis software
subclass of: data processing software
definition: Bruker software for data analysis.
has_obo_namespace: MS
id: MS:1000736

Axiom
annotated source: QuantAnalysis
annotated property: definition
annotated target: Bruker software for data analysis.
database_cross_reference: PSI:MS

spControl
type: Class
subclass of: Bruker software
subclass of: acquisition software
definition: Bruker software for data acquisition.
has_obo_namespace: MS
id: MS:1000737

Axiom
annotated source: spControl
annotated property: definition
annotated target: Bruker software for data acquisition.
database_cross_reference: PSI:MS

TargetAnalysis
type: Class
subclass of: Bruker software
definition: Bruker TargetAnalysis software.
has_obo_namespace: MS
id: MS:1000738

Axiom
annotated source: TargetAnalysis
annotated property: definition
annotated target: Bruker TargetAnalysis software.
database_cross_reference: PSI:MS

WARP-LC
type: Class
subclass of: Bruker software
subclass of: quantitation software name
definition: Bruker WARP-LC software.
has_obo_namespace: MS
id: MS:1000739

Axiom
annotated source: WARP-LC
annotated property: definition
annotated target: Bruker WARP-LC software.
database_cross_reference: PSI:MS

parameter file
type: Class
subclass of: mass spectrometer file format
definition: Parameter file used to configure the acquisition of raw data on the instrument.
has_obo_namespace: MS
id: MS:1000740

Axiom
annotated source: parameter file
annotated property: definition
annotated target: Parameter file used to configure the acquisition of raw data on the instrument.
database_cross_reference: PSI:MS

Conversion to dta
type: Class
subclass of: file format conversion
definition: Conversion to dta format.
has_obo_namespace: MS
id: MS:1000741

Axiom
annotated source: Conversion to dta
annotated property: definition
annotated target: Conversion to dta format.
database_cross_reference: PSI:MS

Bioworks SRF format
type: Class
subclass of: mass spectrometer file format
subclass of: intermediate analysis format
definition: Thermo Finnigan SRF file format.
has_obo_namespace: MS
id: MS:1000742

Axiom
annotated source: Bioworks SRF format
annotated property: definition
annotated target: Thermo Finnigan SRF file format.
database_cross_reference: PSI:MS

TSQ Quantum Ultra AM
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific TSQ Quantum Ultra AM.
has_obo_namespace: MS
id: MS:1000743

Axiom
annotated source: TSQ Quantum Ultra AM
annotated property: definition
annotated target: Thermo Scientific TSQ Quantum Ultra AM.
database_cross_reference: PSI:MS

selected ion m/z
type: Class
subclass of: ion selection attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Mass-to-charge ratio of an selected ion.
has_obo_namespace: MS
id: MS:1000744

Axiom
annotated source: selected ion m/z
annotated property: definition
annotated target: Mass-to-charge ratio of an selected ion.
database_cross_reference: PSI:MS

retention time alignment
type: Class
subclass of: data processing action
definition: The correction of the spectrum scan times, as used e.g. in label-free proteomics.
has_obo_namespace: MS
id: MS:1000745

Axiom
annotated source: retention time alignment
annotated property: definition
annotated target: The correction of the spectrum scan times, as used e.g. in label-free proteomics.
database_cross_reference: PSI:MS

high intensity data point removal
type: Class
subclass of: data filtering
definition: The removal of very high intensity data points.
has_obo_namespace: MS
id: MS:1000746

Axiom
annotated source: high intensity data point removal
annotated property: definition
annotated target: The removal of very high intensity data points.
database_cross_reference: PSI:MS

completion time
type: Class
subclass of: data processing parameter
subclass of: Restriction
  on property: has value type
  some values from: dateTime
definition: The time that a data processing action was finished.
has_obo_namespace: MS
id: MS:1000747

Axiom
annotated source: completion time
annotated property: definition
annotated target: The time that a data processing action was finished.
database_cross_reference: PSI:MS

SSQ 7000
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan SSQ 7000 MS.
has_obo_namespace: MS
id: MS:1000748

Axiom
annotated source: SSQ 7000
annotated property: definition
annotated target: ThermoFinnigan SSQ 7000 MS.
database_cross_reference: PSI:MS

TSQ 7000
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan TSQ 7000 MS.
has_obo_namespace: MS
id: MS:1000749

Axiom
annotated source: TSQ 7000
annotated property: definition
annotated target: ThermoFinnigan TSQ 7000 MS.
database_cross_reference: PSI:MS

TSQ
type: Class
subclass of: Finnigan MAT instrument model
definition: ThermoFinnigan TSQ MS.
has_obo_namespace: MS
id: MS:1000750

Axiom
annotated source: TSQ
annotated property: definition
annotated target: ThermoFinnigan TSQ MS.
database_cross_reference: PSI:MS

TSQ Quantum Ultra
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific TSQ Quantum Ultra.
has_obo_namespace: MS
id: MS:1000751

Axiom
annotated source: TSQ Quantum Ultra
annotated property: definition
annotated target: Thermo Scientific TSQ Quantum Ultra.
database_cross_reference: PSI:MS

TOPP software
type: Class
subclass of: analysis software
subclass of: data processing software
definition: TOPP (The OpenMS proteomics pipeline) software.
has_obo_namespace: MS
id: MS:1000752

Axiom
annotated source: TOPP software
annotated property: definition
annotated target: TOPP (The OpenMS proteomics pipeline) software.
database_cross_reference: PSI:MS

BaselineFilter
type: Class
subclass of: TOPP software
definition: Removes the baseline from profile spectra using a top-hat filter.
has_obo_namespace: MS
id: MS:1000753

Axiom
annotated source: BaselineFilter
annotated property: definition
annotated target: Removes the baseline from profile spectra using a top-hat filter.
database_cross_reference: PSI:MS

DBExporter
type: Class
subclass of: TOPP software
definition: Exports data from an OpenMS database to a file.
has_obo_namespace: MS
id: MS:1000754

Axiom
annotated source: DBExporter
annotated property: definition
annotated target: Exports data from an OpenMS database to a file.
database_cross_reference: PSI:MS

DBImporter
type: Class
subclass of: TOPP software
definition: Imports data to an OpenMS database.
has_obo_namespace: MS
id: MS:1000755

Axiom
annotated source: DBImporter
annotated property: definition
annotated target: Imports data to an OpenMS database.
database_cross_reference: PSI:MS

FileConverter
type: Class
subclass of: TOPP software
definition: Converts between different MS file formats.
has_obo_namespace: MS
id: MS:1000756

Axiom
annotated source: FileConverter
annotated property: definition
annotated target: Converts between different MS file formats.
database_cross_reference: PSI:MS

FileFilter
type: Class
subclass of: TOPP software
definition: Extracts or manipulates portions of data from peak, feature or consensus feature files.
has_obo_namespace: MS
id: MS:1000757

Axiom
annotated source: FileFilter
annotated property: definition
annotated target: Extracts or manipulates portions of data from peak, feature or consensus feature files.
database_cross_reference: PSI:MS

FileMerger
type: Class
subclass of: TOPP software
definition: Merges several MS files into one file.
has_obo_namespace: MS
id: MS:1000758

Axiom
annotated source: FileMerger
annotated property: definition
annotated target: Merges several MS files into one file.
database_cross_reference: PSI:MS

InternalCalibration
type: Class
subclass of: TOPP software
definition: Applies an internal calibration.
has_obo_namespace: MS
id: MS:1000759

Axiom
annotated source: InternalCalibration
annotated property: definition
annotated target: Applies an internal calibration.
database_cross_reference: PSI:MS

MapAligner
type: Class
subclass of: TOPP software
definition: OBSOLETE Corrects retention time distortions between maps.
has_obo_namespace: MS
id: MS:1000760
comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP map aligner' (MS:1002147) branch.
deprecated: true

Axiom
annotated source: MapAligner
annotated property: definition
annotated target: OBSOLETE Corrects retention time distortions between maps.
database_cross_reference: PSI:MS

MapNormalizer
type: Class
subclass of: TOPP software
definition: Normalizes peak intensities in an MS run.
has_obo_namespace: MS
id: MS:1000761

Axiom
annotated source: MapNormalizer
annotated property: definition
annotated target: Normalizes peak intensities in an MS run.
database_cross_reference: PSI:MS

NoiseFilter
type: Class
subclass of: TOPP software
definition: OBSOLETE Removes noise from profile spectra by using different smoothing techniques.
has_obo_namespace: MS
id: MS:1000762
comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP noise filter' (MS:1002131) branch.
deprecated: true

Axiom
annotated source: NoiseFilter
annotated property: definition
annotated target: OBSOLETE Removes noise from profile spectra by using different smoothing techniques.
database_cross_reference: PSI:MS

PeakPicker
type: Class
subclass of: TOPP software
definition: OBSOLETE Finds mass spectrometric peaks in profile mass spectra.
has_obo_namespace: MS
id: MS:1000763
comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP peak picker' (MS:1002134) branch.
deprecated: true

Axiom
annotated source: PeakPicker
annotated property: definition
annotated target: OBSOLETE Finds mass spectrometric peaks in profile mass spectra.
database_cross_reference: PSI:MS

Resampler
type: Class
subclass of: TOPP software
definition: Transforms an LC/MS map into a resampled map or a png image.
has_obo_namespace: MS
id: MS:1000764

Axiom
annotated source: Resampler
annotated property: definition
annotated target: Transforms an LC/MS map into a resampled map or a png image.
database_cross_reference: PSI:MS

SpectraFilter
type: Class
subclass of: TOPP software
definition: OBSOLETE Applies a filter to peak spectra.
has_obo_namespace: MS
id: MS:1000765
comment: This term was made obsolete, because it is replaced by the terms under the 'TOPP spectra filter' (MS:1002137) branch.
deprecated: true

Axiom
annotated source: SpectraFilter
annotated property: definition
annotated target: OBSOLETE Applies a filter to peak spectra.
database_cross_reference: PSI:MS

TOFCalibration
type: Class
subclass of: TOPP software
definition: Applies time of flight calibration.
has_obo_namespace: MS
id: MS:1000766

Axiom
annotated source: TOFCalibration
annotated property: definition
annotated target: Applies time of flight calibration.
database_cross_reference: PSI:MS

native spectrum identifier format
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source data file
definition: Describes how the native spectrum identifiers are formatted.
has_exact_synonym: nativeID format
has_obo_namespace: MS
id: MS:1000767

Axiom
annotated source: native spectrum identifier format
annotated property: definition
annotated target: Describes how the native spectrum identifiers are formatted.
database_cross_reference: PSI:MS

Thermo nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger.
has_obo_namespace: MS
id: MS:1000768

Axiom
annotated source: Thermo nativeID format
annotated property: definition
annotated target: Native format defined by controllerType=xsd:nonNegativeInteger controllerNumber=xsd:positiveInteger scan=xsd:positiveInteger.
database_cross_reference: PSI:MS

Waters nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000769

Axiom
annotated source: Waters nativeID format
annotated property: definition
annotated target: Native format defined by function=xsd:positiveInteger process=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

WIFF nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000770

Axiom
annotated source: WIFF nativeID format
annotated property: definition
annotated target: Native format defined by sample=xsd:nonNegativeInteger period=xsd:nonNegativeInteger cycle=xsd:nonNegativeInteger experiment=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

Bruker/Agilent YEP nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by scan=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000771

Axiom
annotated source: Bruker/Agilent YEP nativeID format
annotated property: definition
annotated target: Native format defined by scan=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

Bruker BAF nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by scan=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000772

Axiom
annotated source: Bruker BAF nativeID format
annotated property: definition
annotated target: Native format defined by scan=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

Bruker FID nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by file=xsd:IDREF.
has_obo_namespace: MS
id: MS:1000773
comment: The nativeID must be the same as the source file ID.

Axiom
annotated source: Bruker FID nativeID format
annotated property: definition
annotated target: Native format defined by file=xsd:IDREF.
database_cross_reference: PSI:MS

multiple peak list nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by index=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000774
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.

Axiom
annotated source: multiple peak list nativeID format
annotated property: definition
annotated target: Native format defined by index=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

single peak list nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by file=xsd:IDREF.
has_obo_namespace: MS
id: MS:1000775
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.

Axiom
annotated source: single peak list nativeID format
annotated property: definition
annotated target: Native format defined by file=xsd:IDREF.
database_cross_reference: PSI:MS

scan number only nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by scan=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000776
comment: Used for conversion from mzXML, or DTA folder where native scan numbers can be derived.

Axiom
annotated source: scan number only nativeID format
annotated property: definition
annotated target: Native format defined by scan=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

spectrum identifier nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by spectrum=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000777
comment: Used for conversion from mzData. The spectrum id attribute is referenced.

Axiom
annotated source: spectrum identifier nativeID format
annotated property: definition
annotated target: Native format defined by spectrum=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

charge state calculation
type: Class
subclass of: data processing action
definition: A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm.
has_obo_namespace: MS
id: MS:1000778

Axiom
annotated source: charge state calculation
annotated property: definition
annotated target: A process that infers the charge state of an MSn spectrum's precursor(s) by the application of some algorithm.
database_cross_reference: PSI:MS

below precursor intensity dominance charge state calculation
type: Class
subclass of: charge state calculation
definition: Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z.
has_obo_namespace: MS
id: MS:1000779

Axiom
annotated source: below precursor intensity dominance charge state calculation
annotated property: definition
annotated target: Infers charge state as single or ambiguously multiple by determining the fraction of intensity below the precursor m/z.
database_cross_reference: PSI:MS

precursor recalculation
type: Class
subclass of: data processing action
definition: A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions.
has_obo_namespace: MS
id: MS:1000780

Axiom
annotated source: precursor recalculation
annotated property: definition
annotated target: A process that recalculates existing precursor selected ions with one or more algorithmically determined precursor selected ions.
database_cross_reference: PSI:MS

msPrefix precursor recalculation
type: Class
subclass of: precursor recalculation
definition: Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans.
has_obo_namespace: MS
id: MS:1000781

Axiom
annotated source: msPrefix precursor recalculation
annotated property: definition
annotated target: Recalculates one or more precursor selected ions by peak detection in the isolation windows of high accuracy MS precursor scans.
database_cross_reference: PSI:MS

Savitzky-Golay smoothing
type: Class
subclass of: smoothing
definition: 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.
has_obo_namespace: MS
id: MS:1000782

Axiom
annotated source: Savitzky-Golay smoothing
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

LOWESS smoothing
type: Class
subclass of: smoothing
definition: 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.
has_obo_namespace: MS
id: MS:1000783

Axiom
annotated source: LOWESS smoothing
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Gaussian smoothing
type: Class
subclass of: smoothing
definition: Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function.
has_exact_synonym: Weierstrass transform
has_exact_synonym: binomial smoothing
has_obo_namespace: MS
id: MS:1000784

Axiom
annotated source: Gaussian smoothing
annotated property: definition
annotated target: Reduces intensity spikes by convolving the data with a one-dimensional Gaussian function.
database_cross_reference: PSI:MS

moving average smoothing
type: Class
subclass of: smoothing
definition: Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
has_exact_synonym: box smoothing
has_exact_synonym: boxcar smoothing
has_exact_synonym: sliding average smoothing
has_obo_namespace: MS
id: MS:1000785

Axiom
annotated source: moving average smoothing
annotated property: definition
annotated target: Reduces intensity spikes by averaging each point with two or more adjacent points. The more adjacent points that used, the stronger the smoothing effect.
database_cross_reference: PSI:MS

non-standard data array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
database_cross_reference: binary-data-type:MS:1000519
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000522
database_cross_reference: binary-data-type:MS:1000523
database_cross_reference: binary-data-type:MS:1001479
has_obo_namespace: MS
id: MS:1000786

Axiom
annotated source: non-standard data array
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

32-bit integer
type: Axiom
annotated source: non-standard data array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000519

32-bit float
type: Axiom
annotated source: non-standard data array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit integer
type: Axiom
annotated source: non-standard data array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000522

64-bit float
type: Axiom
annotated source: non-standard data array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

null-terminated ASCII string
type: Axiom
annotated source: non-standard data array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1001479

inclusive low intensity threshold
type: Class
subclass of: data processing parameter
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
subclass of: Restriction
  on property: has_units
  some values from: UO_0000269
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Threshold at or below which some action is taken.
has_obo_namespace: MS
id: MS:1000787

Axiom
annotated source: inclusive low intensity threshold
annotated property: definition
annotated target: Threshold at or below which some action is taken.
database_cross_reference: PSI:MS

inclusive high intensity threshold
type: Class
subclass of: data processing parameter
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
subclass of: Restriction
  on property: has_units
  some values from: UO_0000269
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Threshold at or above which some action is taken.
has_obo_namespace: MS
id: MS:1000788

Axiom
annotated source: inclusive high intensity threshold
annotated property: definition
annotated target: Threshold at or above which some action is taken.
database_cross_reference: PSI:MS

enhanced multiply charged spectrum
type: Class
subclass of: MS1 spectrum
definition: MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions.
has_obo_namespace: MS
id: MS:1000789

Axiom
annotated source: enhanced multiply charged spectrum
annotated property: definition
annotated target: MS1 spectrum that is enriched in multiply-charged ions compared to singly-charged ions.
database_cross_reference: PSI:MS

time-delayed fragmentation spectrum
type: Class
subclass of: MSn spectrum
definition: 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.
has_obo_namespace: MS
id: MS:1000790

Axiom
annotated source: time-delayed fragmentation spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

enhanced resolution scan
type: Class
definition: OBSOLETE Scan with enhanced resolution.
has_obo_namespace: MS
id: MS:1000791
comment: This term was made obsolete because it was merged with zoom scan (MS:1000497).
deprecated: true

Axiom
annotated source: enhanced resolution scan
annotated property: definition
annotated target: OBSOLETE Scan with enhanced resolution.
database_cross_reference: PSI:MS

isolation window attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: scan
definition: Isolation window parameter.
has_obo_namespace: MS
id: MS:1000792

Axiom
annotated source: isolation window attribute
annotated property: definition
annotated target: Isolation window parameter.
database_cross_reference: PSI:MS

isolation window upper limit
type: Class
subclass of: isolation window attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The highest m/z being isolated in an isolation window.
has_obo_namespace: MS
id: MS:1000793
comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.
deprecated: true

Axiom
annotated source: isolation window upper limit
annotated property: definition
annotated target: OBSOLETE The highest m/z being isolated in an isolation window.
database_cross_reference: PSI:MS

isolation window lower limit
type: Class
subclass of: isolation window attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The lowest m/z being isolated in an isolation window.
has_obo_namespace: MS
id: MS:1000794
comment: This term was obsoleted in favour of using a target, lower, upper offset scheme. See terms 1000827-1000829.
deprecated: true

Axiom
annotated source: isolation window lower limit
annotated property: definition
annotated target: OBSOLETE The lowest m/z being isolated in an isolation window.
database_cross_reference: PSI:MS

no combination
type: Class
subclass of: spectra combination
definition: Use this term if only one scan was recorded or there is no information about scans available.
has_obo_namespace: MS
id: MS:1000795

Axiom
annotated source: no combination
annotated property: definition
annotated target: Use this term if only one scan was recorded or there is no information about scans available.
database_cross_reference: PSI:MS

spectrum title
type: Class
subclass of: spectrum attribute
subclass of: spectrum identification result details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file.
has_obo_namespace: MS
id: MS:1000796
comment: This is the preferred storage place for the spectrum TITLE from an MGF peak list.

Axiom
annotated source: spectrum title
annotated property: definition
annotated target: Free-form text title describing a spectrum, usually a series of key value pairs as used in an MGF file.
database_cross_reference: PSI:MS

peak list scans
type: Class
subclass of: spectrum identification result details
subclass of: MS_1003058
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000797
comment: This is the preferred storage place for the spectrum SCANS attribute from an MGF peak list.

Axiom
annotated source: peak list scans
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

peak list raw scans
type: Class
subclass of: spectrum identification result details
subclass of: MS_1003058
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000798
comment: This is the preferred storage place for the spectrum RAWSCANS attribute from an MGF peak list.

Axiom
annotated source: peak list raw scans
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

custom unreleased software tool
type: Class
subclass of: software
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000799

Axiom
annotated source: custom unreleased software tool
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mass resolving power
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000800

Axiom
annotated source: mass resolving power
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

area peak picking
type: Class
subclass of: peak picking
definition: 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.
has_exact_synonym: sum peak picking
has_obo_namespace: MS
id: MS:1000801

Axiom
annotated source: area peak picking
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

height peak picking
type: Class
subclass of: peak picking
definition: 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.
has_exact_synonym: max peak picking
has_obo_namespace: MS
id: MS:1000802

Axiom
annotated source: height peak picking
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

analyzer scan offset
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value.
has_obo_namespace: MS
id: MS:1000803

Axiom
annotated source: analyzer scan offset
annotated property: definition
annotated target: Offset between two analyzers in a constant neutral loss or neutral gain scan. The value corresponds to the neutral loss or neutral gain value.
database_cross_reference: PSI:MS

electromagnetic radiation spectrum
type: Class
subclass of: data file content
subclass of: spectrum type
definition: A plot of the relative intensity of electromagnetic radiation as a function of the wavelength.
has_exact_synonym: EMR spectrum
has_obo_namespace: MS
id: MS:1000804

Axiom
annotated source: electromagnetic radiation spectrum
annotated property: definition
annotated target: A plot of the relative intensity of electromagnetic radiation as a function of the wavelength.
database_cross_reference: PSI:MS

emission spectrum
type: Class
subclass of: data file content
subclass of: spectrum type
definition: A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited.
has_obo_namespace: MS
id: MS:1000805

Axiom
annotated source: emission spectrum
annotated property: definition
annotated target: A plot of the relative intensity of electromagnetic radiation emitted by atoms or molecules when excited.
database_cross_reference: PSI:MS

absorption spectrum
type: Class
subclass of: data file content
subclass of: spectrum type
definition: A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited.
has_obo_namespace: MS
id: MS:1000806

Axiom
annotated source: absorption spectrum
annotated property: definition
annotated target: A plot of the relative intensity of electromagnetic radiation absorbed by atoms or molecules when excited.
database_cross_reference: PSI:MS

Th/s
type: Class
subclass of: UO_0000000
definition: Unit describing the scan rate of a spectrum in Thomson per second.
has_obo_namespace: MS
id: MS:1000807

Axiom
annotated source: Th/s
annotated property: definition
annotated target: Unit describing the scan rate of a spectrum in Thomson per second.
database_cross_reference: PSI:MS

chromatogram attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: chromatogram
definition: Chromatogram properties that are associated with a value.
has_obo_namespace: MS
id: MS:1000808

Axiom
annotated source: chromatogram attribute
annotated property: definition
annotated target: Chromatogram properties that are associated with a value.
database_cross_reference: PSI:MS

chromatogram title
type: Class
subclass of: chromatogram attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A free-form text title describing a chromatogram.
has_obo_namespace: MS
id: MS:1000809
comment: This is the preferred storage place for the spectrum title.

Axiom
annotated source: chromatogram title
annotated property: definition
annotated target: A free-form text title describing a chromatogram.
database_cross_reference: PSI:MS

ion current chromatogram
type: Class
subclass of: data file content
subclass of: chromatogram type
definition: Representation of the current of ions versus time.
has_obo_namespace: MS
id: MS:1000810

Axiom
annotated source: ion current chromatogram
annotated property: definition
annotated target: Representation of the current of ions versus time.
database_cross_reference: PSI:MS

electromagnetic radiation chromatogram
type: Class
subclass of: data file content
subclass of: chromatogram type
definition: Representation of electromagnetic properties versus time.
has_exact_synonym: EMR radiation chromatogram
has_obo_namespace: MS
id: MS:1000811

Axiom
annotated source: electromagnetic radiation chromatogram
annotated property: definition
annotated target: Representation of electromagnetic properties versus time.
database_cross_reference: PSI:MS

absorption chromatogram
type: Class
subclass of: electromagnetic radiation chromatogram
definition: Representation of light absorbed by the sample versus time.
has_obo_namespace: MS
id: MS:1000812

Axiom
annotated source: absorption chromatogram
annotated property: definition
annotated target: Representation of light absorbed by the sample versus time.
database_cross_reference: PSI:MS

emission chromatogram
type: Class
subclass of: electromagnetic radiation chromatogram
definition: Representation of light emitted by the sample versus time.
has_obo_namespace: MS
id: MS:1000813

Axiom
annotated source: emission chromatogram
annotated property: definition
annotated target: Representation of light emitted by the sample versus time.
database_cross_reference: PSI:MS

counts per second
type: Class
subclass of: intensity unit
definition: The number of counted events observed per second in one or a group of elements of a detector.
has_obo_namespace: MS
id: MS:1000814

Axiom
annotated source: counts per second
annotated property: definition
annotated target: The number of counted events observed per second in one or a group of elements of a detector.
database_cross_reference: PSI:MS

Bruker BAF format
type: Class
subclass of: mass spectrometer file format
definition: Bruker BAF raw file format.
has_obo_namespace: MS
id: MS:1000815

Axiom
annotated source: Bruker BAF format
annotated property: definition
annotated target: Bruker BAF raw file format.
database_cross_reference: PSI:MS

Bruker U2 format
type: Class
subclass of: mass spectrometer file format
definition: Bruker HyStar U2 file format.
has_obo_namespace: MS
id: MS:1000816

Axiom
annotated source: Bruker U2 format
annotated property: definition
annotated target: Bruker HyStar U2 file format.
database_cross_reference: PSI:MS

HyStar
type: Class
subclass of: Bruker software
definition: Bruker software for hyphenated experiments.
has_obo_namespace: MS
id: MS:1000817

Axiom
annotated source: HyStar
annotated property: definition
annotated target: Bruker software for hyphenated experiments.
database_cross_reference: PSI:MS

Acquity UPLC PDA
type: Class
subclass of: Waters instrument model
subclass of: photodiode array detector
definition: Acquity UPLC Photodiode Array Detector.
has_obo_namespace: MS
id: MS:1000818

Axiom
annotated source: Acquity UPLC PDA
annotated property: definition
annotated target: Acquity UPLC Photodiode Array Detector.
database_cross_reference: PSI:MS

Acquity UPLC FLR
type: Class
subclass of: Waters instrument model
subclass of: MS_1002308
definition: Acquity UPLC Fluorescence Detector.
has_obo_namespace: MS
id: MS:1000819

Axiom
annotated source: Acquity UPLC FLR
annotated property: definition
annotated target: Acquity UPLC Fluorescence Detector.
database_cross_reference: PSI:MS

flow rate array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has_units
  some values from: UO_0000271
definition: A data array of flow rate measurements.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000820

Axiom
annotated source: flow rate array
annotated property: definition
annotated target: A data array of flow rate measurements.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: flow rate array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: flow rate array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

pressure array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has_units
  some values from: UO_0000110
definition: A data array of pressure measurements.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000821

Axiom
annotated source: pressure array
annotated property: definition
annotated target: A data array of pressure measurements.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: pressure array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: pressure array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

temperature array
type: Class
subclass of: binary data array
subclass of: Restriction
  on property: has_units
  some values from: UO_0000012
subclass of: Restriction
  on property: has_units
  some values from: UO_0000027
definition: A data array of temperature measurements.
database_cross_reference: binary-data-type:MS:1000521
database_cross_reference: binary-data-type:MS:1000523
has_obo_namespace: MS
id: MS:1000822

Axiom
annotated source: temperature array
annotated property: definition
annotated target: A data array of temperature measurements.
database_cross_reference: PSI:MS

32-bit float
type: Axiom
annotated source: temperature array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000521

64-bit float
type: Axiom
annotated source: temperature array
annotated property: database_cross_reference
annotated target: binary-data-type:MS:1000523

Bruker U2 nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000823

Axiom
annotated source: Bruker U2 nativeID format
annotated property: definition
annotated target: Native format defined by declaration=xsd:nonNegativeInteger collection=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

no nativeID format
type: Class
subclass of: native spectrum identifier format
definition: No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format.
has_obo_namespace: MS
id: MS:1000824

Axiom
annotated source: no nativeID format
annotated property: definition
annotated target: No nativeID format indicates that the file tagged with this term does not contain spectra that can have a nativeID format.
database_cross_reference: PSI:MS

Bruker FID format
type: Class
subclass of: mass spectrometer file format
definition: Bruker FID file format.
has_obo_namespace: MS
id: MS:1000825

Axiom
annotated source: Bruker FID format
annotated property: definition
annotated target: Bruker FID file format.
database_cross_reference: PSI:MS

elution time
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography.
has_obo_namespace: MS
id: MS:1000826

Axiom
annotated source: elution time
annotated property: definition
annotated target: The time of elution from all used chromatographic columns (one or more) in the chromatographic separation step, relative to the start of the chromatography.
database_cross_reference: PSI:MS

isolation window target m/z
type: Class
subclass of: isolation window attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The primary or reference m/z about which the isolation window is defined.
has_obo_namespace: MS
id: MS:1000827

Axiom
annotated source: isolation window target m/z
annotated property: definition
annotated target: The primary or reference m/z about which the isolation window is defined.
database_cross_reference: PSI:MS

isolation window lower offset
type: Class
subclass of: isolation window attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000828

Axiom
annotated source: isolation window lower offset
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

isolation window upper offset
type: Class
subclass of: isolation window attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000829

Axiom
annotated source: isolation window upper offset
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

precision
type: Class
subclass of: mass analyzer attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has_units
  some values from: UO_0000169
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation.
has_obo_namespace: MS
id: MS:1000830
comment: See MS:1000014 for the related term of accuracy.

Axiom
annotated source: precision
annotated property: definition
annotated target: Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation.
database_cross_reference: PSI:MS

sample preparation
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: sample attribute
definition: Properties of the preparation steps which took place before the measurement was performed.
has_obo_namespace: MS
id: MS:1000831

Axiom
annotated source: sample preparation
annotated property: definition
annotated target: Properties of the preparation steps which took place before the measurement was performed.
database_cross_reference: PSI:MS

MALDI matrix application
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sample preparation
definition: Attributes to describe the technique how the sample is prepared with the matrix solution.
has_obo_namespace: MS
id: MS:1000832

Axiom
annotated source: MALDI matrix application
annotated property: definition
annotated target: Attributes to describe the technique how the sample is prepared with the matrix solution.
database_cross_reference: PSI:MS

matrix application type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MALDI matrix application
definition: Describes the technique how the matrix is put on the sample target.
has_obo_namespace: MS
id: MS:1000833

Axiom
annotated source: matrix application type
annotated property: definition
annotated target: Describes the technique how the matrix is put on the sample target.
database_cross_reference: PSI:MS

matrix solution
type: Class
subclass of: MALDI matrix application
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Describes the chemical solution used as matrix.
has_obo_namespace: MS
id: MS:1000834

Axiom
annotated source: matrix solution
annotated property: definition
annotated target: Describes the chemical solution used as matrix.
database_cross_reference: PSI:MS

matrix solution concentration
type: Class
subclass of: MALDI matrix application
subclass of: Restriction
  on property: has_units
  some values from: UO_0000175
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Concentration of the chemical solution used as matrix.
has_obo_namespace: MS
id: MS:1000835

Axiom
annotated source: matrix solution concentration
annotated property: definition
annotated target: Concentration of the chemical solution used as matrix.
database_cross_reference: PSI:MS

dried droplet MALDI matrix preparation
type: Class
subclass of: matrix application type
definition: Dried droplet in MALDI matrix preparation.
has_obo_namespace: MS
id: MS:1000836

Axiom
annotated source: dried droplet MALDI matrix preparation
annotated property: definition
annotated target: Dried droplet in MALDI matrix preparation.
database_cross_reference: PSI:MS

printed MALDI matrix preparation
type: Class
subclass of: matrix application type
definition: Printed MALDI matrix preparation.
has_obo_namespace: MS
id: MS:1000837

Axiom
annotated source: printed MALDI matrix preparation
annotated property: definition
annotated target: Printed MALDI matrix preparation.
database_cross_reference: PSI:MS

sprayed MALDI matrix preparation
type: Class
subclass of: matrix application type
definition: Sprayed MALDI matrix preparation.
has_obo_namespace: MS
id: MS:1000838

Axiom
annotated source: sprayed MALDI matrix preparation
annotated property: definition
annotated target: Sprayed MALDI matrix preparation.
database_cross_reference: PSI:MS

precoated MALDI sample plate
type: Class
subclass of: matrix application type
subclass of: sample plate type
definition: Precoated MALDI sample plate.
has_obo_namespace: MS
id: MS:1000839

Axiom
annotated source: precoated MALDI sample plate
annotated property: definition
annotated target: Precoated MALDI sample plate.
database_cross_reference: PSI:MS

laser
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source attribute
definition: 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.
has_obo_namespace: MS
id: MS:1000840

Axiom
annotated source: laser
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

laser attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: laser
definition: Laser properties that are associated with a value.
has_obo_namespace: MS
id: MS:1000841

Axiom
annotated source: laser attribute
annotated property: definition
annotated target: Laser properties that are associated with a value.
database_cross_reference: PSI:MS

laser type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: laser
definition: Type of laser used for desorption purpose.
has_obo_namespace: MS
id: MS:1000842

Axiom
annotated source: laser type
annotated property: definition
annotated target: Type of laser used for desorption purpose.
database_cross_reference: PSI:MS

wavelength
type: Class
subclass of: laser attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000018
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The distance between two peaks of the emitted laser beam.
has_obo_namespace: MS
id: MS:1000843
comment: This term was made obsolete because it was redundant with the Pato Ontology term wavelength (UO:0001242).
deprecated: true

Axiom
annotated source: wavelength
annotated property: definition
annotated target: OBSOLETE The distance between two peaks of the emitted laser beam.
database_cross_reference: PSI:MS

focus diameter x
type: Class
subclass of: laser attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000017
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Describes the diameter of the laser beam in x direction.
has_obo_namespace: MS
id: MS:1000844

Axiom
annotated source: focus diameter x
annotated property: definition
annotated target: Describes the diameter of the laser beam in x direction.
database_cross_reference: PSI:MS

focus diameter y
type: Class
subclass of: laser attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000017
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Describes the diameter of the laser beam in y direction.
has_obo_namespace: MS
id: MS:1000845

Axiom
annotated source: focus diameter y
annotated property: definition
annotated target: Describes the diameter of the laser beam in y direction.
database_cross_reference: PSI:MS

pulse energy
type: Class
subclass of: laser attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000112
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Describes output energy of the laser system. May be attenuated by filters or other means.
has_obo_namespace: MS
id: MS:1000846

Axiom
annotated source: pulse energy
annotated property: definition
annotated target: Describes output energy of the laser system. May be attenuated by filters or other means.
database_cross_reference: PSI:MS

pulse duration
type: Class
subclass of: laser attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000150
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Describes how long the laser beam was emitted from the laser device.
has_obo_namespace: MS
id: MS:1000847

Axiom
annotated source: pulse duration
annotated property: definition
annotated target: Describes how long the laser beam was emitted from the laser device.
database_cross_reference: PSI:MS

attenuation
type: Class
subclass of: laser attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Describes the reduction of the intensity of the laser beam energy.
has_obo_namespace: MS
id: MS:1000848

Axiom
annotated source: attenuation
annotated property: definition
annotated target: Describes the reduction of the intensity of the laser beam energy.
database_cross_reference: PSI:MS

impact angle
type: Class
subclass of: laser attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000185
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Describes the angle between the laser beam and the sample target.
has_obo_namespace: MS
id: MS:1000849

Axiom
annotated source: impact angle
annotated property: definition
annotated target: Describes the angle between the laser beam and the sample target.
database_cross_reference: PSI:MS

gas laser
type: Class
subclass of: laser type
definition: Laser which is powered by a gaseous medium.
has_obo_namespace: MS
id: MS:1000850

Axiom
annotated source: gas laser
annotated property: definition
annotated target: Laser which is powered by a gaseous medium.
database_cross_reference: PSI:MS

solid-state laser
type: Class
subclass of: laser type
definition: Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states.
has_obo_namespace: MS
id: MS:1000851

Axiom
annotated source: solid-state laser
annotated property: definition
annotated target: Solid state laser materials are commonly made by doping a crystalline solid host with ions that provide the required energy states.
database_cross_reference: PSI:MS

dye-laser
type: Class
subclass of: laser type
definition: Dye lasers use an organic dye as the gain medium.
has_obo_namespace: MS
id: MS:1000852

Axiom
annotated source: dye-laser
annotated property: definition
annotated target: Dye lasers use an organic dye as the gain medium.
database_cross_reference: PSI:MS

free electron laser
type: Class
subclass of: laser type
definition: Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term.
has_obo_namespace: MS
id: MS:1000853

Axiom
annotated source: free electron laser
annotated property: definition
annotated target: Free electron laser uses a relativistic electron beam as the lasing medium which move freely through a magnetic structure, hence the term.
database_cross_reference: PSI:MS

LTQ XL
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific LTQ XL MS.
has_obo_namespace: MS
id: MS:1000854

Axiom
annotated source: LTQ XL
annotated property: definition
annotated target: Thermo Scientific LTQ XL MS.
database_cross_reference: PSI:MS

LTQ Velos
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific LTQ Velos MS.
has_obo_namespace: MS
id: MS:1000855

Axiom
annotated source: LTQ Velos
annotated property: definition
annotated target: Thermo Scientific LTQ Velos MS.
database_cross_reference: PSI:MS

LTQ Velos/ETD
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific LTQ Velos MS with ETD.
has_exact_synonym: LTQ Velos ETD
has_obo_namespace: MS
id: MS:1000856

Axiom
annotated source: LTQ Velos/ETD
annotated property: definition
annotated target: Thermo Scientific LTQ Velos MS with ETD.
database_cross_reference: PSI:MS

run attribute
type: Class
subclass of: object attribute
definition: Properties of the described run.
has_obo_namespace: MS
id: MS:1000857

Axiom
annotated source: run attribute
annotated property: definition
annotated target: Properties of the described run.
database_cross_reference: PSI:MS

fraction identifier
type: Class
subclass of: run attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Identifier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information.
has_obo_namespace: MS
id: MS:1000858

Axiom
annotated source: fraction identifier
annotated property: definition
annotated target: Identifier string that describes the sample fraction. This identifier should contain the fraction number(s) or similar information.
database_cross_reference: PSI:MS

molecule
type: Class
subclass of: molecular entity
definition: Group of two or more atoms held together by chemical bonds.
has_obo_namespace: MS
id: MS:1000859

Axiom
annotated source: molecule
annotated property: definition
annotated target: Group of two or more atoms held together by chemical bonds.
database_cross_reference: https://en.wikipedia.org/wiki/Molecule

peptide
type: Class
subclass of: molecule
definition: A molecule of low molecular weight that is composed of two or more amino acid residues.
has_obo_namespace: MS
id: MS:1000860

Axiom
annotated source: peptide
annotated property: definition
annotated target: A molecule of low molecular weight that is composed of two or more amino acid residues.
database_cross_reference: PSI:MS

molecular entity property
type: Class
subclass of: Restriction
  on property: part_of
  some values from: molecular entity
definition: A physical characteristic of a molecular entity.
has_obo_namespace: MS
id: MS:1000861

Axiom
annotated source: molecular entity property
annotated property: definition
annotated target: A physical characteristic of a molecular entity.
database_cross_reference: PSI:MS

isoelectric point
type: Class
subclass of: molecular entity property
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The pH of a solution at which a charged molecule does not migrate in an electric field.
has_exact_synonym: pI
has_obo_namespace: MS
id: MS:1000862

Axiom
annotated source: isoelectric point
annotated property: definition
annotated target: The pH of a solution at which a charged molecule does not migrate in an electric field.
database_cross_reference: PSI:MS

predicted isoelectric point
type: Class
subclass of: isoelectric point
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
has_exact_synonym: predicted pI
has_obo_namespace: MS
id: MS:1000863

Axiom
annotated source: predicted isoelectric point
annotated property: definition
annotated target: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
database_cross_reference: PSI:MS

chemical formula
type: Class
subclass of: MS_1003033
definition: A combination of symbols used to express the chemical composition of a molecule.
has_obo_namespace: MS
id: MS:1000864

Axiom
annotated source: chemical formula
annotated property: definition
annotated target: A combination of symbols used to express the chemical composition of a molecule.
database_cross_reference: EDAM:0846

empirical formula
type: Class
subclass of: chemical formula
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A chemical formula which expresses the proportions of the elements present in a substance.
has_obo_namespace: MS
id: MS:1000865

Axiom
annotated source: empirical formula
annotated property: definition
annotated target: A chemical formula which expresses the proportions of the elements present in a substance.
database_cross_reference: PSI:MS

molecular formula
type: Class
subclass of: chemical formula
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
has_obo_namespace: MS
id: MS:1000866

Axiom
annotated source: molecular formula
annotated property: definition
annotated target: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
database_cross_reference: PSI:MS

structural formula
type: Class
subclass of: chemical formula
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
has_obo_namespace: MS
id: MS:1000867

Axiom
annotated source: structural formula
annotated property: definition
annotated target: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
database_cross_reference: PSI:MS

SMILES string
type: Class
subclass of: structural formula
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000868

Axiom
annotated source: SMILES string
annotated property: definition
annotated target: 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.
database_cross_reference: EDAM:2301

collision gas pressure
type: Class
subclass of: precursor activation attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000110
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The gas pressure of the collision gas used for collisional excitation.
has_obo_namespace: MS
id: MS:1000869

Axiom
annotated source: collision gas pressure
annotated property: definition
annotated target: The gas pressure of the collision gas used for collisional excitation.
database_cross_reference: PSI:MS

4000 QTRAP
type: Class
subclass of: SCIEX instrument model
definition: OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000.
has_obo_namespace: MS
id: MS:1000870
comment: This term was obsoleted because was redundant to MS:1000139.
deprecated: true

Axiom
annotated source: 4000 QTRAP
annotated property: definition
annotated target: OBSOLETE SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000.
database_cross_reference: PSI:MS

SRM software
type: Class
subclass of: software
definition: Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs.
has_obo_namespace: MS
id: MS:1000871

Axiom
annotated source: SRM software
annotated property: definition
annotated target: Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs.
database_cross_reference: PSI:MS

MaRiMba
type: Class
subclass of: SRM software
definition: Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
has_obo_namespace: MS
id: MS:1000872

Axiom
annotated source: MaRiMba
annotated property: definition
annotated target: Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.
database_cross_reference: http://tools.proteomecenter.org/wiki/index.php

peptide attribute calculation software
type: Class
subclass of: software
definition: Software used to predict or calculate numerical attributes of peptides.
has_obo_namespace: MS
id: MS:1000873

Axiom
annotated source: peptide attribute calculation software
annotated property: definition
annotated target: Software used to predict or calculate numerical attributes of peptides.
database_cross_reference: PSI:MS

SSRCalc
type: Class
subclass of: peptide attribute calculation software
definition: Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence.
has_obo_namespace: MS
id: MS:1000874

Axiom
annotated source: SSRCalc
annotated property: definition
annotated target: Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence.
database_cross_reference: http://hs2.proteome.ca/SSRCalc/SSRCalc.html

declustering potential
type: Class
subclass of: source attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Potential difference between the orifice and the skimmer in volts.
has_obo_namespace: MS
id: MS:1000875

Axiom
annotated source: declustering potential
annotated property: definition
annotated target: Potential difference between the orifice and the skimmer in volts.
database_cross_reference: PSI:MS

cone voltage
type: Class
subclass of: source attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Potential difference between the sampling cone/orifice in volts.
has_obo_namespace: MS
id: MS:1000876

Axiom
annotated source: cone voltage
annotated property: definition
annotated target: Potential difference between the sampling cone/orifice in volts.
database_cross_reference: PSI:MS

tube lens voltage
type: Class
subclass of: source attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Potential difference setting of the tube lens in volts.
has_obo_namespace: MS
id: MS:1000877

Axiom
annotated source: tube lens voltage
annotated property: definition
annotated target: Potential difference setting of the tube lens in volts.
database_cross_reference: PSI:MS

external reference identifier
type: Class
subclass of: MS_1002840
definition: An identifier/accession number to an external reference database.
has_obo_namespace: MS
id: MS:1000878

Axiom
annotated source: external reference identifier
annotated property: definition
annotated target: An identifier/accession number to an external reference database.
database_cross_reference: PSI:MS

PubMed identifier
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: integer
definition: A unique identifier for a publication in the PubMed database (MIR:00000015).
has_obo_namespace: MS
id: MS:1000879

Axiom
annotated source: PubMed identifier
annotated property: definition
annotated target: A unique identifier for a publication in the PubMed database (MIR:00000015).
database_cross_reference: PSI:MS

interchannel delay
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The duration of intervals between scanning, during which the instrument configuration is switched.
has_obo_namespace: MS
id: MS:1000880

Axiom
annotated source: interchannel delay
annotated property: definition
annotated target: The duration of intervals between scanning, during which the instrument configuration is switched.
database_cross_reference: PSI:MS

molecular entity
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Proteomics Standards Initiative Mass Spectrometry Vocabularies
definition: Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
has_obo_namespace: MS
id: MS:1000881

Axiom
annotated source: molecular entity
annotated property: definition
annotated target: Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
database_cross_reference: https://en.wikipedia.org/wiki/Molecular_entity

protein
type: Class
subclass of: molecule
definition: 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.
has_obo_namespace: MS
id: MS:1000882

Axiom
annotated source: protein
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

protein short name
type: Class
subclass of: protein attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
has_obo_namespace: MS
id: MS:1000883

Axiom
annotated source: protein short name
annotated property: definition
annotated target: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
database_cross_reference: PSI:MS

protein attribute
type: Class
subclass of: quantification object attribute
subclass of: Restriction
  on property: part_of
  some values from: protein
definition: A nonphysical characteristic attributed to a specific protein.
has_obo_namespace: MS
id: MS:1000884

Axiom
annotated source: protein attribute
annotated property: definition
annotated target: A nonphysical characteristic attributed to a specific protein.
database_cross_reference: PSI:MS

protein accession
type: Class
subclass of: protein attribute
subclass of: MS_1003046
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Identifier for a specific protein in a database.
has_obo_namespace: MS
id: MS:1000885

Axiom
annotated source: protein accession
annotated property: definition
annotated target: Identifier for a specific protein in a database.
database_cross_reference: PSI:MS

protein name
type: Class
subclass of: protein attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A long name describing the function of the protein.
has_obo_namespace: MS
id: MS:1000886

Axiom
annotated source: protein name
annotated property: definition
annotated target: A long name describing the function of the protein.
database_cross_reference: PSI:MS

peptide attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: peptide
definition: Nonphysical characteristic attributed to a peptide.
has_obo_namespace: MS
id: MS:1000887

Axiom
annotated source: peptide attribute
annotated property: definition
annotated target: Nonphysical characteristic attributed to a peptide.
database_cross_reference: PSI:MS

stripped peptide sequence
type: Class
subclass of: MS_1003050
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000888

Axiom
annotated source: stripped peptide sequence
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

peptidoform sequence
type: Class
subclass of: MS_1003050
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000889
comment: Make it more general as there are actually many other ways to display a modified peptide sequence.

Axiom
annotated source: peptidoform sequence
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

peptidoform labeling state
type: Class
subclass of: MS_1003050
definition: A state description of how a peptide might be isotopically or isobarically labelled.
has_obo_namespace: MS
id: MS:1000890

Axiom
annotated source: peptidoform labeling state
annotated property: definition
annotated target: A state description of how a peptide might be isotopically or isobarically labelled.
database_cross_reference: PSI:MS

heavy labeled peptidoform
type: Class
subclass of: peptidoform labeling state
definition: A peptide that has been created or labelled with some heavier-than-usual isotopes.
has_obo_namespace: MS
id: MS:1000891

Axiom
annotated source: heavy labeled peptidoform
annotated property: definition
annotated target: A peptide that has been created or labelled with some heavier-than-usual isotopes.
database_cross_reference: PSI:MS

unlabeled peptidoform
type: Class
subclass of: peptidoform labeling state
definition: A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
has_exact_synonym: light labeled peptide
has_obo_namespace: MS
id: MS:1000892

Axiom
annotated source: unlabeled peptidoform
annotated property: definition
annotated target: A peptide that has not been labelled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
database_cross_reference: PSI:MS

peptidoform group label
type: Class
subclass of: MS_1003050
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1000893

Axiom
annotated source: peptidoform group label
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

retention time
type: Class
subclass of: MS_1003050
subclass of: MS_1003295
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: A time interval from the start of chromatography when an analyte exits a chromatographic column.
has_obo_namespace: MS
id: MS:1000894

Axiom
annotated source: retention time
annotated property: definition
annotated target: A time interval from the start of chromatography when an analyte exits a chromatographic column.
database_cross_reference: PSI:MS

local retention time
type: Class
subclass of: retention time
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup.
has_obo_namespace: MS
id: MS:1000895

Axiom
annotated source: local retention time
annotated property: definition
annotated target: A time interval from the start of chromatography when an analyte exits an unspecified local chromatographic column and instrumental setup.
database_cross_reference: PSI:MS

normalized retention time
type: Class
subclass of: retention time
subclass of: MS_1003295
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup.
has_obo_namespace: MS
id: MS:1000896

Axiom
annotated source: normalized retention time
annotated property: definition
annotated target: A time interval from the start of chromatography when an analyte exits a standardized reference chromatographic column and instrumental setup.
database_cross_reference: PSI:MS

predicted retention time
type: Class
subclass of: retention time
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application.
has_obo_namespace: MS
id: MS:1000897

Axiom
annotated source: predicted retention time
annotated property: definition
annotated target: A time interval from the start of chromatography when an analyte exits a chromatographic column as predicted by a referenced software application.
database_cross_reference: PSI:MS

standard
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Proteomics Standards Initiative Mass Spectrometry Vocabularies
definition: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
has_obo_namespace: MS
id: MS:1000898

Axiom
annotated source: standard
annotated property: definition
annotated target: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
database_cross_reference: PSI:MS

de facto standard
type: Class
subclass of: standard
definition: 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.
has_obo_namespace: MS
id: MS:1000899

Axiom
annotated source: de facto standard
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

minimum information standard
type: Class
subclass of: standard
definition: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
has_obo_namespace: MS
id: MS:1000900

Axiom
annotated source: minimum information standard
annotated property: definition
annotated target: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
database_cross_reference: PSI:MS

retention time normalization standard
type: Class
subclass of: standard
definition: A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column.
has_obo_namespace: MS
id: MS:1000901

Axiom
annotated source: retention time normalization standard
annotated property: definition
annotated target: A standard providing the retention times at which a set of reference compounds exit the reference chromatographic column.
database_cross_reference: PSI:MS

H-PINS retention time normalization standard
type: Class
subclass of: retention time normalization standard
definition: The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column.
has_obo_namespace: MS
id: MS:1000902

Axiom
annotated source: H-PINS retention time normalization standard
annotated property: definition
annotated target: The de facto standard providing the retention times at which a set of halogenated reference peptides exit the reference chromatographic column.
database_cross_reference: DOI:10.1074/mcp.M800569-MCP200
database_cross_reference: PMID:19411281

product ion series ordinal
type: Class
subclass of: product ion attribute
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion).
has_obo_namespace: MS
id: MS:1000903

Axiom
annotated source: product ion series ordinal
annotated property: definition
annotated target: The ordinal of the fragment within a specified ion series. (e.g. 8 for a y8 ion).
database_cross_reference: PSI:PI

product ion m/z delta
type: Class
subclass of: product ion attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
definition: The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z.
has_obo_namespace: MS
id: MS:1000904

Axiom
annotated source: product ion m/z delta
annotated property: definition
annotated target: The difference in m/z of the predicted m/z based on the assigned product ion minus the actual observed peak m/z.
database_cross_reference: PSI:PI

percent of base peak times 100
type: Class
subclass of: intensity unit
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000905

Axiom
annotated source: percent of base peak times 100
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

peak intensity rank
type: Class
subclass of: ion selection attribute
subclass of: Restriction
  on property: part_of
  some values from: peak
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc.
has_obo_namespace: MS
id: MS:1000906

Axiom
annotated source: peak intensity rank
annotated property: definition
annotated target: Ordinal specifying the rank in intensity of a peak in a spectrum. Base peak is 1. The next most intense peak is 2, etc.
database_cross_reference: PSI:MS

peak targeting suitability rank
type: Class
subclass of: ion selection attribute
subclass of: Restriction
  on property: part_of
  some values from: peak
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: 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 suitable peak is 2, etc. Suitability is algorithm and context dependent.
has_obo_namespace: MS
id: MS:1000907

Axiom
annotated source: peak targeting suitability rank
annotated property: definition
annotated target: 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 suitable peak is 2, etc. Suitability is algorithm and context dependent.
database_cross_reference: PSI:MS

transition
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: 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.
has_exact_synonym: reaction
has_obo_namespace: MS
id: MS:1000908

Axiom
annotated source: transition
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

transition validation method
type: Class
subclass of: Restriction
  on property: part_of
  some values from: transition
definition: The strategy used to validate that a transition is effective.
has_obo_namespace: MS
id: MS:1000909

Axiom
annotated source: transition validation method
annotated property: definition
annotated target: The strategy used to validate that a transition is effective.
database_cross_reference: PSI:MS

transition optimized on specified instrument
type: Class
subclass of: transition validation method
definition: 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.
has_obo_namespace: MS
id: MS:1000910

Axiom
annotated source: transition optimized on specified instrument
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

transition validated with an MS/MS spectrum on specified instrument
type: Class
subclass of: transition validation method
definition: 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.
has_obo_namespace: MS
id: MS:1000911

Axiom
annotated source: transition validated with an MS/MS spectrum on specified instrument
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

transition purported from an MS/MS spectrum on a different, specified instrument
type: Class
subclass of: transition validation method
definition: 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).
has_obo_namespace: MS
id: MS:1000912

Axiom
annotated source: transition purported from an MS/MS spectrum on a different, specified instrument
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:MS

transition predicted by informatic analysis
type: Class
subclass of: transition validation method
definition: The transition has been predicted by informatics software without any direct spectral evidence.
has_obo_namespace: MS
id: MS:1000913

Axiom
annotated source: transition predicted by informatic analysis
annotated property: definition
annotated target: The transition has been predicted by informatics software without any direct spectral evidence.
database_cross_reference: PSI:MS

tab delimited text format
type: Class
subclass of: intermediate analysis format
subclass of: file format
definition: A file format that has two or more columns of tabular data where each column is separated by a TAB character.
has_obo_namespace: MS
id: MS:1000914

Axiom
annotated source: tab delimited text format
annotated property: definition
annotated target: A file format that has two or more columns of tabular data where each column is separated by a TAB character.
database_cross_reference: PSI:MS

retention time window attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: retention time
definition: An attribute of a window in time about which a peptide might elute from the column.
has_obo_namespace: MS
id: MS:1000915

Axiom
annotated source: retention time window attribute
annotated property: definition
annotated target: An attribute of a window in time about which a peptide might elute from the column.
database_cross_reference: PSI:MS

retention time window lower offset
type: Class
subclass of: retention time window attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000916

Axiom
annotated source: retention time window lower offset
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

retention time window upper offset
type: Class
subclass of: retention time window attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1000917

Axiom
annotated source: retention time window upper offset
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

target list
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
definition: 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.
has_obo_namespace: MS
id: MS:1000918

Axiom
annotated source: target list
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

target inclusion exclusion priority
type: Class
subclass of: Restriction
  on property: part_of
  some values from: target list
definition: A priority setting specifying whether included or excluded targets have priority over the other.
has_obo_namespace: MS
id: MS:1000919

Axiom
annotated source: target inclusion exclusion priority
annotated property: definition
annotated target: A priority setting specifying whether included or excluded targets have priority over the other.
database_cross_reference: PSI:MS

includes supersede excludes
type: Class
subclass of: target inclusion exclusion priority
definition: A priority setting specifying that included targets have priority over the excluded targets if there is a conflict.
has_obo_namespace: MS
id: MS:1000920

Axiom
annotated source: includes supersede excludes
annotated property: definition
annotated target: A priority setting specifying that included targets have priority over the excluded targets if there is a conflict.
database_cross_reference: PSI:MS

excludes supersede includes
type: Class
subclass of: target inclusion exclusion priority
definition: A priority setting specifying that excluded targets have priority over the included targets if there is a conflict.
has_obo_namespace: MS
id: MS:1000921

Axiom
annotated source: excludes supersede includes
annotated property: definition
annotated target: A priority setting specifying that excluded targets have priority over the included targets if there is a conflict.
database_cross_reference: PSI:MS

Skyline
type: Class
subclass of: SRM software
subclass of: quantitation software name
definition: 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.
has_obo_namespace: MS
id: MS:1000922

Axiom
annotated source: Skyline
annotated property: definition
annotated target: 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.
database_cross_reference: https://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view

TIQAM
type: Class
subclass of: SRM software
definition: Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology.
has_obo_namespace: MS
id: MS:1000923

Axiom
annotated source: TIQAM
annotated property: definition
annotated target: Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology.
database_cross_reference: http://tools.proteomecenter.org/TIQAM/TIQAM.html

MaRiMba
type: Class
definition: 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.
term replaced by: MS:1000872
has_obo_namespace: MS
id: MS:1000924
comment: This term was made obsolete because it was redundant with an existing term (MS:1000872).
deprecated: true

Axiom
annotated source: MaRiMba
annotated property: definition
annotated target: 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.
database_cross_reference: http://tools.proteomecenter.org/wiki/index.php

ATAQS
type: Class
subclass of: SRM software
definition: 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.
has_obo_namespace: MS
id: MS:1000925

Axiom
annotated source: ATAQS
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

product interpretation rank
type: Class
subclass of: product ion attribute
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: 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.
has_obo_namespace: MS
id: MS:1000926

Axiom
annotated source: product interpretation rank
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ion injection time
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000028
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The length of time spent filling an ion trapping device.
has_obo_namespace: MS
id: MS:1000927

Axiom
annotated source: ion injection time
annotated property: definition
annotated target: The length of time spent filling an ion trapping device.
database_cross_reference: PSI:MS

calibration spectrum
type: Class
subclass of: spectrum type
definition: 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.
has_obo_namespace: MS
id: MS:1000928

Axiom
annotated source: calibration spectrum
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Shimadzu Biotech nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1000929

Axiom
annotated source: Shimadzu Biotech nativeID format
annotated property: definition
annotated target: Native format defined by source=xsd:string start=xsd:nonNegativeInteger end=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

Shimadzu Biotech database entity
type: Class
subclass of: mass spectrometer file format
definition: Shimadzu Biotech format.
has_obo_namespace: MS
id: MS:1000930

Axiom
annotated source: Shimadzu Biotech database entity
annotated property: definition
annotated target: Shimadzu Biotech format.
database_cross_reference: PSI:MS

QTRAP 5500
type: Class
subclass of: SCIEX instrument model
definition: Applied Biosystems|MDS SCIEX QTRAP 5500.
has_obo_namespace: MS
id: MS:1000931

Axiom
annotated source: QTRAP 5500
annotated property: definition
annotated target: Applied Biosystems|MDS SCIEX QTRAP 5500.
database_cross_reference: PSI:MS

TripleTOF 5600
type: Class
subclass of: SCIEX instrument model
definition: SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer.
has_obo_namespace: MS
id: MS:1000932

Axiom
annotated source: TripleTOF 5600
annotated property: definition
annotated target: SCIEX TripleTOF 5600, a quadrupole - quadrupole - time-of-flight mass spectrometer.
database_cross_reference: PSI:MS

protein modifications
type: Class
subclass of: protein attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
has_obo_namespace: MS
id: MS:1000933

Axiom
annotated source: protein modifications
annotated property: definition
annotated target: Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
database_cross_reference: PSI:MS

gene name
type: Class
subclass of: protein attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Name of the gene from which the protein is translated.
has_obo_namespace: MS
id: MS:1000934

Axiom
annotated source: gene name
annotated property: definition
annotated target: Name of the gene from which the protein is translated.
database_cross_reference: PSI:MS

6470A Triple Quadrupole LC/MS
type: Class
subclass of: Agilent instrument model
subclass of: MS_1003762
definition: The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
has_obo_namespace: MS
id: MS:1000935

Axiom
annotated source: 6470A Triple Quadrupole LC/MS
annotated property: definition
annotated target: The 6470A Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
database_cross_reference: PSI:MS

6470B Triple Quadrupole LC/MS
type: Class
subclass of: Agilent instrument model
subclass of: MS_1003762
definition: The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
has_obo_namespace: MS
id: MS:1000936

Axiom
annotated source: 6470B Triple Quadrupole LC/MS
annotated property: definition
annotated target: The 6470B Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
database_cross_reference: PSI:MS

6495C Triple Quadrupole LC/MS
type: Class
subclass of: Agilent instrument model
subclass of: MS_1003762
definition: The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
has_obo_namespace: MS
id: MS:1000937

Axiom
annotated source: 6495C Triple Quadrupole LC/MS
annotated property: definition
annotated target: The 6495C Quadrupole LC/MS system is a Agilent liquid chromatography instrument combined with a Agilent triple quadrupole mass spectrometer.
database_cross_reference: PSI:MS

spectrum interpretation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Proteomics Standards Initiative Mass Spectrometry Vocabularies
definition: Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra.
has_obo_namespace: MS
id: MS:1001000

Axiom
annotated source: spectrum interpretation
annotated property: definition
annotated target: Collection of terms from the PSI Proteome Informatics standards describing the interpretation of spectra.
database_cross_reference: PSI:PI

SEQUEST:CleavesAt
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: string
has_obo_namespace: MS
id: MS:1001005

SEQUEST:ViewCV
type: Class
subclass of: MS_1002096
definition: SEQUEST View Input Parameters.
has_obo_namespace: MS
id: MS:1001006

Axiom
annotated source: SEQUEST:ViewCV
annotated property: definition
annotated target: SEQUEST View Input Parameters.
database_cross_reference: PSI:PI

SEQUEST:OutputLines
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: Number of peptide results to show.
has_obo_namespace: MS
id: MS:1001007

Axiom
annotated source: SEQUEST:OutputLines
annotated property: definition
annotated target: Number of peptide results to show.
database_cross_reference: PSI:MS

SEQUEST:DescriptionLines
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Number of full protein descriptions to show for top N peptides.
has_obo_namespace: MS
id: MS:1001009

Axiom
annotated source: SEQUEST:DescriptionLines
annotated property: definition
annotated target: Number of full protein descriptions to show for top N peptides.
database_cross_reference: PSI:MS

de novo search
type: Class
subclass of: search type
definition: A de novo sequencing search (without database).
has_obo_namespace: MS
id: MS:1001010

Axiom
annotated source: de novo search
annotated property: definition
annotated target: A de novo sequencing search (without database).
database_cross_reference: PSI:PI

search database details
type: Class
subclass of: search input details
definition: Details about the database searched.
has_obo_namespace: MS
id: MS:1001011

Axiom
annotated source: search database details
annotated property: definition
annotated target: Details about the database searched.
database_cross_reference: PSI:PI

database source
type: Class
subclass of: search database details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other).
has_obo_namespace: MS
id: MS:1001012

Axiom
annotated source: database source
annotated property: definition
annotated target: The organisation, project or laboratory from where the database is obtained (UniProt, NCBI, EBI, other).
database_cross_reference: PSI:PI

database name
type: Class
subclass of: search database details
definition: The name of the search database (nr, SwissProt or est_human).
has_obo_namespace: MS
id: MS:1001013

Axiom
annotated source: database name
annotated property: definition
annotated target: The name of the search database (nr, SwissProt or est_human).
database_cross_reference: PSI:PI

database local file path
type: Class
subclass of: search database details
definition: OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view.
has_obo_namespace: MS
id: MS:1001014
deprecated: true

Axiom
annotated source: database local file path
annotated property: definition
annotated target: OBSOLETE: Use attribute in mzIdentML instead. Local file path of the search database from the search engine's point of view.
database_cross_reference: PSI:PI

database original uri
type: Class
subclass of: search database details
subclass of: Restriction
  on property: has value type
  some values from: anyURI
definition: URI, from where the search database was originally downloaded.
has_obo_namespace: MS
id: MS:1001015

Axiom
annotated source: database original uri
annotated property: definition
annotated target: URI, from where the search database was originally downloaded.
database_cross_reference: PSI:PI

database version
type: Class
subclass of: search database details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Version of the search database. In mzIdentML use the attribute instead.
has_obo_namespace: MS
id: MS:1001016

Axiom
annotated source: database version
annotated property: definition
annotated target: Version of the search database. In mzIdentML use the attribute instead.
database_cross_reference: PSI:PI

release date
type: Class
subclass of: search database details
subclass of: MS_1003171
subclass of: Restriction
  on property: has structured representation in format
  some values from: mzIdentML format
subclass of: Restriction
  on property: has value type
  some values from: dateTime
definition: Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term.
has_obo_namespace: MS
id: MS:1001017

Axiom
annotated source: release date
annotated property: definition
annotated target: Date and time at which a product was publicly released. For mzIdentML, use the database release date XML attribute instead of this term.
database_cross_reference: PSI:PI

database type
type: Class
subclass of: search database details
definition: Database containing amino acid or nucleic acid sequences.
has_obo_namespace: MS
id: MS:1001018

Axiom
annotated source: database type
annotated property: definition
annotated target: Database containing amino acid or nucleic acid sequences.
database_cross_reference: PSI:PI

database filtering
type: Class
subclass of: search database details
definition: Was there filtering used on the database.
has_obo_namespace: MS
id: MS:1001019

Axiom
annotated source: database filtering
annotated property: definition
annotated target: Was there filtering used on the database.
database_cross_reference: PSI:PI

DB filter taxonomy
type: Class
subclass of: Sequence database filter types
definition: A taxonomy filter was to the database search.
has_obo_namespace: MS
id: MS:1001020

Axiom
annotated source: DB filter taxonomy
annotated property: definition
annotated target: A taxonomy filter was to the database search.
database_cross_reference: PSI:PI

DB filter on accession numbers
type: Class
subclass of: Sequence database filter types
definition: Filtering applied specifically by accession number pattern.
has_obo_namespace: MS
id: MS:1001021

Axiom
annotated source: DB filter on accession numbers
annotated property: definition
annotated target: Filtering applied specifically by accession number pattern.
database_cross_reference: PSI:PI

DB MW filter
type: Class
subclass of: Sequence database filter types
definition: Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value.
has_obo_namespace: MS
id: MS:1001022

Axiom
annotated source: DB MW filter
annotated property: definition
annotated target: Filtering applied specifically by protein molecular weight, specified as either a range or above/below a threshold value.
database_cross_reference: PSI:PI

DB PI filter
type: Class
subclass of: Sequence database filter types
definition: Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value.
has_obo_namespace: MS
id: MS:1001023

Axiom
annotated source: DB PI filter
annotated property: definition
annotated target: Filtering applied specifically by predicted protein isoelectric focussing point (pI), specified as either a range or above/below a threshold value.
database_cross_reference: PSI:PI

translation frame
type: Class
subclass of: search database details
definition: The translated open reading frames from a nucleotide database considered in the search (range: 1-6).
has_obo_namespace: MS
id: MS:1001024

Axiom
annotated source: translation frame
annotated property: definition
annotated target: The translated open reading frames from a nucleotide database considered in the search (range: 1-6).
database_cross_reference: PSI:PI

translation table
type: Class
subclass of: search database details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The translation table used to translate the nucleotides to amino acids.
has_obo_namespace: MS
id: MS:1001025

Axiom
annotated source: translation table
annotated property: definition
annotated target: The translation table used to translate the nucleotides to amino acids.
database_cross_reference: PSI:PI

SEQUEST:NormalizeXCorrValues
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001026

DB filter on sequence pattern
type: Class
subclass of: Sequence database filter types
definition: Filtering applied specifically by amino acid sequence pattern.
has_obo_namespace: MS
id: MS:1001027

Axiom
annotated source: DB filter on sequence pattern
annotated property: definition
annotated target: Filtering applied specifically by amino acid sequence pattern.
database_cross_reference: PSI:PI

SEQUEST:SequenceHeaderFilter
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: string
definition: String in the header of a sequence entry for that entry to be searched.
has_obo_namespace: MS
id: MS:1001028

Axiom
annotated source: SEQUEST:SequenceHeaderFilter
annotated property: definition
annotated target: String in the header of a sequence entry for that entry to be searched.
database_cross_reference: PSI:MS

number of sequences searched
type: Class
subclass of: search database details
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The number of sequences (proteins / nucleotides) from the database search after filtering.
has_obo_namespace: MS
id: MS:1001029

Axiom
annotated source: number of sequences searched
annotated property: definition
annotated target: The number of sequences (proteins / nucleotides) from the database search after filtering.
database_cross_reference: PSI:PI

number of peptide seqs compared to each spectrum
type: Class
subclass of: search database details
subclass of: spectrum identification result details
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: Number of peptide seqs compared to each spectrum.
has_obo_namespace: MS
id: MS:1001030

Axiom
annotated source: number of peptide seqs compared to each spectrum
annotated property: definition
annotated target: Number of peptide seqs compared to each spectrum.
database_cross_reference: PSI:PI

spectral library search
type: Class
subclass of: search type
definition: A search using a library of spectra.
has_obo_namespace: MS
id: MS:1001031

Axiom
annotated source: spectral library search
annotated property: definition
annotated target: A search using a library of spectra.
database_cross_reference: PSI:PI

SEQUEST:SequencePartialFilter
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: string
has_obo_namespace: MS
id: MS:1001032

date / time search performed
type: Class
subclass of: search statistics
definition: OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run.
has_obo_namespace: MS
id: MS:1001035
deprecated: true

Axiom
annotated source: date / time search performed
annotated property: definition
annotated target: OBSOLETE: use attribute in mzIdentML instead. Date and time of the actual search run.
database_cross_reference: PSI:PI

search time taken
type: Class
subclass of: search statistics
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The time taken to complete the search in seconds.
has_obo_namespace: MS
id: MS:1001036

Axiom
annotated source: search time taken
annotated property: definition
annotated target: The time taken to complete the search in seconds.
database_cross_reference: PSI:PI

SEQUEST:ShowFragmentIons
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating that fragment ions should be shown.
has_obo_namespace: MS
id: MS:1001037

Axiom
annotated source: SEQUEST:ShowFragmentIons
annotated property: definition
annotated target: Flag indicating that fragment ions should be shown.
database_cross_reference: PSI:MS

SEQUEST:Consensus
type: Class
subclass of: SEQUEST:ViewCV
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: Specify depth as value of the CVParam.
has_obo_namespace: MS
id: MS:1001038

Axiom
annotated source: SEQUEST:Consensus
annotated property: definition
annotated target: Specify depth as value of the CVParam.
database_cross_reference: PSI:PI

intermediate analysis format
type: Class
subclass of: file format
definition: Type of the source file, the mzIdentML was created from.
has_obo_namespace: MS
id: MS:1001040

Axiom
annotated source: intermediate analysis format
annotated property: definition
annotated target: Type of the source file, the mzIdentML was created from.
database_cross_reference: PSI:PI

SEQUEST:sortCV
type: Class
subclass of: SEQUEST:ViewCV
definition: SEQUEST View / Sort Input Parameters.
has_obo_namespace: MS
id: MS:1001041

Axiom
annotated source: SEQUEST:sortCV
annotated property: definition
annotated target: SEQUEST View / Sort Input Parameters.
database_cross_reference: PSI:PI

SEQUEST:LimitTo
type: Class
subclass of: MS_1002096
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: Specify "number of dtas shown" as value of the CVParam.
has_obo_namespace: MS
id: MS:1001042

Axiom
annotated source: SEQUEST:LimitTo
annotated property: definition
annotated target: Specify "number of dtas shown" as value of the CVParam.
database_cross_reference: PSI:PI

cleavage agent details
type: Class
subclass of: search input details
definition: Details of cleavage agent (enzyme).
has_obo_namespace: MS
id: MS:1001044

Axiom
annotated source: cleavage agent details
annotated property: definition
annotated target: Details of cleavage agent (enzyme).
database_cross_reference: PSI:PI

cleavage agent name
type: Class
subclass of: cleavage agent details
definition: The name of the cleavage agent.
has_obo_namespace: MS
id: MS:1001045

Axiom
annotated source: cleavage agent name
annotated property: definition
annotated target: The name of the cleavage agent.
database_cross_reference: PSI:PI

SEQUEST:sort by dCn
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results by the delta of the normalized correlation score.
has_obo_namespace: MS
id: MS:1001046

Axiom
annotated source: SEQUEST:sort by dCn
annotated property: definition
annotated target: Sort order of SEQUEST search results by the delta of the normalized correlation score.
database_cross_reference: PSI:PI

SEQUEST:sort by dM
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M.
has_obo_namespace: MS
id: MS:1001047

Axiom
annotated source: SEQUEST:sort by dM
annotated property: definition
annotated target: Sort order of SEQUEST search results by the difference between a theoretically calculated and the corresponding experimentally measured molecular mass M.
database_cross_reference: PSI:PI

SEQUEST:sort by Ions
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the ions.
has_obo_namespace: MS
id: MS:1001048

Axiom
annotated source: SEQUEST:sort by Ions
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the ions.
database_cross_reference: PSI:PI

SEQUEST:sort by MH+
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the mass of the protonated ion.
has_obo_namespace: MS
id: MS:1001049

Axiom
annotated source: SEQUEST:sort by MH+
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the mass of the protonated ion.
database_cross_reference: PSI:PI

SEQUEST:sort by P
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the probability.
has_obo_namespace: MS
id: MS:1001050

Axiom
annotated source: SEQUEST:sort by P
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the probability.
database_cross_reference: PSI:PI

multiple enzyme combination rules
type: Class
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any.
has_obo_namespace: MS
id: MS:1001051
deprecated: true

Axiom
annotated source: multiple enzyme combination rules
annotated property: definition
annotated target: OBSOLETE: use attribute independent in mzIdentML instead. Description of multiple enzyme digestion protocol, if any.
database_cross_reference: PSI:PI

SEQUEST:sort by PreviousAminoAcid
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the previous amino acid.
has_obo_namespace: MS
id: MS:1001052

Axiom
annotated source: SEQUEST:sort by PreviousAminoAcid
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the previous amino acid.
database_cross_reference: PSI:PI

SEQUEST:sort by Ref
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the reference.
has_obo_namespace: MS
id: MS:1001053

Axiom
annotated source: SEQUEST:sort by Ref
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the reference.
database_cross_reference: PSI:PI

modification parameters
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: Modification parameters for the search engine run.
has_obo_namespace: MS
id: MS:1001055

Axiom
annotated source: modification parameters
annotated property: definition
annotated target: Modification parameters for the search engine run.
database_cross_reference: PSI:PI

modification specificity rule
type: Class
subclass of: modification parameters
definition: The specificity rules for the modifications applied by the search engine.
has_obo_namespace: MS
id: MS:1001056

Axiom
annotated source: modification specificity rule
annotated property: definition
annotated target: The specificity rules for the modifications applied by the search engine.
database_cross_reference: PSI:PI

tolerance on types
type: Class
subclass of: modification parameters
definition: OBSOLETE: Tolerance on types.
has_obo_namespace: MS
id: MS:1001057
deprecated: true

Axiom
annotated source: tolerance on types
annotated property: definition
annotated target: OBSOLETE: Tolerance on types.
database_cross_reference: PSI:PI

quality estimation by manual validation
type: Class
subclass of: quality estimation method details
definition: The quality estimation was done manually.
has_obo_namespace: MS
id: MS:1001058

Axiom
annotated source: quality estimation by manual validation
annotated property: definition
annotated target: The quality estimation was done manually.
database_cross_reference: PSI:PI

SEQUEST:sort by RSp
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide).
has_obo_namespace: MS
id: MS:1001059

Axiom
annotated source: SEQUEST:sort by RSp
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the result 'Sp' of 'Rank/Sp' in the out file (peptide).
database_cross_reference: PSI:PI

quality estimation method details
type: Class
subclass of: search input details
definition: Method for quality estimation (manually or with decoy database).
has_obo_namespace: MS
id: MS:1001060

Axiom
annotated source: quality estimation method details
annotated property: definition
annotated target: Method for quality estimation (manually or with decoy database).
database_cross_reference: PSI:PI

neutral loss
type: Class
subclass of: modification parameters
definition: OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD.
term replaced by: MS:1000336
has_obo_namespace: MS
id: MS:1001061
deprecated: true

Axiom
annotated source: neutral loss
annotated property: definition
annotated target: OBSOLETE: replaced by MS:1000336 (neutral loss): Leave this to PSI-MOD.
database_cross_reference: PSI:PI

Mascot MGF format
type: Class
subclass of: mass spectrometer file format
definition: Mascot MGF file format.
has_obo_namespace: MS
id: MS:1001062

Axiom
annotated source: Mascot MGF format
annotated property: definition
annotated target: Mascot MGF file format.
database_cross_reference: PSI:MS

TODOscoring model
type: Class
subclass of: search input details
definition: OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms.
term replaced by: MS:1001961
has_obo_namespace: MS
id: MS:1001065
comment: This term was made obsolete and is replaced by the term (MS:1001961).
deprecated: true

Axiom
annotated source: TODOscoring model
annotated property: definition
annotated target: OBSOLETE: There is Phenyx:ScoringModel for Phenyx! Scoring model (more detailed granularity). TODO: add some child terms.
database_cross_reference: PSI:PI

ions series considered in search
type: Class
subclass of: search input details
definition: The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine.
has_obo_namespace: MS
id: MS:1001066

Axiom
annotated source: ions series considered in search
annotated property: definition
annotated target: The description of the DEPRECATED ion fragment series (including charges and neutral losses) that are considered by the search engine.
database_cross_reference: PSI:PI

SEQUEST:sort by Sp
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results by the Sp score.
has_obo_namespace: MS
id: MS:1001068

Axiom
annotated source: SEQUEST:sort by Sp
annotated property: definition
annotated target: Sort order of SEQUEST search results by the Sp score.
database_cross_reference: PSI:PI

SEQUEST:sort by TIC
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the total ion current.
has_obo_namespace: MS
id: MS:1001069

Axiom
annotated source: SEQUEST:sort by TIC
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the total ion current.
database_cross_reference: PSI:PI

SEQUEST:sort by Scan
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the scan number.
has_obo_namespace: MS
id: MS:1001070

Axiom
annotated source: SEQUEST:sort by Scan
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the scan number.
database_cross_reference: PSI:PI

SEQUEST:sort by Sequence
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the sequence.
has_obo_namespace: MS
id: MS:1001071

Axiom
annotated source: SEQUEST:sort by Sequence
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the sequence.
database_cross_reference: PSI:PI

SEQUEST:sort by Sf
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the SEQUEST result 'Sf'.
has_obo_namespace: MS
id: MS:1001072

Axiom
annotated source: SEQUEST:sort by Sf
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the SEQUEST result 'Sf'.
database_cross_reference: PSI:PI

database type amino acid
type: Class
subclass of: database type
definition: Database contains amino acid sequences.
has_obo_namespace: MS
id: MS:1001073

Axiom
annotated source: database type amino acid
annotated property: definition
annotated target: Database contains amino acid sequences.
database_cross_reference: PSI:PI

database type nucleotide
type: Class
subclass of: database type
definition: Database contains nucleic acid sequences.
has_obo_namespace: MS
id: MS:1001079

Axiom
annotated source: database type nucleotide
annotated property: definition
annotated target: Database contains nucleic acid sequences.
database_cross_reference: PSI:PI

search type
type: Class
subclass of: search input details
definition: Enumeration of type of search value (i.e. from PMF, sequence tag, MS2).
has_obo_namespace: MS
id: MS:1001080

Axiom
annotated source: search type
annotated property: definition
annotated target: Enumeration of type of search value (i.e. from PMF, sequence tag, MS2).
database_cross_reference: PSI:PI

pmf search
type: Class
subclass of: search type
definition: A peptide mass fingerprint search.
has_obo_namespace: MS
id: MS:1001081

Axiom
annotated source: pmf search
annotated property: definition
annotated target: A peptide mass fingerprint search.
database_cross_reference: PSI:PI

tag search
type: Class
subclass of: search type
definition: A sequence tag search.
has_obo_namespace: MS
id: MS:1001082

Axiom
annotated source: tag search
annotated property: definition
annotated target: A sequence tag search.
database_cross_reference: PSI:PI

ms-ms search
type: Class
subclass of: search type
definition: An MS2 search (with fragment ions).
has_obo_namespace: MS
id: MS:1001083

Axiom
annotated source: ms-ms search
annotated property: definition
annotated target: An MS2 search (with fragment ions).
database_cross_reference: PSI:PI

database nr
type: Class
subclass of: database name
definition: Non-redundant GenBank sequence database.
has_obo_namespace: MS
id: MS:1001084

Axiom
annotated source: database nr
annotated property: definition
annotated target: Non-redundant GenBank sequence database.
database_cross_reference: PSI:PI

protein-level identification attribute
type: Class
subclass of: MS_1002694
definition: Protein level information.
has_obo_namespace: MS
id: MS:1001085

Axiom
annotated source: protein-level identification attribute
annotated property: definition
annotated target: Protein level information.
database_cross_reference: PSI:PI

SEQUEST:sort by XCorr
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results by the correlation score.
has_obo_namespace: MS
id: MS:1001086

Axiom
annotated source: SEQUEST:sort by XCorr
annotated property: definition
annotated target: Sort order of SEQUEST search results by the correlation score.
database_cross_reference: PSI:PI

SEQUEST:ProcessCV
type: Class
subclass of: MS_1002096
definition: SEQUEST View / Process Input Parameters.
has_obo_namespace: MS
id: MS:1001087

Axiom
annotated source: SEQUEST:ProcessCV
annotated property: definition
annotated target: SEQUEST View / Process Input Parameters.
database_cross_reference: PSI:PI

protein description
type: Class
subclass of: protein-level identification attribute
subclass of: database sequence details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The protein description line from the sequence entry in the source database FASTA file.
has_obo_namespace: MS
id: MS:1001088

Axiom
annotated source: protein description
annotated property: definition
annotated target: The protein description line from the sequence entry in the source database FASTA file.
database_cross_reference: PSI:PI

molecule taxonomy
type: Class
subclass of: protein-level identification attribute
subclass of: database sequence details
subclass of: Sequence database filters
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The taxonomy of the resultant molecule from the search.
has_obo_namespace: MS
id: MS:1001089

Axiom
annotated source: molecule taxonomy
annotated property: definition
annotated target: The taxonomy of the resultant molecule from the search.
database_cross_reference: PSI:PI

taxonomy nomenclature
type: Class
subclass of: molecule taxonomy
definition: 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).
term replaced by: MS:1001467
term replaced by: MS:1001468
term replaced by: MS:1001469
term replaced by: MS:1001470
has_obo_namespace: MS
id: MS:1001090
deprecated: true

Axiom
annotated source: taxonomy nomenclature
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:PI

NoEnzyme
type: Class
subclass of: cleavage agent name
has_obo_namespace: MS
id: MS:1001091
comment: This term was made obsolete because it is ambiguous and is replaced by NoCleavage (MS:1001955) and unspecific cleavage (MS:1001956).
deprecated: true

peptide sequence-level identification statistic
type: Class
subclass of: peptide sequence-level identification attribute
definition: Identification confidence metric for a peptide.
has_obo_namespace: MS
id: MS:1001092

Axiom
annotated source: peptide sequence-level identification statistic
annotated property: definition
annotated target: Identification confidence metric for a peptide.
database_cross_reference: PSI:PI

sequence coverage
type: Class
subclass of: protein-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: decimal
definition: The percent coverage for the protein based upon the matched peptide sequences (can be calculated).
has_obo_namespace: MS
id: MS:1001093

Axiom
annotated source: sequence coverage
annotated property: definition
annotated target: The percent coverage for the protein based upon the matched peptide sequences (can be calculated).
database_cross_reference: PSI:PI

SEQUEST:sort by z
type: Class
subclass of: SEQUEST:sortCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Sort order of SEQUEST search results given by the charge.
has_obo_namespace: MS
id: MS:1001094

Axiom
annotated source: SEQUEST:sort by z
annotated property: definition
annotated target: Sort order of SEQUEST search results given by the charge.
database_cross_reference: PSI:PI

SEQUEST:ProcessAll
type: Class
subclass of: SEQUEST:ProcessCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001095

SEQUEST:TopPercentMostIntense
type: Class
subclass of: SEQUEST:ProcessCV
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Specify "percentage" as value of the CVParam.
has_obo_namespace: MS
id: MS:1001096

Axiom
annotated source: SEQUEST:TopPercentMostIntense
annotated property: definition
annotated target: Specify "percentage" as value of the CVParam.
database_cross_reference: PSI:PI

distinct peptide sequences
type: Class
subclass of: protein-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: This counts distinct sequences hitting the protein without regard to a minimal confidence threshold.
has_obo_namespace: MS
id: MS:1001097

Axiom
annotated source: distinct peptide sequences
annotated property: definition
annotated target: This counts distinct sequences hitting the protein without regard to a minimal confidence threshold.
database_cross_reference: PSI:PI

confident distinct peptide sequences
type: Class
subclass of: protein-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: 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.
has_obo_namespace: MS
id: MS:1001098

Axiom
annotated source: confident distinct peptide sequences
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

confident peptide qualification
type: Class
subclass of: protein-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: 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.
has_obo_namespace: MS
id: MS:1001099

Axiom
annotated source: confident peptide qualification
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

confident peptide sequence number
type: Class
subclass of: protein-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: 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.
has_obo_namespace: MS
id: MS:1001100

Axiom
annotated source: confident peptide sequence number
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

protein group or subset relationship
type: Class
subclass of: protein-level identification attribute
definition: Protein group or subset relationships.
has_obo_namespace: MS
id: MS:1001101

Axiom
annotated source: protein group or subset relationship
annotated property: definition
annotated target: Protein group or subset relationships.
database_cross_reference: PSI:PI

SEQUEST:Chromatogram
type: Class
subclass of: SEQUEST:ViewCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001102

SEQUEST:InfoAndLog
type: Class
subclass of: SEQUEST:ViewCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001103

database UniProtKB/Swiss-Prot
type: Class
subclass of: MS_1002126
definition: The name of the UniProtKB/Swiss-Prot knowledgebase.
has_obo_namespace: MS
id: MS:1001104

Axiom
annotated source: database UniProtKB/Swiss-Prot
annotated property: definition
annotated target: The name of the UniProtKB/Swiss-Prot knowledgebase.
database_cross_reference: PSI:PI

peptide sequence-level identification attribute
type: Class
subclass of: MS_1002694
definition: Peptide level information.
has_obo_namespace: MS
id: MS:1001105

Axiom
annotated source: peptide sequence-level identification attribute
annotated property: definition
annotated target: Peptide level information.
database_cross_reference: PSI:PI

SEQUEST:TopNumber
type: Class
subclass of: SEQUEST:ProcessCV
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: Specify "number" as value of the CVParam.
has_obo_namespace: MS
id: MS:1001106

Axiom
annotated source: SEQUEST:TopNumber
annotated property: definition
annotated target: Specify "number" as value of the CVParam.
database_cross_reference: PSI:PI

data stored in database
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was a data set in a database.
has_obo_namespace: MS
id: MS:1001107

Axiom
annotated source: data stored in database
annotated property: definition
annotated target: Source file for this mzIdentML was a data set in a database.
database_cross_reference: PSI:PI

param: a ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: a ion with charge on the N-terminal side.
has_obo_namespace: MS
id: MS:1001108

Axiom
annotated source: param: a ion
annotated property: definition
annotated target: Parameter information, type of product: a ion with charge on the N-terminal side.
database_cross_reference: PSI:PI

SEQUEST:CullTo
type: Class
subclass of: SEQUEST:ProcessCV
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specify cull string as value of the CVParam.
has_obo_namespace: MS
id: MS:1001109

Axiom
annotated source: SEQUEST:CullTo
annotated property: definition
annotated target: Specify cull string as value of the CVParam.
database_cross_reference: PSI:PI

SEQUEST:modeCV
type: Class
subclass of: MS_1002096
definition: SEQUEST Mode Input Parameters.
has_obo_namespace: MS
id: MS:1001110

Axiom
annotated source: SEQUEST:modeCV
annotated property: definition
annotated target: SEQUEST Mode Input Parameters.
database_cross_reference: PSI:PI

SEQUEST:Full
type: Class
subclass of: SEQUEST:modeCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001111

n-terminal flanking residue
type: Class
subclass of: peptide sequence-level identification attribute
subclass of: MS_1003046
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1001112

Axiom
annotated source: n-terminal flanking residue
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

c-terminal flanking residue
type: Class
subclass of: peptide sequence-level identification attribute
subclass of: MS_1003046
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1001113

Axiom
annotated source: c-terminal flanking residue
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

retention time(s)
type: Class
subclass of: peptide sequence-level identification attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OBSOLETE Retention time of the spectrum from the source file.
has_obo_namespace: MS
id: MS:1001114
comment: This term was made obsolete because scan start time (MS:1000016) should be used instead.
deprecated: true

Axiom
annotated source: retention time(s)
annotated property: definition
annotated target: OBSOLETE Retention time of the spectrum from the source file.
database_cross_reference: PSI:PI

scan number(s)
type: Class
definition: OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData.
has_obo_namespace: MS
id: MS:1001115
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: scan number(s)
annotated property: definition
annotated target: OBSOLETE: use spectrumID attribute of SpectrumIdentificationResult. Take from mzData.
database_cross_reference: PSI:PI

single protein identification statistic
type: Class
subclass of: protein-level identification attribute
definition: 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).
has_obo_namespace: MS
id: MS:1001116

Axiom
annotated source: single protein identification statistic
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:PI

theoretical neutral mass
type: Class
subclass of: peptide sequence-level identification attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier.
has_exact_synonym: theoretical mass
has_obo_namespace: MS
id: MS:1001117

Axiom
annotated source: theoretical neutral mass
annotated property: definition
annotated target: The theoretical neutral mass of the molecule (e.g. the peptide sequence and its modifications) not including its charge carrier.
database_cross_reference: PSI:PI

param: b ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: b ion with charge on the N-terminal side.
has_obo_namespace: MS
id: MS:1001118

Axiom
annotated source: param: b ion
annotated property: definition
annotated target: Parameter information, type of product: b ion with charge on the N-terminal side.
database_cross_reference: PSI:PI

param: c ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: c ion with charge on the N-terminal side.
has_obo_namespace: MS
id: MS:1001119

Axiom
annotated source: param: c ion
annotated property: definition
annotated target: Parameter information, type of product: c ion with charge on the N-terminal side.
database_cross_reference: PSI:PI

SEQUEST:FormatAndLinks
type: Class
subclass of: SEQUEST:modeCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001120

number of matched peaks
type: Class
subclass of: peptide sequence-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: 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.
has_obo_namespace: MS
id: MS:1001121

Axiom
annotated source: number of matched peaks
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

ions series considered
type: Class
subclass of: peptide sequence-level identification attribute
definition: 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).
has_obo_namespace: MS
id: MS:1001122

Axiom
annotated source: ions series considered
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:PI

number of peaks used
type: Class
subclass of: peptide sequence-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: 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.
has_obo_namespace: MS
id: MS:1001123

Axiom
annotated source: number of peaks used
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

number of peaks submitted
type: Class
subclass of: peptide sequence-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: The number of peaks from the original peaks listed that were submitted to the search engine.
has_obo_namespace: MS
id: MS:1001124

Axiom
annotated source: number of peaks submitted
annotated property: definition
annotated target: The number of peaks from the original peaks listed that were submitted to the search engine.
database_cross_reference: PSI:PI

manual validation
type: Class
subclass of: peptide sequence-level identification statistic
subclass of: single protein identification statistic
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Result of quality estimation: decision of a manual validation.
has_obo_namespace: MS
id: MS:1001125

Axiom
annotated source: manual validation
annotated property: definition
annotated target: Result of quality estimation: decision of a manual validation.
database_cross_reference: PSI:PI

SEQUEST:Fast
type: Class
subclass of: SEQUEST:modeCV
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001126

peptide sharing details
type: Class
subclass of: peptide sequence-level identification attribute
definition: Accessions Containing Sequence - Accessions for each protein containing this peptide.
has_obo_namespace: MS
id: MS:1001127

Axiom
annotated source: peptide sharing details
annotated property: definition
annotated target: Accessions Containing Sequence - Accessions for each protein containing this peptide.
database_cross_reference: PSI:PI

SEQUEST:selectCV
type: Class
subclass of: MS_1002096
definition: SEQUEST Select Input Parameters.
has_obo_namespace: MS
id: MS:1001128

Axiom
annotated source: SEQUEST:selectCV
annotated property: definition
annotated target: SEQUEST Select Input Parameters.
database_cross_reference: PSI:PI

quantification information
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: Quantification information.
has_obo_namespace: MS
id: MS:1001129

Axiom
annotated source: quantification information
annotated property: definition
annotated target: Quantification information.
database_cross_reference: PSI:PI

peptide raw area
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OBSOLETE Peptide raw area.
has_obo_namespace: MS
id: MS:1001130
comment: This term was made obsolete because it is replaced by 'MS1 feature area' (MS:1001844).
deprecated: true

Axiom
annotated source: peptide raw area
annotated property: definition
annotated target: OBSOLETE Peptide raw area.
database_cross_reference: PSI:PI

error on peptide area
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Error on peptide area.
has_obo_namespace: MS
id: MS:1001131

Axiom
annotated source: error on peptide area
annotated property: definition
annotated target: Error on peptide area.
database_cross_reference: PSI:PI

peptide ratio
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Peptide ratio.
has_obo_namespace: MS
id: MS:1001132

Axiom
annotated source: peptide ratio
annotated property: definition
annotated target: Peptide ratio.
database_cross_reference: PSI:PI

error on peptide ratio
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Error on peptide ratio.
has_obo_namespace: MS
id: MS:1001133

Axiom
annotated source: error on peptide ratio
annotated property: definition
annotated target: Error on peptide ratio.
database_cross_reference: PSI:PI

protein ratio
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Protein ratio.
has_obo_namespace: MS
id: MS:1001134

Axiom
annotated source: protein ratio
annotated property: definition
annotated target: Protein ratio.
database_cross_reference: PSI:PI

error on protein ratio
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Error on protein ratio.
has_obo_namespace: MS
id: MS:1001135

Axiom
annotated source: error on protein ratio
annotated property: definition
annotated target: Error on protein ratio.
database_cross_reference: PSI:PI

p-value (protein diff from 1 randomly)
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OBSOLETE P-value (protein diff from 1 randomly).
has_obo_namespace: MS
id: MS:1001136
comment: This term was made obsolete because it is replaced by 't-test p-value' (MS:1001855).
deprecated: true

Axiom
annotated source: p-value (protein diff from 1 randomly)
annotated property: definition
annotated target: OBSOLETE P-value (protein diff from 1 randomly).
database_cross_reference: PSI:PI

absolute quantity
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Absolute quantity in terms of real concentration or molecule copy number in sample.
has_obo_namespace: MS
id: MS:1001137

Axiom
annotated source: absolute quantity
annotated property: definition
annotated target: Absolute quantity in terms of real concentration or molecule copy number in sample.
database_cross_reference: PSI:PI

error on absolute quantity
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Error on absolute quantity.
has_obo_namespace: MS
id: MS:1001138

Axiom
annotated source: error on absolute quantity
annotated property: definition
annotated target: Error on absolute quantity.
database_cross_reference: PSI:PI

quantitation software name
type: Class
subclass of: software
subclass of: quantification information
definition: Quantitation software name.
has_obo_namespace: MS
id: MS:1001139

Axiom
annotated source: quantitation software name
annotated property: definition
annotated target: Quantitation software name.
database_cross_reference: PSI:PI

quantitation software version
type: Class
subclass of: quantification information
definition: OBSOLETE Quantitation software version.
has_obo_namespace: MS
id: MS:1001140
comment: This term was made obsolete because part of mzQuantML schema.
deprecated: true

Axiom
annotated source: quantitation software version
annotated property: definition
annotated target: OBSOLETE Quantitation software version.
database_cross_reference: PSI:PI

intensity of precursor ion
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The intensity of the precursor ion.
has_obo_namespace: MS
id: MS:1001141

Axiom
annotated source: intensity of precursor ion
annotated property: definition
annotated target: The intensity of the precursor ion.
database_cross_reference: PSI:PI

database IPI_human
type: Class
subclass of: database name
definition: International Protein Index database for Homo sapiens sequences.
has_obo_namespace: MS
id: MS:1001142

Axiom
annotated source: database IPI_human
annotated property: definition
annotated target: International Protein Index database for Homo sapiens sequences.
database_cross_reference: PSI:PI

PSM-level search engine specific statistic
type: Class
subclass of: MS_1002347
definition: Search engine specific peptide spectrum match scores.
has_obo_namespace: MS
id: MS:1001143

Axiom
annotated source: PSM-level search engine specific statistic
annotated property: definition
annotated target: Search engine specific peptide spectrum match scores.
database_cross_reference: PSI:PI

SEQUEST:SelectDefault
type: Class
subclass of: SEQUEST:selectCV
has_obo_namespace: MS
id: MS:1001144

SEQUEST:SelectAdvancedCV
type: Class
subclass of: SEQUEST:selectCV
definition: SEQUEST Select Advanced Input Parameters.
has_obo_namespace: MS
id: MS:1001145

Axiom
annotated source: SEQUEST:SelectAdvancedCV
annotated property: definition
annotated target: SEQUEST Select Advanced Input Parameters.
database_cross_reference: PSI:PI

param: a ion-NH3 DEPRECATED
type: Class
subclass of: ions series considered in search
definition: Ion a-NH3 parameter information, type of product: a ion with lost ammonia.
has_obo_namespace: MS
id: MS:1001146

Axiom
annotated source: param: a ion-NH3 DEPRECATED
annotated property: definition
annotated target: Ion a-NH3 parameter information, type of product: a ion with lost ammonia.
database_cross_reference: PSI:PI

protein ambiguity group result details
type: Class
subclass of: protein-level identification attribute
subclass of: search engine specific score
has_obo_namespace: MS
id: MS:1001147

param: a ion-H2O DEPRECATED
type: Class
subclass of: ions series considered in search
definition: Ion a-H2O if a significant and fragment includes STED.
has_obo_namespace: MS
id: MS:1001148

Axiom
annotated source: param: a ion-H2O DEPRECATED
annotated property: definition
annotated target: Ion a-H2O if a significant and fragment includes STED.
database_cross_reference: PSI:PI

param: b ion-NH3 DEPRECATED
type: Class
subclass of: ions series considered in search
definition: Ion b-NH3 parameter information, type of product: b ion with lost ammonia.
has_obo_namespace: MS
id: MS:1001149

Axiom
annotated source: param: b ion-NH3 DEPRECATED
annotated property: definition
annotated target: Ion b-NH3 parameter information, type of product: b ion with lost ammonia.
database_cross_reference: PSI:PI

param: b ion-H2O DEPRECATED
type: Class
subclass of: ions series considered in search
definition: Ion b-H2O if b significant and fragment includes STED.
has_obo_namespace: MS
id: MS:1001150

Axiom
annotated source: param: b ion-H2O DEPRECATED
annotated property: definition
annotated target: Ion b-H2O if b significant and fragment includes STED.
database_cross_reference: PSI:PI

param: y ion-NH3 DEPRECATED
type: Class
subclass of: ions series considered in search
definition: Ion y-NH3 parameter information, type of product: y ion with lost ammonia.
has_obo_namespace: MS
id: MS:1001151

Axiom
annotated source: param: y ion-NH3 DEPRECATED
annotated property: definition
annotated target: Ion y-NH3 parameter information, type of product: y ion with lost ammonia.
database_cross_reference: PSI:PI

param: y ion-H2O DEPRECATED
type: Class
subclass of: ions series considered in search
has_obo_namespace: MS
id: MS:1001152
comment: This term was made obsolete - use MS:1001262 and MS:1002455 instead.

search engine specific score
type: Class
subclass of: MS_1002694
definition: Search engine specific scores.
has_obo_namespace: MS
id: MS:1001153

Axiom
annotated source: search engine specific score
annotated property: definition
annotated target: Search engine specific scores.
database_cross_reference: PSI:PI

SEQUEST:probability
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'Probability'.
has_obo_namespace: MS
id: MS:1001154

Axiom
annotated source: SEQUEST:probability
annotated property: definition
annotated target: The SEQUEST result 'Probability'.
database_cross_reference: PSI:PI

SEQUEST:xcorr
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has_order
  some values from: MS_1002108
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'XCorr'.
has_obo_namespace: MS
id: MS:1001155

Axiom
annotated source: SEQUEST:xcorr
annotated property: definition
annotated target: The SEQUEST result 'XCorr'.
database_cross_reference: PSI:PI

SEQUEST:deltacn
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'DeltaCn'.
has_obo_namespace: MS
id: MS:1001156

Axiom
annotated source: SEQUEST:deltacn
annotated property: definition
annotated target: The SEQUEST result 'DeltaCn'.
database_cross_reference: PSI:PI

SEQUEST:sp
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'Sp' (protein).
has_obo_namespace: MS
id: MS:1001157

Axiom
annotated source: SEQUEST:sp
annotated property: definition
annotated target: The SEQUEST result 'Sp' (protein).
database_cross_reference: PSI:PI

SEQUEST:Uniq
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
has_obo_namespace: MS
id: MS:1001158

SEQUEST:expectation value
type: Class
subclass of: search engine specific score
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'Expectation value'.
has_obo_namespace: MS
id: MS:1001159

Axiom
annotated source: SEQUEST:expectation value
annotated property: definition
annotated target: The SEQUEST result 'Expectation value'.
database_cross_reference: PSI:PI

SEQUEST:sf
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'Sf'.
has_obo_namespace: MS
id: MS:1001160

Axiom
annotated source: SEQUEST:sf
annotated property: definition
annotated target: The SEQUEST result 'Sf'.
database_cross_reference: PSI:PI

SEQUEST:matched ions
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: integer
definition: The SEQUEST result 'Matched Ions'.
has_obo_namespace: MS
id: MS:1001161

Axiom
annotated source: SEQUEST:matched ions
annotated property: definition
annotated target: The SEQUEST result 'Matched Ions'.
database_cross_reference: PSI:PI

SEQUEST:total ions
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: integer
definition: The SEQUEST result 'Total Ions'.
has_obo_namespace: MS
id: MS:1001162

Axiom
annotated source: SEQUEST:total ions
annotated property: definition
annotated target: The SEQUEST result 'Total Ions'.
database_cross_reference: PSI:PI

SEQUEST:consensus score
type: Class
subclass of: search engine specific score
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'Consensus Score'.
has_obo_namespace: MS
id: MS:1001163

Axiom
annotated source: SEQUEST:consensus score
annotated property: definition
annotated target: The SEQUEST result 'Consensus Score'.
database_cross_reference: PSI:PI

Paragon:unused protscore
type: Class
subclass of: MS_1002363
subclass of: MS_1002368
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Paragon result 'Unused ProtScore'.
has_obo_namespace: MS
id: MS:1001164

Axiom
annotated source: Paragon:unused protscore
annotated property: definition
annotated target: The Paragon result 'Unused ProtScore'.
database_cross_reference: PSI:PI

Paragon:total protscore
type: Class
subclass of: MS_1002363
subclass of: MS_1002368
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Paragon result 'Total ProtScore'.
has_obo_namespace: MS
id: MS:1001165

Axiom
annotated source: Paragon:total protscore
annotated property: definition
annotated target: The Paragon result 'Total ProtScore'.
database_cross_reference: PSI:PI

Paragon:score
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Paragon result 'Score'.
has_obo_namespace: MS
id: MS:1001166

Axiom
annotated source: Paragon:score
annotated property: definition
annotated target: The Paragon result 'Score'.
database_cross_reference: PSI:PI

Paragon:confidence
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Paragon result 'Confidence'.
has_obo_namespace: MS
id: MS:1001167

Axiom
annotated source: Paragon:confidence
annotated property: definition
annotated target: The Paragon result 'Confidence'.
database_cross_reference: PSI:PI

Paragon:expression error factor
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Paragon result 'Expression Error Factor'.
has_obo_namespace: MS
id: MS:1001168

Axiom
annotated source: Paragon:expression error factor
annotated property: definition
annotated target: The Paragon result 'Expression Error Factor'.
database_cross_reference: PSI:PI

Paragon:expression change p-value
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Paragon result 'Expression change P-value'.
has_obo_namespace: MS
id: MS:1001169

Axiom
annotated source: Paragon:expression change p-value
annotated property: definition
annotated target: The Paragon result 'Expression change P-value'.
database_cross_reference: PSI:PI

Paragon:contrib
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Paragon result 'Contrib'.
has_obo_namespace: MS
id: MS:1001170

Axiom
annotated source: Paragon:contrib
annotated property: definition
annotated target: The Paragon result 'Contrib'.
database_cross_reference: PSI:PI

Mascot:score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Mascot result 'Score'.
has_obo_namespace: MS
id: MS:1001171

Axiom
annotated source: Mascot:score
annotated property: definition
annotated target: The Mascot result 'Score'.
database_cross_reference: PSI:PI

Mascot:expectation value
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Mascot result 'expectation value'.
has_obo_namespace: MS
id: MS:1001172

Axiom
annotated source: Mascot:expectation value
annotated property: definition
annotated target: The Mascot result 'expectation value'.
database_cross_reference: PSI:PI

Mascot:matched ions
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: The Mascot result 'Matched ions'.
has_obo_namespace: MS
id: MS:1001173

Axiom
annotated source: Mascot:matched ions
annotated property: definition
annotated target: The Mascot result 'Matched ions'.
database_cross_reference: PSI:PI

Mascot:total ions
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: The Mascot result 'Total ions'.
has_obo_namespace: MS
id: MS:1001174

Axiom
annotated source: Mascot:total ions
annotated property: definition
annotated target: The Mascot result 'Total ions'.
database_cross_reference: PSI:PI

peptide shared in multiple proteins
type: Class
subclass of: peptide sharing details
definition: A peptide matching multiple proteins.
has_obo_namespace: MS
id: MS:1001175

Axiom
annotated source: peptide shared in multiple proteins
annotated property: definition
annotated target: A peptide matching multiple proteins.
database_cross_reference: PSI:PI

(?<=[KR])(?!P)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Trypsin.
has_obo_namespace: MS
id: MS:1001176

Axiom
annotated source: (?<=[KR])(?!P)
annotated property: definition
annotated target: Regular expression for Trypsin.
database_cross_reference: PSI:PI

number of molecular hypothesis considered
type: Class
subclass of: search statistics
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search.
has_obo_namespace: MS
id: MS:1001177

Axiom
annotated source: number of molecular hypothesis considered
annotated property: definition
annotated target: Number of Molecular Hypothesis Considered - This is the number of molecules (e.g. peptides for proteomics) considered for a particular search.
database_cross_reference: PSI:PI

database EST
type: Class
subclass of: database type nucleotide
definition: Expressed sequence tag nucleotide sequence database.
has_obo_namespace: MS
id: MS:1001178

Axiom
annotated source: database EST
annotated property: definition
annotated target: Expressed sequence tag nucleotide sequence database.
database_cross_reference: PSI:PI

Cleavage agent regular expression
type: Class
subclass of: MS_1002479
subclass of: Restriction
  on property: part_of
  some values from: cleavage agent details
definition: Regular expressions for cleavage enzymes.
has_obo_namespace: MS
id: MS:1001180

Axiom
annotated source: Cleavage agent regular expression
annotated property: definition
annotated target: Regular expressions for cleavage enzymes.
database_cross_reference: PSI:PI

search statistics
type: Class
subclass of: spectrum identification result details
definition: The details of the actual run of the search.
has_obo_namespace: MS
id: MS:1001184

Axiom
annotated source: search statistics
annotated property: definition
annotated target: The details of the actual run of the search.
database_cross_reference: PSI:PI

Mobilion MBI format
type: Class
subclass of: mass spectrometer file format
definition: Mobilion MBI file format.
has_obo_namespace: MS
id: MS:1001185

Axiom
annotated source: Mobilion MBI format
annotated property: definition
annotated target: Mobilion MBI file format.
database_cross_reference: PSI:MS

Mobilion MBI nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1001186

Axiom
annotated source: Mobilion MBI nativeID format
annotated property: definition
annotated target: Native format defined by frame=xsd:nonNegativeInteger scan=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

modification specificity peptide N-term
type: Class
subclass of: modification specificity rule
definition: As parameter for search engine: apply the modification only at the N-terminus of a peptide.
has_obo_namespace: MS
id: MS:1001189

Axiom
annotated source: modification specificity peptide N-term
annotated property: definition
annotated target: As parameter for search engine: apply the modification only at the N-terminus of a peptide.
database_cross_reference: PSI:PI

modification specificity peptide C-term
type: Class
subclass of: modification specificity rule
definition: As parameter for search engine: apply the modification only at the C-terminus of a peptide.
has_obo_namespace: MS
id: MS:1001190

Axiom
annotated source: modification specificity peptide C-term
annotated property: definition
annotated target: As parameter for search engine: apply the modification only at the C-terminus of a peptide.
database_cross_reference: PSI:PI

p-value
type: Class
subclass of: peptide sequence-level identification statistic
subclass of: protein identification confidence metric
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OBSOLETE Quality estimation by p-value.
has_obo_namespace: MS
id: MS:1001191
comment: This term was made obsolete because now is split into peptide and protein terms.
deprecated: true

Axiom
annotated source: p-value
annotated property: definition
annotated target: OBSOLETE Quality estimation by p-value.
database_cross_reference: PSI:PI

Expect value
type: Class
subclass of: peptide sequence-level identification statistic
subclass of: single protein identification statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Result of quality estimation: Expect value.
has_obo_namespace: MS
id: MS:1001192

Axiom
annotated source: Expect value
annotated property: definition
annotated target: Result of quality estimation: Expect value.
database_cross_reference: PSI:PI

confidence score
type: Class
subclass of: peptide sequence-level identification statistic
subclass of: single protein identification statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Result of quality estimation: confidence score.
has_obo_namespace: MS
id: MS:1001193

Axiom
annotated source: confidence score
annotated property: definition
annotated target: Result of quality estimation: confidence score.
database_cross_reference: PSI:PI

quality estimation with decoy database
type: Class
subclass of: quality estimation method details
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Quality estimation by decoy database.
has_obo_namespace: MS
id: MS:1001194

Axiom
annotated source: quality estimation with decoy database
annotated property: definition
annotated target: Quality estimation by decoy database.
database_cross_reference: PSI:PI

decoy DB type reverse
type: Class
subclass of: decoy DB details
definition: Decoy type: Amino acids of protein sequences are used in reverse order.
has_obo_namespace: MS
id: MS:1001195

Axiom
annotated source: decoy DB type reverse
annotated property: definition
annotated target: Decoy type: Amino acids of protein sequences are used in reverse order.
database_cross_reference: PSI:PI

decoy DB type randomized
type: Class
subclass of: decoy DB details
definition: Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass).
has_obo_namespace: MS
id: MS:1001196

Axiom
annotated source: decoy DB type randomized
annotated property: definition
annotated target: Decoy type: Amino acids of protein sequences are randomized (keeping the original protein mass).
database_cross_reference: PSI:PI

DB composition target+decoy
type: Class
subclass of: decoy DB details
definition: Decoy database composition: database contains original (target) and decoy entries.
has_obo_namespace: MS
id: MS:1001197

Axiom
annotated source: DB composition target+decoy
annotated property: definition
annotated target: Decoy database composition: database contains original (target) and decoy entries.
database_cross_reference: PSI:PI

protein identification confidence metric
type: Class
subclass of: single protein identification statistic
definition: Identification confidence metric for a protein.
has_obo_namespace: MS
id: MS:1001198

Axiom
annotated source: protein identification confidence metric
annotated property: definition
annotated target: Identification confidence metric for a protein.
database_cross_reference: PSI:PI

Mascot DAT format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in Mascot DAT file format.
has_obo_namespace: MS
id: MS:1001199

Axiom
annotated source: Mascot DAT format
annotated property: definition
annotated target: Source file for this mzIdentML was in Mascot DAT file format.
database_cross_reference: PSI:PI

SEQUEST out file format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in SEQUEST out file format.
has_obo_namespace: MS
id: MS:1001200

Axiom
annotated source: SEQUEST out file format
annotated property: definition
annotated target: Source file for this mzIdentML was in SEQUEST out file format.
database_cross_reference: PSI:PI

DB MW filter maximum
type: Class
subclass of: Sequence database filters
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has_units
  some values from: UO_0000222
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Maximum value of molecular weight filter.
has_obo_namespace: MS
id: MS:1001201

Axiom
annotated source: DB MW filter maximum
annotated property: definition
annotated target: Maximum value of molecular weight filter.
database_cross_reference: PSI:PI

DB MW filter minimum
type: Class
subclass of: Sequence database filters
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has_units
  some values from: UO_0000222
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Minimum value of molecular weight filter.
has_obo_namespace: MS
id: MS:1001202

Axiom
annotated source: DB MW filter minimum
annotated property: definition
annotated target: Minimum value of molecular weight filter.
database_cross_reference: PSI:PI

DB PI filter maximum
type: Class
subclass of: Sequence database filters
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Maximum value of isoelectric point filter.
has_obo_namespace: MS
id: MS:1001203

Axiom
annotated source: DB PI filter maximum
annotated property: definition
annotated target: Maximum value of isoelectric point filter.
database_cross_reference: PSI:PI

DB PI filter minimum
type: Class
subclass of: Sequence database filters
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Minimum value of isoelectric point filter.
has_obo_namespace: MS
id: MS:1001204

Axiom
annotated source: DB PI filter minimum
annotated property: definition
annotated target: Minimum value of isoelectric point filter.
database_cross_reference: PSI:PI

Mascot
type: Class
subclass of: analysis software
definition: The name of the Mascot search engine.
has_obo_namespace: MS
id: MS:1001207

Axiom
annotated source: Mascot
annotated property: definition
annotated target: The name of the Mascot search engine.
database_cross_reference: PSI:PI

SEQUEST
type: Class
subclass of: analysis software
definition: The name of the SEQUEST search engine.
has_obo_namespace: MS
id: MS:1001208

Axiom
annotated source: SEQUEST
annotated property: definition
annotated target: The name of the SEQUEST search engine.
database_cross_reference: PSI:PI

Phenyx
type: Class
subclass of: analysis software
definition: The name of the Phenyx search engine.
has_obo_namespace: MS
id: MS:1001209

Axiom
annotated source: Phenyx
annotated property: definition
annotated target: The name of the Phenyx search engine.
database_cross_reference: PSI:PI

mass type settings
type: Class
subclass of: search input details
definition: The type of mass difference value to be considered by the search engine (monoisotopic or average).
has_obo_namespace: MS
id: MS:1001210

Axiom
annotated source: mass type settings
annotated property: definition
annotated target: The type of mass difference value to be considered by the search engine (monoisotopic or average).
database_cross_reference: PSI:PI

parent mass type mono
type: Class
subclass of: mass type settings
definition: Mass type setting for parent mass was monoisotopic.
has_obo_namespace: MS
id: MS:1001211

Axiom
annotated source: parent mass type mono
annotated property: definition
annotated target: Mass type setting for parent mass was monoisotopic.
database_cross_reference: PSI:PI

parent mass type average
type: Class
subclass of: mass type settings
definition: Mass type setting for parent mass was average isotopic.
has_obo_namespace: MS
id: MS:1001212

Axiom
annotated source: parent mass type average
annotated property: definition
annotated target: Mass type setting for parent mass was average isotopic.
database_cross_reference: PSI:PI

search result details
type: Class
definition: OBSOLETE: Scores and global result characteristics.
has_obo_namespace: MS
id: MS:1001213
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: search result details
annotated property: definition
annotated target: OBSOLETE: Scores and global result characteristics.
database_cross_reference: PSI:PI

protein-level global FDR
type: Class
subclass of: MS_1002705
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002305
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Estimation of the global false discovery rate of proteins.
has_obo_namespace: MS
id: MS:1001214

Axiom
annotated source: protein-level global FDR
annotated property: definition
annotated target: Estimation of the global false discovery rate of proteins.
database_cross_reference: PSI:PI

SEQUEST:PeptideSp
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST result 'Sp' in out file (peptide).
has_obo_namespace: MS
id: MS:1001215

Axiom
annotated source: SEQUEST:PeptideSp
annotated property: definition
annotated target: The SEQUEST result 'Sp' in out file (peptide).
database_cross_reference: PSI:PI

SEQUEST:PeptideRankSp
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: integer
definition: The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'.
has_obo_namespace: MS
id: MS:1001217

Axiom
annotated source: SEQUEST:PeptideRankSp
annotated property: definition
annotated target: The SEQUEST result 'Sp' of 'Rank/Sp' in out file (peptide). Also called 'rsp'.
database_cross_reference: PSI:PI

SEQUEST:PeptideNumber
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: integer
definition: The SEQUEST result '#' in out file (peptide).
has_obo_namespace: MS
id: MS:1001218

Axiom
annotated source: SEQUEST:PeptideNumber
annotated property: definition
annotated target: The SEQUEST result '#' in out file (peptide).
database_cross_reference: PSI:PI

SEQUEST:PeptideIdnumber
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: integer
definition: The SEQUEST result 'Id#' in out file (peptide).
has_obo_namespace: MS
id: MS:1001219

Axiom
annotated source: SEQUEST:PeptideIdnumber
annotated property: definition
annotated target: The SEQUEST result 'Id#' in out file (peptide).
database_cross_reference: PSI:PI

frag: y ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: y ion.
has_obo_namespace: MS
id: MS:1001220

Axiom
annotated source: frag: y ion
annotated property: definition
annotated target: Fragmentation information, type of product: y ion.
database_cross_reference: PSI:PI

product ion attribute
type: Class
subclass of: MS_1002694
definition: Fragmentation information like ion types.
has_obo_namespace: MS
id: MS:1001221

Axiom
annotated source: product ion attribute
annotated property: definition
annotated target: Fragmentation information like ion types.
database_cross_reference: PSI:PI

frag: b ion - H2O
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: b ion without water.
has_obo_namespace: MS
id: MS:1001222

Axiom
annotated source: frag: b ion - H2O
annotated property: definition
annotated target: Fragmentation information, type of product: b ion without water.
database_cross_reference: PSI:PI

frag: y ion - H2O
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: y ion without water.
has_obo_namespace: MS
id: MS:1001223

Axiom
annotated source: frag: y ion - H2O
annotated property: definition
annotated target: Fragmentation information, type of product: y ion without water.
database_cross_reference: PSI:PI

frag: b ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: b ion.
has_obo_namespace: MS
id: MS:1001224

Axiom
annotated source: frag: b ion
annotated property: definition
annotated target: Fragmentation information, type of product: b ion.
database_cross_reference: PSI:PI

product ion m/z
type: Class
subclass of: product ion attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
definition: The m/z of the product ion.
has_exact_synonym: fragment ion m/z
has_obo_namespace: MS
id: MS:1001225

Axiom
annotated source: product ion m/z
annotated property: definition
annotated target: The m/z of the product ion.
database_cross_reference: PSI:PI

product ion intensity
type: Class
subclass of: product ion attribute
subclass of: Restriction
  on property: has_units
  some values from: number of detector counts
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak
subclass of: Restriction
  on property: has_units
  some values from: counts per second
subclass of: Restriction
  on property: has_units
  some values from: percent of base peak times 100
definition: The intensity of a single product ion.
has_exact_synonym: fragment ion intensity
has_obo_namespace: MS
id: MS:1001226

Axiom
annotated source: product ion intensity
annotated property: definition
annotated target: The intensity of a single product ion.
database_cross_reference: PSI:PI

product ion m/z error
type: Class
subclass of: product ion attribute
subclass of: Restriction
  on property: has_units
  some values from: m/z
subclass of: Restriction
  on property: has_units
  some values from: UO_0000166
subclass of: Restriction
  on property: has_units
  some values from: UO_0000169
definition: The product ion m/z error.
has_obo_namespace: MS
id: MS:1001227

Axiom
annotated source: product ion m/z error
annotated property: definition
annotated target: The product ion m/z error.
database_cross_reference: PSI:PI

frag: x ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: x ion.
has_obo_namespace: MS
id: MS:1001228

Axiom
annotated source: frag: x ion
annotated property: definition
annotated target: Fragmentation information, type of product: x ion.
database_cross_reference: PSI:PI

frag: a ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: a ion.
has_obo_namespace: MS
id: MS:1001229

Axiom
annotated source: frag: a ion
annotated property: definition
annotated target: Fragmentation information, type of product: a ion.
database_cross_reference: PSI:PI

frag: z ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: z ion.
has_obo_namespace: MS
id: MS:1001230

Axiom
annotated source: frag: z ion
annotated property: definition
annotated target: Fragmentation information, type of product: z ion.
database_cross_reference: PSI:PI

frag: c ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: c ion.
has_obo_namespace: MS
id: MS:1001231

Axiom
annotated source: frag: c ion
annotated property: definition
annotated target: Fragmentation information, type of product: c ion.
database_cross_reference: PSI:PI

frag: b ion - NH3
type: Class
subclass of: MS_1002307
definition: Ion b-NH3 fragmentation information, type of product: b ion without ammonia.
has_obo_namespace: MS
id: MS:1001232

Axiom
annotated source: frag: b ion - NH3
annotated property: definition
annotated target: Ion b-NH3 fragmentation information, type of product: b ion without ammonia.
database_cross_reference: PSI:PI

frag: y ion - NH3
type: Class
subclass of: MS_1002307
definition: Ion y-NH3 fragmentation information, type of product: y ion without ammonia.
has_obo_namespace: MS
id: MS:1001233

Axiom
annotated source: frag: y ion - NH3
annotated property: definition
annotated target: Ion y-NH3 fragmentation information, type of product: y ion without ammonia.
database_cross_reference: PSI:PI

frag: a ion - H2O
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: a ion without water.
has_obo_namespace: MS
id: MS:1001234

Axiom
annotated source: frag: a ion - H2O
annotated property: definition
annotated target: Fragmentation information, type of product: a ion without water.
database_cross_reference: PSI:PI

frag: a ion - NH3
type: Class
subclass of: MS_1002307
definition: Ion a-NH3 fragmentation information, type of product: a ion without ammonia.
has_obo_namespace: MS
id: MS:1001235

Axiom
annotated source: frag: a ion - NH3
annotated property: definition
annotated target: Ion a-NH3 fragmentation information, type of product: a ion without ammonia.
database_cross_reference: PSI:PI

frag: d ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: d ion.
has_obo_namespace: MS
id: MS:1001236

Axiom
annotated source: frag: d ion
annotated property: definition
annotated target: Fragmentation information, type of product: d ion.
database_cross_reference: PSI:PI

frag: v ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: v ion.
has_obo_namespace: MS
id: MS:1001237

Axiom
annotated source: frag: v ion
annotated property: definition
annotated target: Fragmentation information, type of product: v ion.
database_cross_reference: PSI:PI

frag: w ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: w ion.
has_obo_namespace: MS
id: MS:1001238

Axiom
annotated source: frag: w ion
annotated property: definition
annotated target: Fragmentation information, type of product: w ion.
database_cross_reference: PSI:PI

frag: immonium ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: immonium ion.
has_obo_namespace: MS
id: MS:1001239

Axiom
annotated source: frag: immonium ion
annotated property: definition
annotated target: Fragmentation information, type of product: immonium ion.
database_cross_reference: PSI:PI

non-identified ion
type: Class
subclass of: product ion attribute
definition: Non-identified ion.
has_obo_namespace: MS
id: MS:1001240

Axiom
annotated source: non-identified ion
annotated property: definition
annotated target: Non-identified ion.
database_cross_reference: PSI:PI

co-eluting ion
type: Class
subclass of: product ion attribute
definition: Co-eluting ion.
has_obo_namespace: MS
id: MS:1001241

Axiom
annotated source: co-eluting ion
annotated property: definition
annotated target: Co-eluting ion.
database_cross_reference: PSI:PI

SEQUEST out folder
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was a SEQUEST folder with its out files.
has_obo_namespace: MS
id: MS:1001242

Axiom
annotated source: SEQUEST out folder
annotated property: definition
annotated target: Source file for this mzIdentML was a SEQUEST folder with its out files.
database_cross_reference: PSI:PI

SEQUEST summary
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was a SEQUEST summary page (proteins).
has_obo_namespace: MS
id: MS:1001243

Axiom
annotated source: SEQUEST summary
annotated property: definition
annotated target: Source file for this mzIdentML was a SEQUEST summary page (proteins).
database_cross_reference: PSI:PI

PerSeptive PKS format
type: Class
subclass of: mass spectrometer file format
definition: PerSeptive peak list file format.
has_obo_namespace: MS
id: MS:1001245

Axiom
annotated source: PerSeptive PKS format
annotated property: definition
annotated target: PerSeptive peak list file format.
database_cross_reference: http://www.matrixscience.com/help/data_file_help.html#PKS

SCIEX API III format
type: Class
subclass of: mass spectrometer file format
definition: PE SCIEX peak list file format.
has_obo_namespace: MS
id: MS:1001246

Axiom
annotated source: SCIEX API III format
annotated property: definition
annotated target: PE SCIEX peak list file format.
database_cross_reference: http://www.matrixscience.com/help/data_file_help.html#API

Bruker XML format
type: Class
subclass of: mass spectrometer file format
definition: Bruker data exchange XML format.
has_obo_namespace: MS
id: MS:1001247

Axiom
annotated source: Bruker XML format
annotated property: definition
annotated target: Bruker data exchange XML format.
database_cross_reference: PSI:PI

search input details
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: Details describing the search input.
has_obo_namespace: MS
id: MS:1001249

Axiom
annotated source: search input details
annotated property: definition
annotated target: Details describing the search input.
database_cross_reference: PSI:PI

local FDR
type: Class
subclass of: peptide sequence-level identification statistic
subclass of: single protein identification statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Result of quality estimation: the local FDR at the current position of a sorted list.
has_obo_namespace: MS
id: MS:1001250

Axiom
annotated source: local FDR
annotated property: definition
annotated target: Result of quality estimation: the local FDR at the current position of a sorted list.
database_cross_reference: PSI:PI

Trypsin
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[KR])(?!P)
definition: Enzyme trypsin.
has_obo_namespace: MS
id: MS:1001251

Axiom
annotated source: Trypsin
annotated property: definition
annotated target: Enzyme trypsin.
database_cross_reference: PSI:PI

DB source EBI
type: Class
subclass of: database source
definition: Database source EBI.
has_obo_namespace: MS
id: MS:1001252

Axiom
annotated source: DB source EBI
annotated property: definition
annotated target: Database source EBI.
database_cross_reference: PSI:PI

DB source NCBI
type: Class
subclass of: database source
definition: Database source NCBI.
has_obo_namespace: MS
id: MS:1001253

Axiom
annotated source: DB source NCBI
annotated property: definition
annotated target: Database source NCBI.
database_cross_reference: PSI:PI

DB source UniProt
type: Class
subclass of: database source
definition: Database source UniProt.
has_obo_namespace: MS
id: MS:1001254

Axiom
annotated source: DB source UniProt
annotated property: definition
annotated target: Database source UniProt.
database_cross_reference: PSI:PI

fragment mass type average
type: Class
subclass of: mass type settings
definition: Mass type setting for fragment mass was average isotopic.
has_obo_namespace: MS
id: MS:1001255

Axiom
annotated source: fragment mass type average
annotated property: definition
annotated target: Mass type setting for fragment mass was average isotopic.
database_cross_reference: PSI:PI

fragment mass type mono
type: Class
subclass of: mass type settings
definition: Mass type setting for fragment mass was monoisotopic.
has_obo_namespace: MS
id: MS:1001256

Axiom
annotated source: fragment mass type mono
annotated property: definition
annotated target: Mass type setting for fragment mass was monoisotopic.
database_cross_reference: PSI:PI

param: v ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: side chain loss v ion.
has_obo_namespace: MS
id: MS:1001257

Axiom
annotated source: param: v ion
annotated property: definition
annotated target: Parameter information, type of product: side chain loss v ion.
database_cross_reference: PSI:PI

param: d ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: side chain loss d ion.
has_obo_namespace: MS
id: MS:1001258

Axiom
annotated source: param: d ion
annotated property: definition
annotated target: Parameter information, type of product: side chain loss d ion.
database_cross_reference: PSI:PI

param: immonium ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: immonium ion.
has_obo_namespace: MS
id: MS:1001259

Axiom
annotated source: param: immonium ion
annotated property: definition
annotated target: Parameter information, type of product: immonium ion.
database_cross_reference: PSI:PI

param: w ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: side chain loss w ion.
has_obo_namespace: MS
id: MS:1001260

Axiom
annotated source: param: w ion
annotated property: definition
annotated target: Parameter information, type of product: side chain loss w ion.
database_cross_reference: PSI:PI

param: x ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: x ion with charge on the C-terminal side.
has_obo_namespace: MS
id: MS:1001261

Axiom
annotated source: param: x ion
annotated property: definition
annotated target: Parameter information, type of product: x ion with charge on the C-terminal side.
database_cross_reference: PSI:PI

param: y ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: y ion with charge on the C-terminal side.
has_obo_namespace: MS
id: MS:1001262

Axiom
annotated source: param: y ion
annotated property: definition
annotated target: Parameter information, type of product: y ion with charge on the C-terminal side.
database_cross_reference: PSI:PI

param: z ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: z ion with charge on the C-terminal side.
has_obo_namespace: MS
id: MS:1001263

Axiom
annotated source: param: z ion
annotated property: definition
annotated target: Parameter information, type of product: z ion with charge on the C-terminal side.
database_cross_reference: PSI:PI

role type
type: Class
subclass of: contact attribute
definition: Role of a Person or Organization.
has_obo_namespace: MS
id: MS:1001266

Axiom
annotated source: role type
annotated property: definition
annotated target: Role of a Person or Organization.
database_cross_reference: PSI:PI

software vendor
type: Class
subclass of: role type
definition: Software vendor role.
has_obo_namespace: MS
id: MS:1001267

Axiom
annotated source: software vendor
annotated property: definition
annotated target: Software vendor role.
database_cross_reference: PSI:PI

programmer
type: Class
subclass of: role type
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Programmer role.
has_obo_namespace: MS
id: MS:1001268

Axiom
annotated source: programmer
annotated property: definition
annotated target: Programmer role.
database_cross_reference: PSI:PI

instrument vendor
type: Class
subclass of: role type
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Instrument vendor role.
has_obo_namespace: MS
id: MS:1001269

Axiom
annotated source: instrument vendor
annotated property: definition
annotated target: Instrument vendor role.
database_cross_reference: PSI:PI

lab personnel
type: Class
subclass of: role type
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Lab personnel role.
has_obo_namespace: MS
id: MS:1001270

Axiom
annotated source: lab personnel
annotated property: definition
annotated target: Lab personnel role.
database_cross_reference: PSI:PI

researcher
type: Class
subclass of: role type
definition: Researcher role.
has_obo_namespace: MS
id: MS:1001271

Axiom
annotated source: researcher
annotated property: definition
annotated target: Researcher role.
database_cross_reference: PSI:PI

(?<=R)(?!P)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Arg-C.
has_obo_namespace: MS
id: MS:1001272

Axiom
annotated source: (?<=R)(?!P)
annotated property: definition
annotated target: Regular expression for Arg-C.
database_cross_reference: PSI:PI

(?=[BD])
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Asp-N.
has_obo_namespace: MS
id: MS:1001273

Axiom
annotated source: (?=[BD])
annotated property: definition
annotated target: Regular expression for Asp-N.
database_cross_reference: PSI:PI

(?=[DE])
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Asp-N-ambic.
has_obo_namespace: MS
id: MS:1001274

Axiom
annotated source: (?=[DE])
annotated property: definition
annotated target: Regular expression for Asp-N-ambic.
database_cross_reference: PSI:PI

ProteinScape SearchEvent
type: Class
subclass of: intermediate analysis format
definition: Source data for this mzIdentML was a ProteinScape SearchEvent.
has_obo_namespace: MS
id: MS:1001275

Axiom
annotated source: ProteinScape SearchEvent
annotated property: definition
annotated target: Source data for this mzIdentML was a ProteinScape SearchEvent.
database_cross_reference: PSI:PI

ProteinScape Gel
type: Class
subclass of: intermediate analysis format
definition: Source data for this mzIdentML was a ProteinScape Gel.
has_obo_namespace: MS
id: MS:1001276

Axiom
annotated source: ProteinScape Gel
annotated property: definition
annotated target: Source data for this mzIdentML was a ProteinScape Gel.
database_cross_reference: PSI:PI

decoy DB accession regexp
type: Class
subclass of: decoy DB details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specify the regular expression for decoy accession numbers.
has_obo_namespace: MS
id: MS:1001283

Axiom
annotated source: decoy DB accession regexp
annotated property: definition
annotated target: Specify the regular expression for decoy accession numbers.
database_cross_reference: PSI:PI

decoy DB derived from
type: Class
subclass of: decoy DB details
definition: OBSOLETE The name of the database, the search database was derived from.
has_obo_namespace: MS
id: MS:1001284
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.
deprecated: true

Axiom
annotated source: decoy DB derived from
annotated property: definition
annotated target: OBSOLETE The name of the database, the search database was derived from.
database_cross_reference: PSI:PI

database IPI_mouse
type: Class
subclass of: database name
definition: International Protein Index database for Mus musculus sequences.
has_obo_namespace: MS
id: MS:1001285

Axiom
annotated source: database IPI_mouse
annotated property: definition
annotated target: International Protein Index database for Mus musculus sequences.
database_cross_reference: PSI:PI

database IPI_rat
type: Class
subclass of: database name
definition: International Protein Index database for Rattus norvegicus sequences.
has_obo_namespace: MS
id: MS:1001286

Axiom
annotated source: database IPI_rat
annotated property: definition
annotated target: International Protein Index database for Rattus norvegicus sequences.
database_cross_reference: PSI:PI

database IPI_zebrafish
type: Class
subclass of: database name
definition: International Protein Index database for Danio rerio sequences.
has_obo_namespace: MS
id: MS:1001287

Axiom
annotated source: database IPI_zebrafish
annotated property: definition
annotated target: International Protein Index database for Danio rerio sequences.
database_cross_reference: PSI:PI

database IPI_chicken
type: Class
subclass of: database name
definition: International Protein Index database for Gallus gallus sequences.
has_obo_namespace: MS
id: MS:1001288

Axiom
annotated source: database IPI_chicken
annotated property: definition
annotated target: International Protein Index database for Gallus gallus sequences.
database_cross_reference: PSI:PI

database IPI_cow
type: Class
subclass of: database name
definition: International Protein Index database for Bos taurus sequences.
has_obo_namespace: MS
id: MS:1001289

Axiom
annotated source: database IPI_cow
annotated property: definition
annotated target: International Protein Index database for Bos taurus sequences.
database_cross_reference: PSI:PI

database IPI_arabidopsis
type: Class
subclass of: database name
definition: International Protein Index database for Arabidopsis thaliana sequences.
has_obo_namespace: MS
id: MS:1001290

Axiom
annotated source: database IPI_arabidopsis
annotated property: definition
annotated target: International Protein Index database for Arabidopsis thaliana sequences.
database_cross_reference: PSI:PI

decoy DB from nr
type: Class
definition: OBSOLETE Decoy database from a non-redundant GenBank sequence database.
has_obo_namespace: MS
id: MS:1001291
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.
deprecated: true

Axiom
annotated source: decoy DB from nr
annotated property: definition
annotated target: OBSOLETE Decoy database from a non-redundant GenBank sequence database.
database_cross_reference: PSI:PI

decoy DB from IPI_rat
type: Class
definition: OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus.
has_obo_namespace: MS
id: MS:1001292
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.
deprecated: true

Axiom
annotated source: decoy DB from IPI_rat
annotated property: definition
annotated target: OBSOLETE Decoy database from a International Protein Index database for Rattus norvegicus.
database_cross_reference: PSI:PI

decoy DB from IPI_mouse
type: Class
definition: OBSOLETE Decoy database from a International Protein Index database for Mus musculus.
has_obo_namespace: MS
id: MS:1001293
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.
deprecated: true

Axiom
annotated source: decoy DB from IPI_mouse
annotated property: definition
annotated target: OBSOLETE Decoy database from a International Protein Index database for Mus musculus.
database_cross_reference: PSI:PI

decoy DB from IPI_arabidopsis
type: Class
definition: OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana.
has_obo_namespace: MS
id: MS:1001294
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.
deprecated: true

Axiom
annotated source: decoy DB from IPI_arabidopsis
annotated property: definition
annotated target: OBSOLETE Decoy database from a International Protein Index database for Arabidopsis thaliana.
database_cross_reference: PSI:PI

decoy DB from EST
type: Class
definition: OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database.
has_obo_namespace: MS
id: MS:1001295
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.
deprecated: true

Axiom
annotated source: decoy DB from EST
annotated property: definition
annotated target: OBSOLETE Decoy database from an expressed sequence tag nucleotide sequence database.
database_cross_reference: PSI:PI

decoy DB from IPI_zebrafish
type: Class
definition: OBSOLETE Decoy database from a International Protein Index database for Danio rerio.
has_obo_namespace: MS
id: MS:1001296
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.
deprecated: true

Axiom
annotated source: decoy DB from IPI_zebrafish
annotated property: definition
annotated target: OBSOLETE Decoy database from a International Protein Index database for Danio rerio.
database_cross_reference: PSI:PI

decoy DB from UniProtKB/Swiss-Prot
type: Class
definition: OBSOLETE Decoy database from a Swiss-Prot protein sequence database.
has_obo_namespace: MS
id: MS:1001297
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.
deprecated: true

Axiom
annotated source: decoy DB from UniProtKB/Swiss-Prot
annotated property: definition
annotated target: OBSOLETE Decoy database from a Swiss-Prot protein sequence database.
database_cross_reference: PSI:PI

decoy DB from IPI_chicken
type: Class
definition: OBSOLETE Decoy database from a International Protein Index database for Gallus gallus.
has_obo_namespace: MS
id: MS:1001298
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.
deprecated: true

Axiom
annotated source: decoy DB from IPI_chicken
annotated property: definition
annotated target: OBSOLETE Decoy database from a International Protein Index database for Gallus gallus.
database_cross_reference: PSI:PI

decoy DB from IPI_cow
type: Class
definition: OBSOLETE Decoy database from a International Protein Index database for Bos taurus.
has_obo_namespace: MS
id: MS:1001299
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.
deprecated: true

Axiom
annotated source: decoy DB from IPI_cow
annotated property: definition
annotated target: OBSOLETE Decoy database from a International Protein Index database for Bos taurus.
database_cross_reference: PSI:PI

decoy DB from IPI_human
type: Class
definition: OBSOLETE Decoy database from a International Protein Index database for Homo sapiens.
has_obo_namespace: MS
id: MS:1001300
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.
deprecated: true

Axiom
annotated source: decoy DB from IPI_human
annotated property: definition
annotated target: OBSOLETE Decoy database from a International Protein Index database for Homo sapiens.
database_cross_reference: PSI:PI

protein rank
type: Class
subclass of: protein-level identification attribute
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The rank of the protein in a list sorted by the search engine.
has_obo_namespace: MS
id: MS:1001301

Axiom
annotated source: protein rank
annotated property: definition
annotated target: The rank of the protein in a list sorted by the search engine.
database_cross_reference: PSI:PI

search engine specific input parameter
type: Class
subclass of: MS_1002093
definition: Search engine specific input parameters.
has_obo_namespace: MS
id: MS:1001302

Axiom
annotated source: search engine specific input parameter
annotated property: definition
annotated target: Search engine specific input parameters.
database_cross_reference: PSI:PI

Arg-C
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=R)(?!P)
definition: Endoproteinase Arg-C.
has_exact_synonym: Clostripain
has_exact_synonym: Trypsin/R
has_obo_namespace: MS
id: MS:1001303

Axiom
annotated source: Arg-C
annotated property: definition
annotated target: Endoproteinase Arg-C.
database_cross_reference: PSI:PI

Asp-N
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?=[BD])
definition: Endoproteinase Asp-N.
has_obo_namespace: MS
id: MS:1001304

Axiom
annotated source: Asp-N
annotated property: definition
annotated target: Endoproteinase Asp-N.
database_cross_reference: PSI:PI

Asp-N_ambic
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?=[DE])
definition: Enzyme Asp-N, Ammonium Bicarbonate (AmBic).
has_obo_namespace: MS
id: MS:1001305

Axiom
annotated source: Asp-N_ambic
annotated property: definition
annotated target: Enzyme Asp-N, Ammonium Bicarbonate (AmBic).
database_cross_reference: PSI:PI

Chymotrypsin
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[FYWL])(?!P)
definition: Enzyme chymotrypsin.
has_obo_namespace: MS
id: MS:1001306

Axiom
annotated source: Chymotrypsin
annotated property: definition
annotated target: Enzyme chymotrypsin.
database_cross_reference: PSI:PI

CNBr
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=M)
definition: Cyanogen bromide.
has_obo_namespace: MS
id: MS:1001307

Axiom
annotated source: CNBr
annotated property: definition
annotated target: Cyanogen bromide.
database_cross_reference: PSI:PI

Formic_acid
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: ((?<=D))|((?=D))
definition: Formic acid.
has_obo_namespace: MS
id: MS:1001308

Axiom
annotated source: Formic_acid
annotated property: definition
annotated target: Formic acid.
database_cross_reference: PubChem_Compound:284

Lys-C
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=K)(?!P)
definition: Endoproteinase Lys-C.
has_exact_synonym: Trypsin/K
has_obo_namespace: MS
id: MS:1001309

Axiom
annotated source: Lys-C
annotated property: definition
annotated target: Endoproteinase Lys-C.
database_cross_reference: PSI:PI

Lys-C/P
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=K)
definition: Proteinase Lys-C/P.
has_obo_namespace: MS
id: MS:1001310

Axiom
annotated source: Lys-C/P
annotated property: definition
annotated target: Proteinase Lys-C/P.
database_cross_reference: PSI:PI

PepsinA
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[FL])
definition: PepsinA proteinase.
has_obo_namespace: MS
id: MS:1001311

Axiom
annotated source: PepsinA
annotated property: definition
annotated target: PepsinA proteinase.
database_cross_reference: PSI:PI

TrypChymo
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[FYWLKR])(?!P)
definition: Cleavage agent TrypChymo.
has_obo_namespace: MS
id: MS:1001312

Axiom
annotated source: TrypChymo
annotated property: definition
annotated target: Cleavage agent TrypChymo.
database_cross_reference: PSI:PI

Trypsin/P
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[KR])
definition: Cleavage agent Trypsin/P.
has_obo_namespace: MS
id: MS:1001313

Axiom
annotated source: Trypsin/P
annotated property: definition
annotated target: Cleavage agent Trypsin/P.
database_cross_reference: PSI:PI

V8-DE
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[BDEZ])(?!P)
definition: Cleavage agent V8-DE.
has_obo_namespace: MS
id: MS:1001314

Axiom
annotated source: V8-DE
annotated property: definition
annotated target: Cleavage agent V8-DE.
database_cross_reference: PSI:PI

V8-E
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[EZ])(?!P)
definition: Cleavage agent V8-E.
has_obo_namespace: MS
id: MS:1001315

Axiom
annotated source: V8-E
annotated property: definition
annotated target: Cleavage agent V8-E.
database_cross_reference: PSI:PI

Mascot:SigThreshold
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05).
has_obo_namespace: MS
id: MS:1001316

Axiom
annotated source: Mascot:SigThreshold
annotated property: definition
annotated target: Significance threshold below which the p-value of a peptide match must lie to be considered statistically significant (default 0.05).
database_cross_reference: PSI:PI

Mascot:MaxProteinHits
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1001317

Axiom
annotated source: Mascot:MaxProteinHits
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

Mascot:ProteinScoringMethod
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Mascot protein scoring method; either 'Standard' or 'MudPIT'.
has_obo_namespace: MS
id: MS:1001318

Axiom
annotated source: Mascot:ProteinScoringMethod
annotated property: definition
annotated target: Mascot protein scoring method; either 'Standard' or 'MudPIT'.
database_cross_reference: PSI:PI

Mascot:MinMSMSThreshold
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: double
definition: 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.
has_obo_namespace: MS
id: MS:1001319

Axiom
annotated source: Mascot:MinMSMSThreshold
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

Mascot:ShowHomologousProteinsWithSamePeptides
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed.
has_obo_namespace: MS
id: MS:1001320

Axiom
annotated source: Mascot:ShowHomologousProteinsWithSamePeptides
annotated property: definition
annotated target: If true, show (sequence or spectrum) same-set proteins. Otherwise they are suppressed.
database_cross_reference: PSI:PI

Mascot:ShowHomologousProteinsWithSubsetOfPeptides
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed.
has_obo_namespace: MS
id: MS:1001321

Axiom
annotated source: Mascot:ShowHomologousProteinsWithSubsetOfPeptides
annotated property: definition
annotated target: If true, show (sequence or spectrum) sub-set and subsumable proteins. Otherwise they are suppressed.
database_cross_reference: PSI:PI

Mascot:RequireBoldRed
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: 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.
has_obo_namespace: MS
id: MS:1001322

Axiom
annotated source: Mascot:RequireBoldRed
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

Mascot:UseUnigeneClustering
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use.
has_obo_namespace: MS
id: MS:1001323

Axiom
annotated source: Mascot:UseUnigeneClustering
annotated property: definition
annotated target: If true, then the search results are against a nucleic acid database and Unigene clustering is enabled. Otherwise UniGene clustering is not in use.
database_cross_reference: PSI:PI

Mascot:IncludeErrorTolerantMatches
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: 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.
has_obo_namespace: MS
id: MS:1001324

Axiom
annotated source: Mascot:IncludeErrorTolerantMatches
annotated property: definition
annotated target: 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.
database_cross_reference: http://www.matrixscience.com/help/error_tolerant_help.html

Mascot:ShowDecoyMatches
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: 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.
has_obo_namespace: MS
id: MS:1001325

Axiom
annotated source: Mascot:ShowDecoyMatches
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

add_others
type: Class
definition: OBSOLETE.
has_obo_namespace: MS
id: MS:1001326
comment: This former purgatory term was made obsolete.
deprecated: true

Axiom
annotated source: add_others
annotated property: definition
annotated target: OBSOLETE.
database_cross_reference: PSI:PI

Spectronaut
type: Class
subclass of: analysis software
subclass of: MS_1003207
definition: Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data.
has_obo_namespace: MS
id: MS:1001327

Axiom
annotated source: Spectronaut
annotated property: definition
annotated target: Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data.
database_cross_reference: https://doi.org/10.1074/mcp.M114.044305

OMSSA:evalue
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OMSSA E-value.
has_obo_namespace: MS
id: MS:1001328

Axiom
annotated source: OMSSA:evalue
annotated property: definition
annotated target: OMSSA E-value.
database_cross_reference: PSI:PI

OMSSA:pvalue
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OMSSA p-value.
has_obo_namespace: MS
id: MS:1001329

Axiom
annotated source: OMSSA:pvalue
annotated property: definition
annotated target: OMSSA p-value.
database_cross_reference: PSI:PI

X!Tandem:expect
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The X!Tandem expectation value.
has_obo_namespace: MS
id: MS:1001330

Axiom
annotated source: X!Tandem:expect
annotated property: definition
annotated target: The X!Tandem expectation value.
database_cross_reference: PSI:PI

X!Tandem:hyperscore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The X!Tandem hyperscore.
has_obo_namespace: MS
id: MS:1001331

Axiom
annotated source: X!Tandem:hyperscore
annotated property: definition
annotated target: The X!Tandem hyperscore.
database_cross_reference: PSI:PI

(?<=[FYWL])(?!P)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Chymotrypsin.
has_obo_namespace: MS
id: MS:1001332

Axiom
annotated source: (?<=[FYWL])(?!P)
annotated property: definition
annotated target: Regular expression for Chymotrypsin.
database_cross_reference: PSI:PI

(?<=M)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for CNBr.
has_obo_namespace: MS
id: MS:1001333

Axiom
annotated source: (?<=M)
annotated property: definition
annotated target: Regular expression for CNBr.
database_cross_reference: PSI:PI

((?<=D))|((?=D))
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for formic acid.
has_obo_namespace: MS
id: MS:1001334

Axiom
annotated source: ((?<=D))|((?=D))
annotated property: definition
annotated target: Regular expression for formic acid.
database_cross_reference: PSI:PI

(?<=K)(?!P)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Lys-C.
has_obo_namespace: MS
id: MS:1001335

Axiom
annotated source: (?<=K)(?!P)
annotated property: definition
annotated target: Regular expression for Lys-C.
database_cross_reference: PSI:PI

(?<=K)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Lys-C/P.
has_obo_namespace: MS
id: MS:1001336

Axiom
annotated source: (?<=K)
annotated property: definition
annotated target: Regular expression for Lys-C/P.
database_cross_reference: PSI:PI

(?<=[FL])
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for PepsinA.
has_obo_namespace: MS
id: MS:1001337

Axiom
annotated source: (?<=[FL])
annotated property: definition
annotated target: Regular expression for PepsinA.
database_cross_reference: PSI:PI

(?<=[FYWLKR])(?!P)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for TrypChymo.
has_obo_namespace: MS
id: MS:1001338

Axiom
annotated source: (?<=[FYWLKR])(?!P)
annotated property: definition
annotated target: Regular expression for TrypChymo.
database_cross_reference: PSI:PI

(?<=[KR])
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for Trypsin/P.
has_obo_namespace: MS
id: MS:1001339

Axiom
annotated source: (?<=[KR])
annotated property: definition
annotated target: Regular expression for Trypsin/P.
database_cross_reference: PSI:PI

(?<=[BDEZ])(?!P)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for V8-DE.
has_obo_namespace: MS
id: MS:1001340

Axiom
annotated source: (?<=[BDEZ])(?!P)
annotated property: definition
annotated target: Regular expression for V8-DE.
database_cross_reference: PSI:PI

(?<=[EZ])(?!P)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for V8-E.
has_obo_namespace: MS
id: MS:1001341

Axiom
annotated source: (?<=[EZ])(?!P)
annotated property: definition
annotated target: Regular expression for V8-E.
database_cross_reference: PSI:PI

database sequence details
type: Class
subclass of: search database details
definition: Details about a single database sequence.
has_obo_namespace: MS
id: MS:1001342

Axiom
annotated source: database sequence details
annotated property: definition
annotated target: Details about a single database sequence.
database_cross_reference: PSI:PI

NA sequence
type: Class
subclass of: database sequence details
definition: The sequence is a nucleic acid sequence.
has_obo_namespace: MS
id: MS:1001343

Axiom
annotated source: NA sequence
annotated property: definition
annotated target: The sequence is a nucleic acid sequence.
database_cross_reference: PSI:PI

AA sequence
type: Class
subclass of: database sequence details
definition: The sequence is a amino acid sequence.
has_obo_namespace: MS
id: MS:1001344

Axiom
annotated source: AA sequence
annotated property: definition
annotated target: The sequence is a amino acid sequence.
database_cross_reference: PSI:PI

mass table source
type: Class
subclass of: mass table options
definition: Children of this term specify the source of the mass table used.
has_obo_namespace: MS
id: MS:1001345

Axiom
annotated source: mass table source
annotated property: definition
annotated target: Children of this term specify the source of the mass table used.
database_cross_reference: PSI:PI

AAIndex mass table
type: Class
subclass of: mass table source
definition: The masses used in the mass table are taken from AAIndex.
has_obo_namespace: MS
id: MS:1001346

Axiom
annotated source: AAIndex mass table
annotated property: definition
annotated target: The masses used in the mass table are taken from AAIndex.
database_cross_reference: PSI:PI

database file formats
type: Class
subclass of: search database details
definition: The children of this term define file formats of the sequence database used.
has_obo_namespace: MS
id: MS:1001347

Axiom
annotated source: database file formats
annotated property: definition
annotated target: The children of this term define file formats of the sequence database used.
database_cross_reference: PSI:PI

FASTA format
type: Class
subclass of: database file formats
definition: The sequence database was stored in the FASTA format.
has_obo_namespace: MS
id: MS:1001348

Axiom
annotated source: FASTA format
annotated property: definition
annotated target: The sequence database was stored in the FASTA format.
database_cross_reference: PSI:PI

ASN.1
type: Class
subclass of: database file formats
definition: The sequence database was stored in the Abstract Syntax Notation 1 format.
has_obo_namespace: MS
id: MS:1001349

Axiom
annotated source: ASN.1
annotated property: definition
annotated target: The sequence database was stored in the Abstract Syntax Notation 1 format.
database_cross_reference: PSI:PI

NCBI *.p*
type: Class
subclass of: database file formats
definition: The sequence database was stored in the NCBI formatdb (*.p*) format.
has_obo_namespace: MS
id: MS:1001350

Axiom
annotated source: NCBI *.p*
annotated property: definition
annotated target: The sequence database was stored in the NCBI formatdb (*.p*) format.
database_cross_reference: PSI:PI

clustal aln
type: Class
subclass of: database file formats
definition: ClustalW ALN (multiple alignment) format.
has_obo_namespace: MS
id: MS:1001351

Axiom
annotated source: clustal aln
annotated property: definition
annotated target: ClustalW ALN (multiple alignment) format.
database_cross_reference: PSI:PI

embl em
type: Class
subclass of: database file formats
definition: EMBL entry format.
has_obo_namespace: MS
id: MS:1001352

Axiom
annotated source: embl em
annotated property: definition
annotated target: EMBL entry format.
database_cross_reference: PSI:PI

NBRF PIR
type: Class
subclass of: database file formats
definition: The NBRF PIR was used as format.
has_obo_namespace: MS
id: MS:1001353

Axiom
annotated source: NBRF PIR
annotated property: definition
annotated target: The NBRF PIR was used as format.
database_cross_reference: PSI:PI

mass table options
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: Root node for options for the mass table used.
has_obo_namespace: MS
id: MS:1001354

Axiom
annotated source: mass table options
annotated property: definition
annotated target: Root node for options for the mass table used.
database_cross_reference: PSI:PI

peptide descriptions
type: Class
subclass of: peptide sequence-level identification attribute
definition: Descriptions of peptides.
has_obo_namespace: MS
id: MS:1001355

Axiom
annotated source: peptide descriptions
annotated property: definition
annotated target: Descriptions of peptides.
database_cross_reference: PSI:PI

spectrum descriptions
type: Class
subclass of: search input details
definition: Descriptions of the input spectra.
has_obo_namespace: MS
id: MS:1001356

Axiom
annotated source: spectrum descriptions
annotated property: definition
annotated target: Descriptions of the input spectra.
database_cross_reference: PSI:PI

spectrum quality descriptions
type: Class
subclass of: spectrum descriptions
definition: Description of the quality of the input spectrum.
has_obo_namespace: MS
id: MS:1001357

Axiom
annotated source: spectrum quality descriptions
annotated property: definition
annotated target: Description of the quality of the input spectrum.
database_cross_reference: PSI:PI

msmsEval quality
type: Class
subclass of: spectrum quality descriptions
subclass of: Restriction
  on property: has value type
  some values from: double
definition: This term reports the quality of the spectrum assigned by msmsEval.
has_obo_namespace: MS
id: MS:1001358

Axiom
annotated source: msmsEval quality
annotated property: definition
annotated target: This term reports the quality of the spectrum assigned by msmsEval.
database_cross_reference: PSI:PI

ambiguous residues
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: Children of this term describe ambiguous residues.
has_obo_namespace: MS
id: MS:1001359

Axiom
annotated source: ambiguous residues
annotated property: definition
annotated target: Children of this term describe ambiguous residues.
database_cross_reference: PSI:PI

alternate single letter codes
type: Class
subclass of: ambiguous residues
subclass of: Restriction
  on property: has value type
  some values from: string
definition: List of standard residue one letter codes which are used to replace a non-standard.
has_obo_namespace: MS
id: MS:1001360

Axiom
annotated source: alternate single letter codes
annotated property: definition
annotated target: List of standard residue one letter codes which are used to replace a non-standard.
database_cross_reference: PSI:PI

alternate mass
type: Class
subclass of: ambiguous residues
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: List of masses a non-standard letter code is replaced with.
has_obo_namespace: MS
id: MS:1001361

Axiom
annotated source: alternate mass
annotated property: definition
annotated target: List of masses a non-standard letter code is replaced with.
database_cross_reference: PSI:PI

number of unmatched peaks
type: Class
subclass of: MS_1002345
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: The number of unmatched peaks.
has_obo_namespace: MS
id: MS:1001362

Axiom
annotated source: number of unmatched peaks
annotated property: definition
annotated target: The number of unmatched peaks.
database_cross_reference: PSI:PI

peptide unique to one protein
type: Class
subclass of: peptide sharing details
definition: A peptide matching only one.
has_obo_namespace: MS
id: MS:1001363

Axiom
annotated source: peptide unique to one protein
annotated property: definition
annotated target: A peptide matching only one.
database_cross_reference: PSI:PI

peptide sequence-level global FDR
type: Class
subclass of: MS_1002703
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002305
subclass of: Restriction
  on property: has value type
  some values from: double
definition: 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).
has_obo_namespace: MS
id: MS:1001364

Axiom
annotated source: peptide sequence-level global FDR
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:PI

frag: internal yb ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: internal yb ion.
has_obo_namespace: MS
id: MS:1001365

Axiom
annotated source: frag: internal yb ion
annotated property: definition
annotated target: Fragmentation information, type of product: internal yb ion.
database_cross_reference: PSI:PI

frag: internal ya ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: internal ya ion.
has_obo_namespace: MS
id: MS:1001366

Axiom
annotated source: frag: internal ya ion
annotated property: definition
annotated target: Fragmentation information, type of product: internal ya ion.
database_cross_reference: PSI:PI

frag: z+1 ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: z+1 ion.
has_obo_namespace: MS
id: MS:1001367

Axiom
annotated source: frag: z+1 ion
annotated property: definition
annotated target: Fragmentation information, type of product: z+1 ion.
database_cross_reference: PSI:PI

frag: z+2 ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: z+2 ion.
has_obo_namespace: MS
id: MS:1001368

Axiom
annotated source: frag: z+2 ion
annotated property: definition
annotated target: Fragmentation information, type of product: z+2 ion.
database_cross_reference: PSI:PI

text format
type: Class
subclass of: mass spectrometer file format
definition: Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search.
has_obo_namespace: MS
id: MS:1001369

Axiom
annotated source: text format
annotated property: definition
annotated target: Simple text file format of "m/z [intensity]" values for a PMF (or single MS2) search.
database_cross_reference: PSI:PI

Mascot:homology threshold
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Mascot result 'homology threshold'.
has_obo_namespace: MS
id: MS:1001370

Axiom
annotated source: Mascot:homology threshold
annotated property: definition
annotated target: The Mascot result 'homology threshold'.
database_cross_reference: PSI:PI

Mascot:identity threshold
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Mascot result 'identity threshold'.
has_obo_namespace: MS
id: MS:1001371

Axiom
annotated source: Mascot:identity threshold
annotated property: definition
annotated target: The Mascot result 'identity threshold'.
database_cross_reference: PSI:PI

SEQUEST:Sequences
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
has_obo_namespace: MS
id: MS:1001372

SEQUEST:TIC
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: SEQUEST total ion current.
has_obo_namespace: MS
id: MS:1001373

Axiom
annotated source: SEQUEST:TIC
annotated property: definition
annotated target: SEQUEST total ion current.
database_cross_reference: PSI:PI

SEQUEST:Sum
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
has_obo_namespace: MS
id: MS:1001374

Phenyx:Instrument Type
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The instrument type parameter value in Phenyx.
has_obo_namespace: MS
id: MS:1001375

Axiom
annotated source: Phenyx:Instrument Type
annotated property: definition
annotated target: The instrument type parameter value in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Scoring Model
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The selected scoring model in Phenyx.
has_obo_namespace: MS
id: MS:1001376

Axiom
annotated source: Phenyx:Scoring Model
annotated property: definition
annotated target: The selected scoring model in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Default Parent Charge
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The default parent charge value in Phenyx.
has_obo_namespace: MS
id: MS:1001377

Axiom
annotated source: Phenyx:Default Parent Charge
annotated property: definition
annotated target: The default parent charge value in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Trust Parent Charge
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct.
has_obo_namespace: MS
id: MS:1001378

Axiom
annotated source: Phenyx:Trust Parent Charge
annotated property: definition
annotated target: The parameter in Phenyx that specifies if the experimental charge state is to be considered as correct.
database_cross_reference: PSI:PI

Phenyx:Turbo
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: The turbo mode parameter in Phenyx.
has_obo_namespace: MS
id: MS:1001379

Axiom
annotated source: Phenyx:Turbo
annotated property: definition
annotated target: The turbo mode parameter in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Turbo:ErrorTol
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx.
has_obo_namespace: MS
id: MS:1001380

Axiom
annotated source: Phenyx:Turbo:ErrorTol
annotated property: definition
annotated target: The maximal allowed fragment m/z error filter considered in the turbo mode of Phenyx.
database_cross_reference: PSI:PI

Phenyx:Turbo:Coverage
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx.
has_obo_namespace: MS
id: MS:1001381

Axiom
annotated source: Phenyx:Turbo:Coverage
annotated property: definition
annotated target: The minimal peptide sequence coverage value, expressed in percent, considered in the turbo mode of Phenyx.
database_cross_reference: PSI:PI

Phenyx:Turbo:Series
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The list of ion series considered in the turbo mode of Phenyx.
has_obo_namespace: MS
id: MS:1001382

Axiom
annotated source: Phenyx:Turbo:Series
annotated property: definition
annotated target: The list of ion series considered in the turbo mode of Phenyx.
database_cross_reference: PSI:PI

Phenyx:MinPepLength
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The minimal number of residues for a peptide to be considered for a valid identification in Phenyx.
has_obo_namespace: MS
id: MS:1001383

Axiom
annotated source: Phenyx:MinPepLength
annotated property: definition
annotated target: The minimal number of residues for a peptide to be considered for a valid identification in Phenyx.
database_cross_reference: PSI:PI

Phenyx:MinPepzscore
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx.
has_obo_namespace: MS
id: MS:1001384

Axiom
annotated source: Phenyx:MinPepzscore
annotated property: definition
annotated target: The minimal peptide z-score for a peptide to be considered for a valid identification in Phenyx.
database_cross_reference: PSI:PI

Phenyx:MaxPepPvalue
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx.
has_obo_namespace: MS
id: MS:1001385

Axiom
annotated source: Phenyx:MaxPepPvalue
annotated property: definition
annotated target: The maximal peptide p-value for a peptide to be considered for a valid identification in Phenyx.
database_cross_reference: PSI:PI

Phenyx:AC Score
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx.
has_obo_namespace: MS
id: MS:1001386

Axiom
annotated source: Phenyx:AC Score
annotated property: definition
annotated target: The minimal protein score required for a protein database entry to be displayed in the list of identified proteins in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Conflict Resolution
type: Class
subclass of: MS_1002097
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used.
has_obo_namespace: MS
id: MS:1001387

Axiom
annotated source: Phenyx:Conflict Resolution
annotated property: definition
annotated target: The parameter in Phenyx that specifies if the conflict resolution algorithm is to be used.
database_cross_reference: PSI:PI

Phenyx:AC
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The primary sequence database identifier of a protein in Phenyx.
has_obo_namespace: MS
id: MS:1001388

Axiom
annotated source: Phenyx:AC
annotated property: definition
annotated target: The primary sequence database identifier of a protein in Phenyx.
database_cross_reference: PSI:PI

Phenyx:ID
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A secondary sequence database identifier of a protein in Phenyx.
has_obo_namespace: MS
id: MS:1001389

Axiom
annotated source: Phenyx:ID
annotated property: definition
annotated target: A secondary sequence database identifier of a protein in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Score
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The protein score of a protein match in Phenyx.
has_obo_namespace: MS
id: MS:1001390

Axiom
annotated source: Phenyx:Score
annotated property: definition
annotated target: The protein score of a protein match in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Peptides1
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: First number of phenyx result "#Peptides".
has_obo_namespace: MS
id: MS:1001391

Axiom
annotated source: Phenyx:Peptides1
annotated property: definition
annotated target: First number of phenyx result "#Peptides".
database_cross_reference: PSI:PI

Phenyx:Peptides2
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: Second number of phenyx result "#Peptides".
has_obo_namespace: MS
id: MS:1001392

Axiom
annotated source: Phenyx:Peptides2
annotated property: definition
annotated target: Second number of phenyx result "#Peptides".
database_cross_reference: PSI:PI

Phenyx:Auto
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: The value of the automatic peptide acceptance filter in Phenyx.
has_obo_namespace: MS
id: MS:1001393

Axiom
annotated source: Phenyx:Auto
annotated property: definition
annotated target: The value of the automatic peptide acceptance filter in Phenyx.
database_cross_reference: PSI:PI

Phenyx:User
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: The value of the user-defined peptide acceptance filter in Phenyx.
has_obo_namespace: MS
id: MS:1001394

Axiom
annotated source: Phenyx:User
annotated property: definition
annotated target: The value of the user-defined peptide acceptance filter in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Pepzscore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The z-score value of a peptide sequence match in Phenyx.
has_obo_namespace: MS
id: MS:1001395

Axiom
annotated source: Phenyx:Pepzscore
annotated property: definition
annotated target: The z-score value of a peptide sequence match in Phenyx.
database_cross_reference: PSI:PI

Phenyx:PepPvalue
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: MS_1002358
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The p-value of a peptide sequence match in Phenyx.
has_obo_namespace: MS
id: MS:1001396

Axiom
annotated source: Phenyx:PepPvalue
annotated property: definition
annotated target: The p-value of a peptide sequence match in Phenyx.
database_cross_reference: PSI:PI

Phenyx:NumberOfMC
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The number of missed cleavages of a peptide sequence in Phenyx.
has_obo_namespace: MS
id: MS:1001397

Axiom
annotated source: Phenyx:NumberOfMC
annotated property: definition
annotated target: The number of missed cleavages of a peptide sequence in Phenyx.
database_cross_reference: PSI:PI

Phenyx:Modif
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx.
has_obo_namespace: MS
id: MS:1001398

Axiom
annotated source: Phenyx:Modif
annotated property: definition
annotated target: The expression of the nature and position(s) of modified residue(s) on a matched peptide sequence in Phenyx.
database_cross_reference: PSI:PI

OMSSA csv format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in OMSSA csv file format.
has_obo_namespace: MS
id: MS:1001399

Axiom
annotated source: OMSSA csv format
annotated property: definition
annotated target: Source file for this mzIdentML was in OMSSA csv file format.
database_cross_reference: PSI:PI

OMSSA xml format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in OMSSA xml file format.
has_obo_namespace: MS
id: MS:1001400

Axiom
annotated source: OMSSA xml format
annotated property: definition
annotated target: Source file for this mzIdentML was in OMSSA xml file format.
database_cross_reference: PSI:PI

X!Tandem xml format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in X!Tandem xml file format.
has_obo_namespace: MS
id: MS:1001401

Axiom
annotated source: X!Tandem xml format
annotated property: definition
annotated target: Source file for this mzIdentML was in X!Tandem xml file format.
database_cross_reference: PSI:PI

spectrum identification result details
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: This subsection describes terms which can describe details of spectrum identification results.
has_obo_namespace: MS
id: MS:1001405

Axiom
annotated source: spectrum identification result details
annotated property: definition
annotated target: This subsection describes terms which can describe details of spectrum identification results.
database_cross_reference: PSI:PI

param: internal yb ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: internal yb ion.
has_obo_namespace: MS
id: MS:1001406

Axiom
annotated source: param: internal yb ion
annotated property: definition
annotated target: Parameter information, type of product: internal yb ion.
database_cross_reference: PSI:PI

param: internal ya ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: internal ya ion.
has_obo_namespace: MS
id: MS:1001407

Axiom
annotated source: param: internal ya ion
annotated property: definition
annotated target: Parameter information, type of product: internal ya ion.
database_cross_reference: PSI:PI

param: z+1 ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: z+1 ion.
has_obo_namespace: MS
id: MS:1001408

Axiom
annotated source: param: z+1 ion
annotated property: definition
annotated target: Parameter information, type of product: z+1 ion.
database_cross_reference: PSI:PI

param: z+2 ion
type: Class
subclass of: MS_1002473
definition: Parameter information, type of product: z+2 ion.
has_obo_namespace: MS
id: MS:1001409

Axiom
annotated source: param: z+2 ion
annotated property: definition
annotated target: Parameter information, type of product: z+2 ion.
database_cross_reference: PSI:PI

translation start codons
type: Class
subclass of: search database details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The translation start codons used to translate the nucleotides to amino acids.
has_obo_namespace: MS
id: MS:1001410

Axiom
annotated source: translation start codons
annotated property: definition
annotated target: The translation start codons used to translate the nucleotides to amino acids.
database_cross_reference: PSI:PI

search tolerance specification
type: Class
subclass of: search input details
definition: Specification of the search tolerance.
has_obo_namespace: MS
id: MS:1001411

Axiom
annotated source: search tolerance specification
annotated property: definition
annotated target: Specification of the search tolerance.
database_cross_reference: PSI:PI

search tolerance plus value
type: Class
subclass of: search tolerance specification
subclass of: Restriction
  on property: has_units
  some values from: UO_0000166
subclass of: Restriction
  on property: has_units
  some values from: UO_0000169
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
has_obo_namespace: MS
id: MS:1001412

search tolerance minus value
type: Class
subclass of: search tolerance specification
subclass of: Restriction
  on property: has_units
  some values from: UO_0000166
subclass of: Restriction
  on property: has_units
  some values from: UO_0000169
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
has_obo_namespace: MS
id: MS:1001413

MGF scans
type: Class
subclass of: spectrum identification result details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file.
term replaced by: MS:1000797
has_obo_namespace: MS
id: MS:1001414
deprecated: true

Axiom
annotated source: MGF scans
annotated property: definition
annotated target: OBSOLETE: replaced by MS:1000797 (peak list scans): This term can hold the scans attribute from an MGF input file.
database_cross_reference: PSI:PI

MGF raw scans
type: Class
subclass of: spectrum identification result details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file.
term replaced by: MS:1000798
has_obo_namespace: MS
id: MS:1001415
deprecated: true

Axiom
annotated source: MGF raw scans
annotated property: definition
annotated target: OBSOLETE: replaced by MS:1000798 (peak list raw scans): This term can hold the raw scans attribute from an MGF input file.
database_cross_reference: PSI:PI

spectrum title
type: Class
subclass of: spectrum identification result details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE.
term replaced by: MS:1000796
has_obo_namespace: MS
id: MS:1001416
deprecated: true

Axiom
annotated source: spectrum title
annotated property: definition
annotated target: OBSOLETE: replaced by MS:1000796 (spectrum title): Holds the spectrum title from different input file formats, e.g. MGF TITLE.
database_cross_reference: PSI:PI

SpectraST:dot
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: SpectraST dot product of two spectra, measuring spectral similarity.
has_obo_namespace: MS
id: MS:1001417

Axiom
annotated source: SpectraST:dot
annotated property: definition
annotated target: SpectraST dot product of two spectra, measuring spectral similarity.
database_cross_reference: PSI:PI

SpectraST:dot_bias
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: SpectraST measure of how much of the dot product is dominated by a few peaks.
has_obo_namespace: MS
id: MS:1001418

Axiom
annotated source: SpectraST:dot_bias
annotated property: definition
annotated target: SpectraST measure of how much of the dot product is dominated by a few peaks.
database_cross_reference: PSI:PI

SpectraST:discriminant score F
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: SpectraST spectrum score.
has_obo_namespace: MS
id: MS:1001419

Axiom
annotated source: SpectraST:discriminant score F
annotated property: definition
annotated target: SpectraST spectrum score.
database_cross_reference: PSI:PI

SpectraST:delta
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: SpectraST normalised difference between dot product of top hit and runner-up.
has_obo_namespace: MS
id: MS:1001420

Axiom
annotated source: SpectraST:delta
annotated property: definition
annotated target: SpectraST normalised difference between dot product of top hit and runner-up.
database_cross_reference: PSI:PI

pepXML format
type: Class
subclass of: intermediate analysis format
definition: The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers.
has_obo_namespace: MS
id: MS:1001421

Axiom
annotated source: pepXML format
annotated property: definition
annotated target: The XML-based pepXML file format for encoding PSM information, created and maintained by the Trans-Proteomic Pipeline developers.
database_cross_reference: PSI:PI

protXML format
type: Class
subclass of: intermediate analysis format
definition: The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers.
has_obo_namespace: MS
id: MS:1001422

Axiom
annotated source: protXML format
annotated property: definition
annotated target: The XML-based protXML file format for encoding protein identifications, created and maintained by the Trans-Proteomic Pipeline developers.
database_cross_reference: PSI:PI

translation table description
type: Class
subclass of: search database details
subclass of: Restriction
  on property: has value type
  some values from: anyURI
definition: A URL that describes the translation table used to translate the nucleotides to amino acids.
has_obo_namespace: MS
id: MS:1001423

Axiom
annotated source: translation table description
annotated property: definition
annotated target: A URL that describes the translation table used to translate the nucleotides to amino acids.
database_cross_reference: PSI:PI

ProteinExtractor:Methodname
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Name of the used method in the ProteinExtractor algorithm.
has_obo_namespace: MS
id: MS:1001424

Axiom
annotated source: ProteinExtractor:Methodname
annotated property: definition
annotated target: Name of the used method in the ProteinExtractor algorithm.
database_cross_reference: PSI:PI

ProteinExtractor:GenerateNonRedundant
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating if a non redundant scoring should be generated.
has_obo_namespace: MS
id: MS:1001425

Axiom
annotated source: ProteinExtractor:GenerateNonRedundant
annotated property: definition
annotated target: Flag indicating if a non redundant scoring should be generated.
database_cross_reference: PSI:PI

ProteinExtractor:IncludeIdentified
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating if identified proteins should be included.
has_obo_namespace: MS
id: MS:1001426

Axiom
annotated source: ProteinExtractor:IncludeIdentified
annotated property: definition
annotated target: Flag indicating if identified proteins should be included.
database_cross_reference: PSI:PI

ProteinExtractor:MaxNumberOfProteins
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The maximum number of proteins to consider.
has_obo_namespace: MS
id: MS:1001427

Axiom
annotated source: ProteinExtractor:MaxNumberOfProteins
annotated property: definition
annotated target: The maximum number of proteins to consider.
database_cross_reference: PSI:PI

ProteinExtractor:MaxProteinMass
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The maximum considered mass for a protein.
has_obo_namespace: MS
id: MS:1001428

Axiom
annotated source: ProteinExtractor:MaxProteinMass
annotated property: definition
annotated target: The maximum considered mass for a protein.
database_cross_reference: PSI:PI

ProteinExtractor:MinNumberOfPeptides
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The minimum number of proteins to consider.
has_obo_namespace: MS
id: MS:1001429

Axiom
annotated source: ProteinExtractor:MinNumberOfPeptides
annotated property: definition
annotated target: The minimum number of proteins to consider.
database_cross_reference: PSI:PI

ProteinExtractor:UseMascot
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001430

Axiom
annotated source: ProteinExtractor:UseMascot
annotated property: definition
annotated target: Flag indicating to include Mascot scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: PSI:PI

ProteinExtractor:MascotPeptideScoreThreshold
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001431

Axiom
annotated source: ProteinExtractor:MascotPeptideScoreThreshold
annotated property: definition
annotated target: Only peptides with scores higher than that threshold are taken into account in Mascot scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:MascotUniqueScore
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation.
has_obo_namespace: MS
id: MS:1001432

Axiom
annotated source: ProteinExtractor:MascotUniqueScore
annotated property: definition
annotated target: In the final result each protein must have at least one peptide above this Mascot score threshold in ProteinExtractor meta score calculation.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:MascotUseIdentityScore
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: boolean
has_obo_namespace: MS
id: MS:1001433

ProteinExtractor:MascotWeighting
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
has_obo_namespace: MS
id: MS:1001434

Axiom
annotated source: ProteinExtractor:MascotWeighting
annotated property: definition
annotated target: Influence of Mascot search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:UseSequest
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001435

Axiom
annotated source: ProteinExtractor:UseSequest
annotated property: definition
annotated target: Flag indicating to include SEQUEST scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: PSI:PI

ProteinExtractor:SequestPeptideScoreThreshold
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001436

Axiom
annotated source: ProteinExtractor:SequestPeptideScoreThreshold
annotated property: definition
annotated target: Only peptides with scores higher than that threshold are taken into account in SEQUEST scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:SequestUniqueScore
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation.
has_obo_namespace: MS
id: MS:1001437

Axiom
annotated source: ProteinExtractor:SequestUniqueScore
annotated property: definition
annotated target: In the final result each protein must have at least one peptide above this SEQUEST score threshold in ProteinExtractor meta score calculation.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:SequestWeighting
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
has_obo_namespace: MS
id: MS:1001438

Axiom
annotated source: ProteinExtractor:SequestWeighting
annotated property: definition
annotated target: Influence of SEQUEST search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:UseProteinSolver
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001439

Axiom
annotated source: ProteinExtractor:UseProteinSolver
annotated property: definition
annotated target: Flag indicating to include ProteinSolver scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: PSI:PI

ProteinExtractor:ProteinSolverPeptideScoreThreshold
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001440

Axiom
annotated source: ProteinExtractor:ProteinSolverPeptideScoreThreshold
annotated property: definition
annotated target: Only peptides with scores higher than that threshold are taken into account in ProteinSolver scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:ProteinSolverUniqueScore
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation.
has_obo_namespace: MS
id: MS:1001441

Axiom
annotated source: ProteinExtractor:ProteinSolverUniqueScore
annotated property: definition
annotated target: In the final result each protein must have at least one peptide above this ProteinSolver score threshold in ProteinExtractor meta score calculation.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:ProteinSolverWeighting
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
has_obo_namespace: MS
id: MS:1001442

Axiom
annotated source: ProteinExtractor:ProteinSolverWeighting
annotated property: definition
annotated target: Influence of ProteinSolver search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:UsePhenyx
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001443

Axiom
annotated source: ProteinExtractor:UsePhenyx
annotated property: definition
annotated target: Flag indicating to include Phenyx scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: PSI:PI

ProteinExtractor:PhenyxPeptideScoreThreshold
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score.
has_obo_namespace: MS
id: MS:1001444

Axiom
annotated source: ProteinExtractor:PhenyxPeptideScoreThreshold
annotated property: definition
annotated target: Only peptides with scores higher than that threshold are taken into account in Phenyx scoring for calculation of the ProteinExtractor meta score.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:PhenyxUniqueScore
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation.
has_obo_namespace: MS
id: MS:1001445

Axiom
annotated source: ProteinExtractor:PhenyxUniqueScore
annotated property: definition
annotated target: In the final result each protein must have at least one peptide above this Phenyx score threshold in ProteinExtractor meta score calculation.
database_cross_reference: DOI:10.4172/jpb.1000056

ProteinExtractor:PhenyxWeighting
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
has_obo_namespace: MS
id: MS:1001446

Axiom
annotated source: ProteinExtractor:PhenyxWeighting
annotated property: definition
annotated target: Influence of Phenyx search engine in the process of merging the search engine specific protein lists into the global protein list of ProteinExtractor.
database_cross_reference: DOI:10.4172/jpb.1000056

prot:FDR threshold
type: Class
subclass of: MS_1002485
subclass of: Restriction
  on property: has value type
  some values from: double
definition: False-discovery rate threshold for proteins.
has_obo_namespace: MS
id: MS:1001447

Axiom
annotated source: prot:FDR threshold
annotated property: definition
annotated target: False-discovery rate threshold for proteins.
database_cross_reference: PSI:PI

pep:FDR threshold
type: Class
subclass of: MS_1002484
subclass of: Restriction
  on property: has value type
  some values from: double
definition: False-discovery rate threshold for peptides.
has_obo_namespace: MS
id: MS:1001448

Axiom
annotated source: pep:FDR threshold
annotated property: definition
annotated target: False-discovery rate threshold for peptides.
database_cross_reference: PSI:PI

OMSSA e-value threshold
type: Class
subclass of: MS_1002099
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Threshold for OMSSA e-value for quality estimation.
has_obo_namespace: MS
id: MS:1001449

Axiom
annotated source: OMSSA e-value threshold
annotated property: definition
annotated target: Threshold for OMSSA e-value for quality estimation.
database_cross_reference: PSI:PI

decoy DB details
type: Class
subclass of: search database details
definition: Details of decoy generation and database structure.
has_obo_namespace: MS
id: MS:1001450

Axiom
annotated source: decoy DB details
annotated property: definition
annotated target: Details of decoy generation and database structure.
database_cross_reference: PSI:PI

decoy DB generation algorithm
type: Class
subclass of: decoy DB details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Name of algorithm used for decoy generation.
has_obo_namespace: MS
id: MS:1001451

Axiom
annotated source: decoy DB generation algorithm
annotated property: definition
annotated target: Name of algorithm used for decoy generation.
database_cross_reference: PSI:PI

decoy DB type shuffle
type: Class
subclass of: decoy DB details
definition: Decoy type: Amino acids of protein sequences are used in a random order.
has_obo_namespace: MS
id: MS:1001452

Axiom
annotated source: decoy DB type shuffle
annotated property: definition
annotated target: Decoy type: Amino acids of protein sequences are used in a random order.
database_cross_reference: PSI:PI

DB composition only decoy
type: Class
subclass of: decoy DB details
definition: Decoy database composition: database contains only decoy entries.
has_obo_namespace: MS
id: MS:1001453

Axiom
annotated source: DB composition only decoy
annotated property: definition
annotated target: Decoy database composition: database contains only decoy entries.
database_cross_reference: PSI:PI

quality estimation with implicit decoy sequences
type: Class
subclass of: quality estimation method details
definition: Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy).
has_obo_namespace: MS
id: MS:1001454

Axiom
annotated source: quality estimation with implicit decoy sequences
annotated property: definition
annotated target: Decoy entries are generated during the search, not explicitly stored in a database (like Mascot Decoy).
database_cross_reference: PSI:PI

acquisition software
type: Class
subclass of: software
definition: Acquisition software.
has_obo_namespace: MS
id: MS:1001455

Axiom
annotated source: acquisition software
annotated property: definition
annotated target: Acquisition software.
database_cross_reference: PSI:MS

analysis software
type: Class
subclass of: software
definition: Analysis software.
has_obo_namespace: MS
id: MS:1001456

Axiom
annotated source: analysis software
annotated property: definition
annotated target: Analysis software.
database_cross_reference: PSI:MS

data processing software
type: Class
subclass of: software
definition: Data processing software.
has_obo_namespace: MS
id: MS:1001457

Axiom
annotated source: data processing software
annotated property: definition
annotated target: Data processing software.
database_cross_reference: PSI:MS

spectrum generation information
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Proteomics Standards Initiative Mass Spectrometry Vocabularies
definition: Vocabularies describing the spectrum generation information.
has_obo_namespace: MS
id: MS:1001458

Axiom
annotated source: spectrum generation information
annotated property: definition
annotated target: Vocabularies describing the spectrum generation information.
database_cross_reference: PSI:PI

file format
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Proteomics Standards Initiative Mass Spectrometry Vocabularies
definition: Format of data files.
has_obo_namespace: MS
id: MS:1001459

Axiom
annotated source: file format
annotated property: definition
annotated target: Format of data files.
database_cross_reference: PSI:MS

unknown modification
type: Class
subclass of: peptide modification details
definition: This term should be given if the modification was unknown.
has_obo_namespace: MS
id: MS:1001460

Axiom
annotated source: unknown modification
annotated property: definition
annotated target: This term should be given if the modification was unknown.
database_cross_reference: PSI:PI

greylag
type: Class
subclass of: analysis software
definition: Greylag identification software.
has_obo_namespace: MS
id: MS:1001461

Axiom
annotated source: greylag
annotated property: definition
annotated target: Greylag identification software.
database_cross_reference: http://greylag.org/

PEFF format
type: Class
subclass of: database file formats
definition: The sequence database was stored in the PEFF (PSI enhanced FastA file) format.
has_obo_namespace: MS
id: MS:1001462

Axiom
annotated source: PEFF format
annotated property: definition
annotated target: The sequence database was stored in the PEFF (PSI enhanced FastA file) format.
database_cross_reference: PSI:PI

Phenyx XML format
type: Class
subclass of: mass spectrometer file format
subclass of: intermediate analysis format
definition: Phenyx open XML file format.
has_obo_namespace: MS
id: MS:1001463

Axiom
annotated source: Phenyx XML format
annotated property: definition
annotated target: Phenyx open XML file format.
database_cross_reference: PSI:PI

DTASelect format
type: Class
subclass of: intermediate analysis format
definition: DTASelect file format.
has_obo_namespace: MS
id: MS:1001464

Axiom
annotated source: DTASelect format
annotated property: definition
annotated target: DTASelect file format.
database_cross_reference: PMID:12643522
database_cross_reference: http://www.scripps.edu/cravatt/protomap/dtaselect_instructions.html

MS2 format
type: Class
subclass of: mass spectrometer file format
definition: MS2 file format for MS2 spectral data.
has_obo_namespace: MS
id: MS:1001466

Axiom
annotated source: MS2 format
annotated property: definition
annotated target: MS2 file format for MS2 spectral data.
database_cross_reference: DOI:10.1002/rcm.1603
database_cross_reference: PMID:15317041
database_cross_reference: http://fields.scripps.edu/sequest/SQTFormat.html

taxonomy: NCBI TaxID
type: Class
subclass of: molecule taxonomy
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens.
has_obo_namespace: MS
id: MS:1001467

Axiom
annotated source: taxonomy: NCBI TaxID
annotated property: definition
annotated target: This term is used if a NCBI TaxID is specified, e.g. 9606 for Homo sapiens.
database_cross_reference: PSI:PI

taxonomy: common name
type: Class
subclass of: molecule taxonomy
subclass of: Restriction
  on property: has value type
  some values from: string
definition: This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
has_obo_namespace: MS
id: MS:1001468

Axiom
annotated source: taxonomy: common name
annotated property: definition
annotated target: This term is used if a common name is specified, e.g. human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
database_cross_reference: PSI:PI

taxonomy: scientific name
type: Class
subclass of: molecule taxonomy
subclass of: Restriction
  on property: has value type
  some values from: string
definition: This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
has_obo_namespace: MS
id: MS:1001469

Axiom
annotated source: taxonomy: scientific name
annotated property: definition
annotated target: This term is used if a scientific name is specified, e.g. Homo sapiens. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
database_cross_reference: PSI:PI

taxonomy: Swiss-Prot ID
type: Class
subclass of: molecule taxonomy
subclass of: Restriction
  on property: has value type
  some values from: string
definition: This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
has_obo_namespace: MS
id: MS:1001470

Axiom
annotated source: taxonomy: Swiss-Prot ID
annotated property: definition
annotated target: This term is used if a swiss prot taxonomy id is specified, e.g. Human. Recommend using MS:1001467 (taxonomy: NCBI TaxID) where possible.
database_cross_reference: PSI:PI

peptide modification details
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: The children of this term can be used to describe modifications.
has_obo_namespace: MS
id: MS:1001471

Axiom
annotated source: peptide modification details
annotated property: definition
annotated target: The children of this term can be used to describe modifications.
database_cross_reference: PSI:PI

selected ion monitoring chromatogram
type: Class
subclass of: ion current chromatogram
definition: Representation of an array of the measurements of a selectively monitored ion versus time.
has_exact_synonym: SIM chromatogram
has_obo_namespace: MS
id: MS:1001472

Axiom
annotated source: selected ion monitoring chromatogram
annotated property: definition
annotated target: Representation of an array of the measurements of a selectively monitored ion versus time.
database_cross_reference: PSI:MS

selected reaction monitoring chromatogram
type: Class
subclass of: ion current chromatogram
definition: Representation of an array of the measurements of a selectively monitored reaction versus time.
has_exact_synonym: SRM chromatogram
has_obo_namespace: MS
id: MS:1001473

Axiom
annotated source: selected reaction monitoring chromatogram
annotated property: definition
annotated target: Representation of an array of the measurements of a selectively monitored reaction versus time.
database_cross_reference: PSI:MS

consecutive reaction monitoring chromatogram
type: Class
subclass of: ion current chromatogram
definition: OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time.
has_exact_synonym: CRM chromatogram
has_obo_namespace: MS
id: MS:1001474
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.
deprecated: true

Axiom
annotated source: consecutive reaction monitoring chromatogram
annotated property: definition
annotated target: OBSOLETE Representation of an array of the measurements of a series of monitored reactions versus time.
database_cross_reference: PSI:MS

OMSSA
type: Class
subclass of: analysis software
definition: Open Mass Spectrometry Search Algorithm was used to analyze the spectra.
has_obo_namespace: MS
id: MS:1001475

Axiom
annotated source: OMSSA
annotated property: definition
annotated target: Open Mass Spectrometry Search Algorithm was used to analyze the spectra.
database_cross_reference: PSI:PI

X!Tandem
type: Class
subclass of: analysis software
definition: X!Tandem was used to analyze the spectra.
has_obo_namespace: MS
id: MS:1001476

Axiom
annotated source: X!Tandem
annotated property: definition
annotated target: X!Tandem was used to analyze the spectra.
database_cross_reference: PSI:PI

SpectraST
type: Class
subclass of: analysis software
subclass of: MS_1003207
subclass of: MS_1003406
definition: 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.
has_obo_namespace: MS
id: MS:1001477

Axiom
annotated source: SpectraST
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

Mascot Parser
type: Class
subclass of: analysis software
definition: Mascot Parser was used to analyze the spectra.
has_obo_namespace: MS
id: MS:1001478

Axiom
annotated source: Mascot Parser
annotated property: definition
annotated target: Mascot Parser was used to analyze the spectra.
database_cross_reference: PSI:PI

null-terminated ASCII string
type: Class
subclass of: binary data type
definition: Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte.
has_obo_namespace: MS
id: MS:1001479

Axiom
annotated source: null-terminated ASCII string
annotated property: definition
annotated target: Sequence of zero or more non-zero ASCII characters terminated by a single null (0) byte.
database_cross_reference: PSI:MS

SCIEX TOF/TOF nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1001480

Axiom
annotated source: SCIEX TOF/TOF nativeID format
annotated property: definition
annotated target: Native format defined by jobRun=xsd:nonNegativeInteger spotLabel=xsd:string spectrum=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

SCIEX TOF/TOF database
type: Class
subclass of: mass spectrometer file format
definition: Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database.
has_obo_namespace: MS
id: MS:1001481

Axiom
annotated source: SCIEX TOF/TOF database
annotated property: definition
annotated target: Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument database.
database_cross_reference: PSI:MS

5800 TOF/TOF
type: Class
subclass of: SCIEX instrument model
definition: SCIEX 5800 TOF-TOF Analyzer.
has_obo_namespace: MS
id: MS:1001482

Axiom
annotated source: 5800 TOF/TOF
annotated property: definition
annotated target: SCIEX 5800 TOF-TOF Analyzer.
database_cross_reference: PSI:MS

SCIEX TOF/TOF Series Explorer Software
type: Class
subclass of: SCIEX software
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
definition: SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis.
has_obo_namespace: MS
id: MS:1001483

Axiom
annotated source: SCIEX TOF/TOF Series Explorer Software
annotated property: definition
annotated target: SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis.
database_cross_reference: PSI:MS

intensity normalization
type: Class
subclass of: data processing action
definition: Normalization of data point intensities.
has_obo_namespace: MS
id: MS:1001484

Axiom
annotated source: intensity normalization
annotated property: definition
annotated target: Normalization of data point intensities.
database_cross_reference: PSI:MS

m/z calibration
type: Class
subclass of: data processing action
definition: Calibration of data point m/z positions.
has_obo_namespace: MS
id: MS:1001485

Axiom
annotated source: m/z calibration
annotated property: definition
annotated target: Calibration of data point m/z positions.
database_cross_reference: PSI:MS

data filtering
type: Class
subclass of: data processing action
definition: Filtering out part of the data.
has_obo_namespace: MS
id: MS:1001486

Axiom
annotated source: data filtering
annotated property: definition
annotated target: Filtering out part of the data.
database_cross_reference: PSI:MS

ProteinExtractor
type: Class
subclass of: Bruker software
subclass of: analysis software
definition: An algorithm for protein determination/assembly integrated into Bruker's ProteinScape.
has_obo_namespace: MS
id: MS:1001487

Axiom
annotated source: ProteinExtractor
annotated property: definition
annotated target: An algorithm for protein determination/assembly integrated into Bruker's ProteinScape.
database_cross_reference: PSI:MS

Mascot Distiller
type: Class
subclass of: quantitation software name
subclass of: analysis software
definition: Mascot Distiller.
has_obo_namespace: MS
id: MS:1001488

Axiom
annotated source: Mascot Distiller
annotated property: definition
annotated target: Mascot Distiller.
database_cross_reference: PSI:PI

Mascot Integra
type: Class
subclass of: analysis software
definition: Mascot Integra.
has_obo_namespace: MS
id: MS:1001489

Axiom
annotated source: Mascot Integra
annotated property: definition
annotated target: Mascot Integra.
database_cross_reference: PSI:PI

Percolator
type: Class
subclass of: analysis software
definition: Percolator.
has_obo_namespace: MS
id: MS:1001490

Axiom
annotated source: Percolator
annotated property: definition
annotated target: Percolator.
database_cross_reference: PSI:PI

percolator:Q value
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Percolator:Q value.
has_obo_namespace: MS
id: MS:1001491

Axiom
annotated source: percolator:Q value
annotated property: definition
annotated target: Percolator:Q value.
database_cross_reference: PSI:PI

percolator:score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Percolator:score.
has_obo_namespace: MS
id: MS:1001492

Axiom
annotated source: percolator:score
annotated property: definition
annotated target: Percolator:score.
database_cross_reference: PSI:PI

percolator:PEP
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Posterior error probability.
has_obo_namespace: MS
id: MS:1001493

Axiom
annotated source: percolator:PEP
annotated property: definition
annotated target: Posterior error probability.
database_cross_reference: PSI:PI

no threshold
type: Class
subclass of: MS_1002482
definition: In case no threshold was used.
has_obo_namespace: MS
id: MS:1001494

Axiom
annotated source: no threshold
annotated property: definition
annotated target: In case no threshold was used.
database_cross_reference: PSI:PI

ProteinScape:SearchResultId
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The SearchResultId of this peptide as SearchResult in the ProteinScape database.
has_obo_namespace: MS
id: MS:1001495

Axiom
annotated source: ProteinScape:SearchResultId
annotated property: definition
annotated target: The SearchResultId of this peptide as SearchResult in the ProteinScape database.
database_cross_reference: PSI:PI

ProteinScape:SearchEventId
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The SearchEventId of the SearchEvent in the ProteinScape database.
has_obo_namespace: MS
id: MS:1001496

Axiom
annotated source: ProteinScape:SearchEventId
annotated property: definition
annotated target: The SearchEventId of the SearchEvent in the ProteinScape database.
database_cross_reference: PSI:PI

ProteinScape:ProfoundProbability
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Profound probability score stored by ProteinScape.
has_obo_namespace: MS
id: MS:1001497

Axiom
annotated source: ProteinScape:ProfoundProbability
annotated property: definition
annotated target: The Profound probability score stored by ProteinScape.
database_cross_reference: PSI:PI

Profound:z value
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Profound z value.
has_obo_namespace: MS
id: MS:1001498

Axiom
annotated source: Profound:z value
annotated property: definition
annotated target: The Profound z value.
database_cross_reference: PSI:PI

Profound:Cluster
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Profound cluster score.
has_obo_namespace: MS
id: MS:1001499

Axiom
annotated source: Profound:Cluster
annotated property: definition
annotated target: The Profound cluster score.
database_cross_reference: PSI:PI

Profound:ClusterRank
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: The Profound cluster rank.
has_obo_namespace: MS
id: MS:1001500

Axiom
annotated source: Profound:ClusterRank
annotated property: definition
annotated target: The Profound cluster rank.
database_cross_reference: PSI:PI

MSFit:Mowse score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The MSFit Mowse score.
has_obo_namespace: MS
id: MS:1001501

Axiom
annotated source: MSFit:Mowse score
annotated property: definition
annotated target: The MSFit Mowse score.
database_cross_reference: PSI:PI

Sonar:Score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The Sonar score.
has_obo_namespace: MS
id: MS:1001502

Axiom
annotated source: Sonar:Score
annotated property: definition
annotated target: The Sonar score.
database_cross_reference: PSI:PI

ProteinScape:PFFSolverExp
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The ProteinSolver exp value stored by ProteinScape.
has_obo_namespace: MS
id: MS:1001503

Axiom
annotated source: ProteinScape:PFFSolverExp
annotated property: definition
annotated target: The ProteinSolver exp value stored by ProteinScape.
database_cross_reference: PSI:PI

ProteinScape:PFFSolverScore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The ProteinSolver score stored by ProteinScape.
has_obo_namespace: MS
id: MS:1001504

Axiom
annotated source: ProteinScape:PFFSolverScore
annotated property: definition
annotated target: The ProteinSolver score stored by ProteinScape.
database_cross_reference: PSI:PI

ProteinScape:IntensityCoverage
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape.
has_obo_namespace: MS
id: MS:1001505

Axiom
annotated source: ProteinScape:IntensityCoverage
annotated property: definition
annotated target: The intensity coverage of the identified peaks in the spectrum calculated by ProteinScape.
database_cross_reference: PSI:PI

ProteinScape:SequestMetaScore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores.
has_obo_namespace: MS
id: MS:1001506

Axiom
annotated source: ProteinScape:SequestMetaScore
annotated property: definition
annotated target: The SEQUEST meta score calculated by ProteinScape from the original SEQUEST scores.
database_cross_reference: PSI:PI

ProteinExtractor:Score
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The score calculated by ProteinExtractor.
has_obo_namespace: MS
id: MS:1001507

Axiom
annotated source: ProteinExtractor:Score
annotated property: definition
annotated target: The score calculated by ProteinExtractor.
database_cross_reference: PSI:PI

Agilent MassHunter nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by scanId=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1001508

Axiom
annotated source: Agilent MassHunter nativeID format
annotated property: definition
annotated target: Native format defined by scanId=xsd:nonNegativeInteger.
database_cross_reference: PSI:PI

Agilent MassHunter format
type: Class
subclass of: mass spectrometer file format
definition: A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer.
has_obo_namespace: MS
id: MS:1001509

Axiom
annotated source: Agilent MassHunter format
annotated property: definition
annotated target: A data file format found in an Agilent MassHunter directory which contains raw data acquired by an Agilent mass spectrometer.
database_cross_reference: PSI:PI

TSQ Vantage
type: Class
subclass of: Thermo Scientific instrument model
definition: TSQ Vantage.
has_obo_namespace: MS
id: MS:1001510

Axiom
annotated source: TSQ Vantage
annotated property: definition
annotated target: TSQ Vantage.
database_cross_reference: PSI:MS

Sequence database filter types
type: Class
subclass of: database filtering
definition: Filter types which are used to filter a sequence database.
has_obo_namespace: MS
id: MS:1001511

Axiom
annotated source: Sequence database filter types
annotated property: definition
annotated target: Filter types which are used to filter a sequence database.
database_cross_reference: PSI:PI

Sequence database filters
type: Class
subclass of: database filtering
definition: Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search.
has_obo_namespace: MS
id: MS:1001512

Axiom
annotated source: Sequence database filters
annotated property: definition
annotated target: Sequence database filters which actually can contains values, e.g. to limit PI value of the sequences used to search.
database_cross_reference: PSI:PI

DB sequence filter pattern
type: Class
subclass of: Sequence database filters
subclass of: Restriction
  on property: has value type
  some values from: string
definition: DB sequence filter pattern.
has_obo_namespace: MS
id: MS:1001513

Axiom
annotated source: DB sequence filter pattern
annotated property: definition
annotated target: DB sequence filter pattern.
database_cross_reference: PSI:MS

DB accession filter string
type: Class
subclass of: Sequence database filters
subclass of: Restriction
  on property: has value type
  some values from: string
definition: DB accession filter string.
has_obo_namespace: MS
id: MS:1001514

Axiom
annotated source: DB accession filter string
annotated property: definition
annotated target: DB accession filter string.
database_cross_reference: PSI:MS

frag: c ion - H2O
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: c ion without water.
has_obo_namespace: MS
id: MS:1001515

Axiom
annotated source: frag: c ion - H2O
annotated property: definition
annotated target: Fragmentation information, type of product: c ion without water.
database_cross_reference: PSI:PI

frag: c ion - NH3
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: c ion without ammonia.
has_obo_namespace: MS
id: MS:1001516

Axiom
annotated source: frag: c ion - NH3
annotated property: definition
annotated target: Fragmentation information, type of product: c ion without ammonia.
database_cross_reference: PSI:PI

frag: z ion - H2O
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: z ion without water.
has_obo_namespace: MS
id: MS:1001517

Axiom
annotated source: frag: z ion - H2O
annotated property: definition
annotated target: Fragmentation information, type of product: z ion without water.
database_cross_reference: PSI:PI

frag: z ion - NH3
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: z ion without ammonia.
has_obo_namespace: MS
id: MS:1001518

Axiom
annotated source: frag: z ion - NH3
annotated property: definition
annotated target: Fragmentation information, type of product: z ion without ammonia.
database_cross_reference: PSI:PI

frag: x ion - H2O
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: x ion without water.
has_obo_namespace: MS
id: MS:1001519

Axiom
annotated source: frag: x ion - H2O
annotated property: definition
annotated target: Fragmentation information, type of product: x ion without water.
database_cross_reference: PSI:PI

frag: x ion - NH3
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: x ion without ammonia.
has_obo_namespace: MS
id: MS:1001520

Axiom
annotated source: frag: x ion - NH3
annotated property: definition
annotated target: Fragmentation information, type of product: x ion without ammonia.
database_cross_reference: PSI:PI

frag: precursor ion - H2O
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: precursor ion without water.
has_obo_namespace: MS
id: MS:1001521

Axiom
annotated source: frag: precursor ion - H2O
annotated property: definition
annotated target: Fragmentation information, type of product: precursor ion without water.
database_cross_reference: PSI:PI

frag: precursor ion - NH3
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: precursor ion without ammonia.
has_obo_namespace: MS
id: MS:1001522

Axiom
annotated source: frag: precursor ion - NH3
annotated property: definition
annotated target: Fragmentation information, type of product: precursor ion without ammonia.
database_cross_reference: PSI:PI

frag: precursor ion
type: Class
subclass of: MS_1002307
definition: Fragmentation information, type of product: precursor ion.
has_obo_namespace: MS
id: MS:1001523

Axiom
annotated source: frag: precursor ion
annotated property: definition
annotated target: Fragmentation information, type of product: precursor ion.
database_cross_reference: PSI:PI

fragment neutral loss
type: Class
subclass of: peptide modification details
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: This term can describe a neutral loss m/z value that is lost from an ion.
has_obo_namespace: MS
id: MS:1001524

Axiom
annotated source: fragment neutral loss
annotated property: definition
annotated target: This term can describe a neutral loss m/z value that is lost from an ion.
database_cross_reference: PSI:PI

precursor neutral loss
type: Class
subclass of: peptide modification details
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: This term can describe a neutral loss m/z value that is lost from an ion.
has_obo_namespace: MS
id: MS:1001525

Axiom
annotated source: precursor neutral loss
annotated property: definition
annotated target: This term can describe a neutral loss m/z value that is lost from an ion.
database_cross_reference: PSI:PI

spectrum from database integer nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by databasekey=xsd:long.
has_obo_namespace: MS
id: MS:1001526
comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier).

Axiom
annotated source: spectrum from database integer nativeID format
annotated property: definition
annotated target: Native format defined by databasekey=xsd:long.
database_cross_reference: PSI:MS

Proteinscape spectra
type: Class
subclass of: mass spectrometer file format
definition: Spectra from Bruker/Protagen Proteinscape database.
has_obo_namespace: MS
id: MS:1001527

Axiom
annotated source: Proteinscape spectra
annotated property: definition
annotated target: Spectra from Bruker/Protagen Proteinscape database.
database_cross_reference: PSI:MS

Mascot query number
type: Class
subclass of: native spectrum identifier format
subclass of: spectrum identification result details
definition: Native format defined by query=xsd:nonNegativeInteger.
has_obo_namespace: MS
id: MS:1001528
comment: The spectrum (query) number in a Mascot results file, starting from 1.

Axiom
annotated source: Mascot query number
annotated property: definition
annotated target: Native format defined by query=xsd:nonNegativeInteger.
database_cross_reference: PSI:MS

spectra data details
type: Class
subclass of: search input details
definition: Child-terms contain information to map the results back to spectra.
has_obo_namespace: MS
id: MS:1001529

Axiom
annotated source: spectra data details
annotated property: definition
annotated target: Child-terms contain information to map the results back to spectra.
database_cross_reference: PSI:MS

mzML unique identifier
type: Class
subclass of: spectra data details
definition: Native format defined by mzMLid=xsd:IDREF.
has_obo_namespace: MS
id: MS:1001530
comment: A unique identifier of a spectrum stored in an mzML file.

Axiom
annotated source: mzML unique identifier
annotated property: definition
annotated target: Native format defined by mzMLid=xsd:IDREF.
database_cross_reference: PSI:MS

spectrum from ProteinScape database nativeID format
type: Class
subclass of: native spectrum identifier format
subclass of: spectra data details
definition: Native format defined by databasekey=xsd:long.
has_obo_namespace: MS
id: MS:1001531
comment: A unique identifier of a spectrum stored in a ProteinScape database.

Axiom
annotated source: spectrum from ProteinScape database nativeID format
annotated property: definition
annotated target: Native format defined by databasekey=xsd:long.
database_cross_reference: PSI:MS

spectrum from database string nativeID format
type: Class
subclass of: native spectrum identifier format
subclass of: spectra data details
definition: Native format defined by databasekey=xsd:string.
has_obo_namespace: MS
id: MS:1001532
comment: A unique identifier of a spectrum stored in a database (e.g. a PRIMARY KEY identifier).

Axiom
annotated source: spectrum from database string nativeID format
annotated property: definition
annotated target: Native format defined by databasekey=xsd:string.
database_cross_reference: PSI:MS

Bruker Daltonics esquire series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' esquire series.
has_obo_namespace: MS
id: MS:1001533

Axiom
annotated source: Bruker Daltonics esquire series
annotated property: definition
annotated target: Bruker Daltonics' esquire series.
database_cross_reference: PSI:MS

Bruker Daltonics flex series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' flex series.
has_obo_namespace: MS
id: MS:1001534

Axiom
annotated source: Bruker Daltonics flex series
annotated property: definition
annotated target: Bruker Daltonics' flex series.
database_cross_reference: PSI:MS

Bruker Daltonics BioTOF series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' BioTOF series.
has_obo_namespace: MS
id: MS:1001535

Axiom
annotated source: Bruker Daltonics BioTOF series
annotated property: definition
annotated target: Bruker Daltonics' BioTOF series.
database_cross_reference: PSI:MS

Bruker Daltonics micrOTOF series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' micrOTOF series.
has_obo_namespace: MS
id: MS:1001536

Axiom
annotated source: Bruker Daltonics micrOTOF series
annotated property: definition
annotated target: Bruker Daltonics' micrOTOF series.
database_cross_reference: PSI:MS

BioTOF
type: Class
subclass of: Bruker Daltonics BioTOF series
definition: Bruker Daltonics' BioTOF: ESI TOF.
has_obo_namespace: MS
id: MS:1001537

Axiom
annotated source: BioTOF
annotated property: definition
annotated target: Bruker Daltonics' BioTOF: ESI TOF.
database_cross_reference: PSI:MS

BioTOF III
type: Class
subclass of: Bruker Daltonics BioTOF series
definition: Bruker Daltonics' BioTOF III: ESI TOF.
has_obo_namespace: MS
id: MS:1001538

Axiom
annotated source: BioTOF III
annotated property: definition
annotated target: Bruker Daltonics' BioTOF III: ESI TOF.
database_cross_reference: PSI:MS

UltroTOF-Q
type: Class
subclass of: Bruker Daltonics BioTOF series
definition: Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional).
has_obo_namespace: MS
id: MS:1001539

Axiom
annotated source: UltroTOF-Q
annotated property: definition
annotated target: Bruker Daltonics' UltroTOF-Q: ESI Q-TOF (MALDI optional).
database_cross_reference: PSI:MS

micrOTOF II
type: Class
subclass of: Bruker Daltonics micrOTOF series
definition: Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1001540

Axiom
annotated source: micrOTOF II
annotated property: definition
annotated target: Bruker Daltonics' micrOTOF II: ESI TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

maXis
type: Class
subclass of: Bruker Daltonics maXis series
definition: Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI.
has_obo_namespace: MS
id: MS:1001541

Axiom
annotated source: maXis
annotated property: definition
annotated target: Bruker Daltonics' maXis: ESI Q-TOF, Nanospray, APCI, APPI.
database_cross_reference: PSI:MS

amaZon ETD
type: Class
subclass of: Bruker Daltonics amaZon series
definition: Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR.
has_obo_namespace: MS
id: MS:1001542

Axiom
annotated source: amaZon ETD
annotated property: definition
annotated target: Bruker Daltonics' amaZon ETD: ESI quadrupole ion trap, Nanospray, APCI, APPI, ETD, PTR.
database_cross_reference: PSI:MS

microflex LRF
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' microflex LRF: MALDI TOF.
has_obo_namespace: MS
id: MS:1001543

Axiom
annotated source: microflex LRF
annotated property: definition
annotated target: Bruker Daltonics' microflex LRF: MALDI TOF.
database_cross_reference: PSI:MS

ultrafleXtreme
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' ultrafleXtreme: MALDI TOF.
has_obo_namespace: MS
id: MS:1001544

Axiom
annotated source: ultrafleXtreme
annotated property: definition
annotated target: Bruker Daltonics' ultrafleXtreme: MALDI TOF.
database_cross_reference: PSI:MS

Bruker Daltonics amaZon series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' amaZon series.
has_obo_namespace: MS
id: MS:1001545

Axiom
annotated source: Bruker Daltonics amaZon series
annotated property: definition
annotated target: Bruker Daltonics' amaZon series.
database_cross_reference: PSI:MS

amaZon X
type: Class
subclass of: Bruker Daltonics amaZon series
definition: Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
has_obo_namespace: MS
id: MS:1001546

Axiom
annotated source: amaZon X
annotated property: definition
annotated target: Bruker Daltonics' amaZon X: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
database_cross_reference: PSI:MS

Bruker Daltonics maXis series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' maXis series.
has_obo_namespace: MS
id: MS:1001547

Axiom
annotated source: Bruker Daltonics maXis series
annotated property: definition
annotated target: Bruker Daltonics' maXis series.
database_cross_reference: PSI:MS

Bruker Daltonics solarix series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
has_obo_namespace: MS
id: MS:1001548

Axiom
annotated source: Bruker Daltonics solarix series
annotated property: definition
annotated target: Bruker Daltonics' solarix: ESI quadrupole ion trap, APCI, APPI, ETD, PTR.
database_cross_reference: PSI:MS

solariX
type: Class
subclass of: Bruker Daltonics solarix series
definition: Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR.
has_obo_namespace: MS
id: MS:1001549

Axiom
annotated source: solariX
annotated property: definition
annotated target: Bruker Daltonics' solariX: ESI, MALDI, Qh-FT_ICR.
database_cross_reference: PSI:MS

microflex II
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' microflex II: MALDI TOF.
has_obo_namespace: MS
id: MS:1001550

Axiom
annotated source: microflex II
annotated property: definition
annotated target: Bruker Daltonics' microflex II: MALDI TOF.
database_cross_reference: PSI:MS

autoflex II TOF/TOF
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF.
has_obo_namespace: MS
id: MS:1001553

Axiom
annotated source: autoflex II TOF/TOF
annotated property: definition
annotated target: Bruker Daltonics' autoflex II TOF/TOF: MALDI TOF.
database_cross_reference: PSI:MS

autoflex III TOF/TOF smartbeam
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF.
has_obo_namespace: MS
id: MS:1001554

Axiom
annotated source: autoflex III TOF/TOF smartbeam
annotated property: definition
annotated target: Bruker Daltonics' autoflex III TOF/TOF smartbeam: MALDI TOF.
database_cross_reference: PSI:MS

autoflex
type: Class
subclass of: Bruker Daltonics flex series
definition: Bruker Daltonics' autoflex: MALDI TOF.
has_obo_namespace: MS
id: MS:1001555

Axiom
annotated source: autoflex
annotated property: definition
annotated target: Bruker Daltonics' autoflex: MALDI TOF.
database_cross_reference: PSI:MS

Bruker Daltonics apex series
type: Class
subclass of: Bruker Daltonics instrument model
definition: Bruker Daltonics' apex series.
has_obo_namespace: MS
id: MS:1001556

Axiom
annotated source: Bruker Daltonics apex series
annotated property: definition
annotated target: Bruker Daltonics' apex series.
database_cross_reference: PSI:MS

Shimadzu Corporation software
type: Class
subclass of: software
definition: Shimadzu Corporation software.
has_obo_namespace: MS
id: MS:1001557

Axiom
annotated source: Shimadzu Corporation software
annotated property: definition
annotated target: Shimadzu Corporation software.
database_cross_reference: PSI:MS

MALDI Solutions
type: Class
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
subclass of: Shimadzu Corporation software
definition: Shimadzu Biotech software for data acquisition, processing, and analysis.
has_obo_namespace: MS
id: MS:1001558

Axiom
annotated source: MALDI Solutions
annotated property: definition
annotated target: Shimadzu Biotech software for data acquisition, processing, and analysis.
database_cross_reference: PSI:MS

SCIEX TOF/TOF T2D nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Native format defined by file=xsd:IDREF.
has_obo_namespace: MS
id: MS:1001559

Axiom
annotated source: SCIEX TOF/TOF T2D nativeID format
annotated property: definition
annotated target: Native format defined by file=xsd:IDREF.
database_cross_reference: PSI:MS

SCIEX TOF/TOF T2D format
type: Class
subclass of: mass spectrometer file format
definition: Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format.
has_obo_namespace: MS
id: MS:1001560

Axiom
annotated source: SCIEX TOF/TOF T2D format
annotated property: definition
annotated target: Applied Biosystems/MDS Analytical Technologies TOF/TOF instrument export format.
database_cross_reference: PSI:MS

Scaffold
type: Class
subclass of: analysis software
definition: Scaffold analysis software.
has_obo_namespace: MS
id: MS:1001561

Axiom
annotated source: Scaffold
annotated property: definition
annotated target: Scaffold analysis software.
database_cross_reference: http://www.proteomesoftware.com

Scaffold nativeID format
type: Class
subclass of: native spectrum identifier format
definition: Scaffold native ID format.
has_obo_namespace: MS
id: MS:1001562

Axiom
annotated source: Scaffold nativeID format
annotated property: definition
annotated target: Scaffold native ID format.
database_cross_reference: PSI:MS

SEQUEST SQT format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in SEQUEST SQT format.
has_obo_namespace: MS
id: MS:1001563

Axiom
annotated source: SEQUEST SQT format
annotated property: definition
annotated target: Source file for this mzIdentML was in SEQUEST SQT format.
database_cross_reference: PSI:PI

Discoverer MSF format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format.
has_obo_namespace: MS
id: MS:1001564

Axiom
annotated source: Discoverer MSF format
annotated property: definition
annotated target: Source file for this mzIdentML was in Thermo Scientific Discoverer MSF format.
database_cross_reference: PSI:PI

IdentityE XML format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in Waters IdentityE XML format.
has_obo_namespace: MS
id: MS:1001565

Axiom
annotated source: IdentityE XML format
annotated property: definition
annotated target: Source file for this mzIdentML was in Waters IdentityE XML format.
database_cross_reference: PSI:PI

ProteinLynx XML format
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in Waters ProteinLynx XML format.
has_obo_namespace: MS
id: MS:1001566

Axiom
annotated source: ProteinLynx XML format
annotated property: definition
annotated target: Source file for this mzIdentML was in Waters ProteinLynx XML format.
database_cross_reference: PSI:PI

SpectrumMill directories
type: Class
subclass of: intermediate analysis format
definition: Source file for this mzIdentML was in Agilent SpectrumMill directory format.
has_obo_namespace: MS
id: MS:1001567

Axiom
annotated source: SpectrumMill directories
annotated property: definition
annotated target: Source file for this mzIdentML was in Agilent SpectrumMill directory format.
database_cross_reference: PSI:PI

Scaffold:Peptide Probability
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Scaffold peptide probability score.
has_obo_namespace: MS
id: MS:1001568

Axiom
annotated source: Scaffold:Peptide Probability
annotated property: definition
annotated target: Scaffold peptide probability score.
database_cross_reference: PSI:PI

IdentityE Score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Waters IdentityE peptide score.
has_obo_namespace: MS
id: MS:1001569

Axiom
annotated source: IdentityE Score
annotated property: definition
annotated target: Waters IdentityE peptide score.
database_cross_reference: PSI:PI

ProteinLynx:Log Likelihood
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: ProteinLynx log likelihood score.
has_obo_namespace: MS
id: MS:1001570

Axiom
annotated source: ProteinLynx:Log Likelihood
annotated property: definition
annotated target: ProteinLynx log likelihood score.
database_cross_reference: PSI:PI

ProteinLynx:Ladder Score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Waters ProteinLynx Ladder score.
has_obo_namespace: MS
id: MS:1001571

Axiom
annotated source: ProteinLynx:Ladder Score
annotated property: definition
annotated target: Waters ProteinLynx Ladder score.
database_cross_reference: PSI:PI

SpectrumMill:Score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Spectrum mill peptide score.
has_obo_namespace: MS
id: MS:1001572

Axiom
annotated source: SpectrumMill:Score
annotated property: definition
annotated target: Spectrum mill peptide score.
database_cross_reference: PSI:PI

SpectrumMill:SPI
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: SpectrumMill SPI score (%).
has_obo_namespace: MS
id: MS:1001573

Axiom
annotated source: SpectrumMill:SPI
annotated property: definition
annotated target: SpectrumMill SPI score (%).
database_cross_reference: PSI:PI

report only spectra assigned to identified proteins
type: Class
subclass of: quality estimation method details
definition: Flag indicating to report only the spectra assigned to identified proteins.
has_obo_namespace: MS
id: MS:1001574

Axiom
annotated source: report only spectra assigned to identified proteins
annotated property: definition
annotated target: Flag indicating to report only the spectra assigned to identified proteins.
database_cross_reference: PSI:PI

Scaffold: Minimum Peptide Count
type: Class
subclass of: MS_1002106
subclass of: Restriction
  on property: has value type
  some values from: positiveInteger
definition: Minimum number of peptides a protein must have to be accepted.
has_obo_namespace: MS
id: MS:1001575

Axiom
annotated source: Scaffold: Minimum Peptide Count
annotated property: definition
annotated target: Minimum number of peptides a protein must have to be accepted.
database_cross_reference: PSI:PI

Scaffold: Minimum Protein Probability
type: Class
subclass of: MS_1002106
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Minimum protein probability a protein must have to be accepted.
has_obo_namespace: MS
id: MS:1001576

Axiom
annotated source: Scaffold: Minimum Protein Probability
annotated property: definition
annotated target: Minimum protein probability a protein must have to be accepted.
database_cross_reference: PSI:PI

Scaffold: Minimum Peptide Probability
type: Class
subclass of: MS_1002106
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Minimum probability a peptide must have to be accepted for protein scoring.
has_obo_namespace: MS
id: MS:1001577

Axiom
annotated source: Scaffold: Minimum Peptide Probability
annotated property: definition
annotated target: Minimum probability a peptide must have to be accepted for protein scoring.
database_cross_reference: PSI:PI

minimum number of enzymatic termini
type: Class
subclass of: MS_1002094
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: Minimum number of enzymatic termini a peptide must have to be accepted.
has_obo_namespace: MS
id: MS:1001578

Axiom
annotated source: minimum number of enzymatic termini
annotated property: definition
annotated target: Minimum number of enzymatic termini a peptide must have to be accepted.
database_cross_reference: PSI:PI

Scaffold:Protein Probability
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Scaffold protein probability score.
has_obo_namespace: MS
id: MS:1001579

Axiom
annotated source: Scaffold:Protein Probability
annotated property: definition
annotated target: Scaffold protein probability score.
database_cross_reference: PSI:PI

SpectrumMill:Discriminant Score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Discriminant score from Agilent SpectrumMill software.
has_obo_namespace: MS
id: MS:1001580

Axiom
annotated source: SpectrumMill:Discriminant Score
annotated property: definition
annotated target: Discriminant score from Agilent SpectrumMill software.
database_cross_reference: PSI:PI

FAIMS compensation voltage
type: Class
subclass of: ion selection attribute
subclass of: MS_1002892
subclass of: MS_1003254
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.
has_exact_synonym: FAIMS CV
has_obo_namespace: MS
id: MS:1001581

Axiom
annotated source: FAIMS compensation voltage
annotated property: definition
annotated target: The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion.
database_cross_reference: PSI:MS

XCMS
type: Class
subclass of: analysis software
subclass of: data processing software
definition: Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data.
has_obo_namespace: MS
id: MS:1001582

Axiom
annotated source: XCMS
annotated property: definition
annotated target: Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data.
database_cross_reference: PSI:MS

MaxQuant
type: Class
subclass of: quantitation software name
subclass of: analysis software
definition: MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data.
has_obo_namespace: MS
id: MS:1001583

Axiom
annotated source: MaxQuant
annotated property: definition
annotated target: MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data.
database_cross_reference: PSI:MS

combined pmf + ms-ms search
type: Class
subclass of: search type
definition: Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF).
has_obo_namespace: MS
id: MS:1001584

Axiom
annotated source: combined pmf + ms-ms search
annotated property: definition
annotated target: Search that includes data from Peptide Mass Fingerprint (PMF) and MS2 (aka Peptide Fragment Fingerprint - PFF).
database_cross_reference: PSI:MS

MyriMatch
type: Class
subclass of: analysis software
definition: Tabb Lab software for directly comparing peptides in a database to tandem mass spectra.
has_obo_namespace: MS
id: MS:1001585

Axiom
annotated source: MyriMatch
annotated property: definition
annotated target: Tabb Lab software for directly comparing peptides in a database to tandem mass spectra.
database_cross_reference: PSI:MS

DirecTag
type: Class
subclass of: analysis software
definition: Tabb Lab software for generating sequence tags from tandem mass spectra.
has_obo_namespace: MS
id: MS:1001586

Axiom
annotated source: DirecTag
annotated property: definition
annotated target: Tabb Lab software for generating sequence tags from tandem mass spectra.
database_cross_reference: PSI:MS

TagRecon
type: Class
subclass of: analysis software
definition: Tabb Lab software for reconciling sequence tags to a protein database.
has_obo_namespace: MS
id: MS:1001587

Axiom
annotated source: TagRecon
annotated property: definition
annotated target: Tabb Lab software for reconciling sequence tags to a protein database.
database_cross_reference: PSI:MS

Pepitome
type: Class
subclass of: analysis software
definition: Tabb Lab software for spectral library searches on tandem mass spectra.
has_obo_namespace: MS
id: MS:1001588

Axiom
annotated source: Pepitome
annotated property: definition
annotated target: Tabb Lab software for spectral library searches on tandem mass spectra.
database_cross_reference: PSI:MS

MyriMatch:MVH
type: Class
subclass of: PSM-level search engine specific statistic
definition: 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.
has_exact_synonym: Pepitome:MVH
has_exact_synonym: TagRecon:MVH
has_obo_namespace: MS
id: MS:1001589

Axiom
annotated source: MyriMatch:MVH
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

MyriMatch:mzFidelity
type: Class
subclass of: PSM-level search engine specific statistic
definition: 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.
has_exact_synonym: Pepitome:mzFidelity
has_exact_synonym: TagRecon:mzFidelity
has_obo_namespace: MS
id: MS:1001590

Axiom
annotated source: MyriMatch:mzFidelity
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

anchor protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A representative protein selected from a set of sequence same-set or spectrum same-set proteins.
has_obo_namespace: MS
id: MS:1001591

Axiom
annotated source: anchor protein
annotated property: definition
annotated target: A representative protein selected from a set of sequence same-set or spectrum same-set proteins.
database_cross_reference: PSI:MS

family member protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A protein with significant homology to another protein, but some distinguishing peptide matches.
has_obo_namespace: MS
id: MS:1001592

Axiom
annotated source: family member protein
annotated property: definition
annotated target: A protein with significant homology to another protein, but some distinguishing peptide matches.
database_cross_reference: PSI:MS

group member with undefined relationship OR ortholog protein
type: Class
subclass of: protein group or subset relationship
definition: TO ENDETAIL: a really generic relationship OR ortholog protein.
has_obo_namespace: MS
id: MS:1001593

Axiom
annotated source: group member with undefined relationship OR ortholog protein
annotated property: definition
annotated target: TO ENDETAIL: a really generic relationship OR ortholog protein.
database_cross_reference: PSI:MS

sequence same-set protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences.
has_obo_namespace: MS
id: MS:1001594

Axiom
annotated source: sequence same-set protein
annotated property: definition
annotated target: A protein which is indistinguishable or equivalent to another protein, having matches to an identical set of peptide sequences.
database_cross_reference: PSI:MS

spectrum same-set protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1001595

Axiom
annotated source: spectrum same-set protein
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

sequence sub-set protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches.
has_obo_namespace: MS
id: MS:1001596

Axiom
annotated source: sequence sub-set protein
annotated property: definition
annotated target: A protein with a sub-set of the peptide sequence matches for another protein, and no distinguishing peptide matches.
database_cross_reference: PSI:MS

spectrum sub-set protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1001597

Axiom
annotated source: spectrum sub-set protein
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

sequence subsumable protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins.
has_obo_namespace: MS
id: MS:1001598

Axiom
annotated source: sequence subsumable protein
annotated property: definition
annotated target: A sequence same-set or sequence sub-set protein where the matches are distributed across two or more proteins.
database_cross_reference: PSI:MS

spectrum subsumable protein
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins.
has_obo_namespace: MS
id: MS:1001599

Axiom
annotated source: spectrum subsumable protein
annotated property: definition
annotated target: A spectrum same-set or spectrum sub-set protein where the matches are distributed across two or more proteins.
database_cross_reference: PSI:MS

protein inference confidence category
type: Class
subclass of: protein group or subset relationship
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable).
has_obo_namespace: MS
id: MS:1001600

Axiom
annotated source: protein inference confidence category
annotated property: definition
annotated target: Confidence category of inferred protein (conclusive, non conclusive, ambiguous group or indistinguishable).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Files:Raw File names
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Name and location of the .raw file or files.
has_obo_namespace: MS
id: MS:1001601
comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Spectrum Files:Raw File names
annotated property: definition
annotated target: OBSOLETE Name and location of the .raw file or files.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SRF File Selector:SRF File Path
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Path and name of the .srf (SEQUEST Result Format) file.
has_obo_namespace: MS
id: MS:1001602
comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:SRF File Selector:SRF File Path
annotated property: definition
annotated target: OBSOLETE Path and name of the .srf (SEQUEST Result Format) file.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Ionization Source
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc).
has_obo_namespace: MS
id: MS:1001603
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.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Ionization Source
annotated property: definition
annotated target: OBSOLETE Ionization source (electro-, nano-, thermospray, electron impact, APCI, MALDI, FAB etc).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Activation Type
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any).
has_obo_namespace: MS
id: MS:1001604
comment: This term was made obsolete because it's recommended to use one of the 'ionization type' terms (MS:1000008) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Activation Type
annotated property: definition
annotated target: OBSOLETE Fragmentation method used (CID, MPD, ECD, PQD, ETD, HCD, Any).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Lower RT Limit
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Lower retention-time limit.
has_obo_namespace: MS
id: MS:1001605

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Lower RT Limit
annotated property: definition
annotated target: Lower retention-time limit.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mass Analyzer
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS).
has_obo_namespace: MS
id: MS:1001606
comment: This term was made obsolete because it's recommended to use mass analyzer type (MS:1000443) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Mass Analyzer
annotated property: definition
annotated target: OBSOLETE Type of mass spectrometer used (ITMS, FTMS, TOFMS, SQMS, TQMS, SectorMS).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Max Precursor Mass
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Maximum mass limit of a singly charged precursor ion.
has_obo_namespace: MS
id: MS:1001607

Axiom
annotated source: ProteomeDiscoverer:Max Precursor Mass
annotated property: definition
annotated target: Maximum mass limit of a singly charged precursor ion.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Min Precursor Mass
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Minimum mass limit of a singly charged precursor ion.
has_obo_namespace: MS
id: MS:1001608

Axiom
annotated source: ProteomeDiscoverer:Min Precursor Mass
annotated property: definition
annotated target: Minimum mass limit of a singly charged precursor ion.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: 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.
has_obo_namespace: MS
id: MS:1001609

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Minimum Peak Count
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ProteomeDiscoverer:MS Order
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Level of the mass spectrum (MS2 ... MS10).
has_obo_namespace: MS
id: MS:1001610
comment: This term was made obsolete because it's recommended to use MS1 spectrum (MS:1000579) or MSn spectrum (MS:1000580) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:MS Order
annotated property: definition
annotated target: OBSOLETE Level of the mass spectrum (MS2 ... MS10).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Polarity Mode
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Polarity mode (positive or negative).
has_obo_namespace: MS
id: MS:1001611
comment: This term was made obsolete because it's recommended to use scan polarity (MS:1000465) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Polarity Mode
annotated property: definition
annotated target: OBSOLETE Polarity mode (positive or negative).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Precursor Selection
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3).
has_obo_namespace: MS
id: MS:1001612

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Precursor Selection
annotated property: definition
annotated target: Determines which precursor mass to use for a given MSn scan. This option applies only to higher-order MSn scans (n >= 3).
database_cross_reference: PSI:MS

ProteomeDiscoverer:SN Threshold
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Signal-to-Noise ratio below which peaks are removed.
has_obo_namespace: MS
id: MS:1001613

Axiom
annotated source: ProteomeDiscoverer:SN Threshold
annotated property: definition
annotated target: Signal-to-Noise ratio below which peaks are removed.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Scan Type
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)).
has_obo_namespace: MS
id: MS:1001614
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.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Scan Type
annotated property: definition
annotated target: OBSOLETE Scan type for the precursor ion (full, Single Ion Monitoring (SIM), Single Reaction Monitoring (SRM)).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1001615

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Total Intensity Threshold
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header.
has_obo_namespace: MS
id: MS:1001616

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Unrecognized Activation Type Replacements
annotated property: definition
annotated target: Specifies the fragmentation method to use in the search algorithm if it is not included in the scan header.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Specifies the charge state of the precursor ions, if it is not defined in the scan header.
has_obo_namespace: MS
id: MS:1001617

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Unrecognized Charge Replacements
annotated property: definition
annotated target: Specifies the charge state of the precursor ions, if it is not defined in the scan header.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header.
has_obo_namespace: MS
id: MS:1001618

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Unrecognized Mass Analyzer Replacements
annotated property: definition
annotated target: Specifies the mass spectrometer to use to produce the spectra, if it is not included in the scan header.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header.
has_obo_namespace: MS
id: MS:1001619

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Unrecognized MS Order Replacements
annotated property: definition
annotated target: Specifies the MS scan order used to produce the product spectra, if it is not included in the scan header.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specifies the polarity of the ions monitored if it is not included in the scan header.
has_obo_namespace: MS
id: MS:1001620

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Unrecognized Polarity Replacements
annotated property: definition
annotated target: Specifies the polarity of the ions monitored if it is not included in the scan header.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Upper RT Limit
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Upper retention-time limit.
has_obo_namespace: MS
id: MS:1001621

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Upper RT Limit
annotated property: definition
annotated target: Upper retention-time limit.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors.
has_obo_namespace: MS
id: MS:1001622

Axiom
annotated source: ProteomeDiscoverer:Non-Fragment Filter:Mass Window Offset
annotated property: definition
annotated target: Specifies the size of the mass-to-charge ratio (m/z) window in daltons used to remove precursors.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Maximum allowed mass of a neutral loss.
has_obo_namespace: MS
id: MS:1001623

Axiom
annotated source: ProteomeDiscoverer:Non-Fragment Filter:Maximum Neutral Loss Mass
annotated property: definition
annotated target: Maximum allowed mass of a neutral loss.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed.
has_obo_namespace: MS
id: MS:1001624

Axiom
annotated source: ProteomeDiscoverer:Non-Fragment Filter:Remove Charge Reduced Precursor
annotated property: definition
annotated target: Determines whether the charge-reduced precursor peaks found in an ETD or ECD spectrum are removed.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether neutral loss peaks are removed from ETD and ECD spectra.
has_obo_namespace: MS
id: MS:1001625

Axiom
annotated source: ProteomeDiscoverer:Non-Fragment Filter:Remove Neutral Loss Peaks
annotated property: definition
annotated target: Determines whether neutral loss peaks are removed from ETD and ECD spectra.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra.
has_obo_namespace: MS
id: MS:1001626

Axiom
annotated source: ProteomeDiscoverer:Non-Fragment Filter:Remove Only Known Masses
annotated property: definition
annotated target: Determines whether overtone peaks are removed from LTQ FT or LTQ FT Ultra ECD spectra.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum.
has_obo_namespace: MS
id: MS:1001627

Axiom
annotated source: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Overtones
annotated property: definition
annotated target: Determines whether precursor overtone peaks in the spectrum are removed from the input spectrum.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether precursor artifact peaks from the MS2 input spectra are removed.
has_obo_namespace: MS
id: MS:1001628

Axiom
annotated source: ProteomeDiscoverer:Non-Fragment Filter:Remove Precursor Peak
annotated property: definition
annotated target: Determines whether precursor artifact peaks from the MS2 input spectra are removed.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type.
has_obo_namespace: MS
id: MS:1001629

Axiom
annotated source: ProteomeDiscoverer:Spectrum Grouper:Allow Mass Analyzer Mismatch
annotated property: definition
annotated target: Determines whether the fragment spectrum for scans with the same precursor mass is grouped, regardless of mass analyzer and activation type.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether spectra from different MS order scans can be grouped together.
has_obo_namespace: MS
id: MS:1001630

Axiom
annotated source: ProteomeDiscoverer:Spectrum Grouper:Allow MS Order Mismatch
annotated property: definition
annotated target: Determines whether spectra from different MS order scans can be grouped together.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species.
has_obo_namespace: MS
id: MS:1001631
comment: This term was made obsolete because it's recommended to use retention time window width (MS:1001907) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Spectrum Grouper:Max RT Difference
annotated property: definition
annotated target: OBSOLETE Chromatographic window where precursors to be grouped must reside to be considered the same species.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis.
has_obo_namespace: MS
id: MS:1001632

Axiom
annotated source: ProteomeDiscoverer:Spectrum Grouper:Precursor Mass Criterion
annotated property: definition
annotated target: Groups spectra measured within the given mass and retention-time tolerances into a single spectrum for analysis.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Highest Charge
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Highest charge state that is allowed for the deconvolution of multiply charged data.
has_obo_namespace: MS
id: MS:1001633

Axiom
annotated source: ProteomeDiscoverer:Xtract:Highest Charge
annotated property: definition
annotated target: Highest charge state that is allowed for the deconvolution of multiply charged data.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Highest MZ
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
has_obo_namespace: MS
id: MS:1001634
comment: This term was made obsolete because it's recommended to use scan window upper limit (MS:1000500) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Xtract:Highest MZ
annotated property: definition
annotated target: OBSOLETE Highest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Lowest Charge
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Lowest charge state that is allowed for the deconvolution of multiply charged data.
has_obo_namespace: MS
id: MS:1001635

Axiom
annotated source: ProteomeDiscoverer:Xtract:Lowest Charge
annotated property: definition
annotated target: Lowest charge state that is allowed for the deconvolution of multiply charged data.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Lowest MZ
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
has_obo_namespace: MS
id: MS:1001636
comment: This term was made obsolete because it's recommended to use scan window lower limit (MS:1000501) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Xtract:Lowest MZ
annotated property: definition
annotated target: OBSOLETE Lowest mass-to-charge (mz) value for spectral peaks in the measured spectrum that are considered for Xtract.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Monoisotopic Mass Only
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum.
has_obo_namespace: MS
id: MS:1001637

Axiom
annotated source: ProteomeDiscoverer:Xtract:Monoisotopic Mass Only
annotated property: definition
annotated target: Determines whether the isotopic pattern, i.e. all isotopes of a mass are removed from the spectrum.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Overlapping Remainder
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted).
has_obo_namespace: MS
id: MS:1001638

Axiom
annotated source: ProteomeDiscoverer:Xtract:Overlapping Remainder
annotated property: definition
annotated target: Fraction of the more abundant peak that an overlapping multiplet must exceed in order to be processed (deconvoluted).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Required Fitting Accuracy
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Accuracy required for a pattern fit to be considered valid.
has_obo_namespace: MS
id: MS:1001639

Axiom
annotated source: ProteomeDiscoverer:Xtract:Required Fitting Accuracy
annotated property: definition
annotated target: Accuracy required for a pattern fit to be considered valid.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Xtract:Resolution At 400
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Resolution at mass 400.
has_obo_namespace: MS
id: MS:1001640

Axiom
annotated source: ProteomeDiscoverer:Xtract:Resolution At 400
annotated property: definition
annotated target: Resolution at mass 400.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Lowest Charge State
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Minimum charge state below which peptides are filtered out.
has_obo_namespace: MS
id: MS:1001641

Axiom
annotated source: ProteomeDiscoverer:Lowest Charge State
annotated property: definition
annotated target: Minimum charge state below which peptides are filtered out.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Highest Charge State
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum charge above which peptides are filtered out.
has_obo_namespace: MS
id: MS:1001642

Axiom
annotated source: ProteomeDiscoverer:Highest Charge State
annotated property: definition
annotated target: Maximum charge above which peptides are filtered out.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether spectra with scores above the threshold score are retained rather than filtered out.
has_obo_namespace: MS
id: MS:1001643

Axiom
annotated source: ProteomeDiscoverer:Spectrum Score Filter:Let Pass Above Scores
annotated property: definition
annotated target: Determines whether spectra with scores above the threshold score are retained rather than filtered out.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Dynamic Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Determine dynamic post-translational modifications (PTMs).
has_obo_namespace: MS
id: MS:1001644

Axiom
annotated source: ProteomeDiscoverer:Dynamic Modification
annotated property: definition
annotated target: Determine dynamic post-translational modifications (PTMs).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Static Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Static Modification to all occurrences of a named amino acid.
has_obo_namespace: MS
id: MS:1001645

Axiom
annotated source: ProteomeDiscoverer:Static Modification
annotated property: definition
annotated target: Static Modification to all occurrences of a named amino acid.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Decoy Search
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database.
has_obo_namespace: MS
id: MS:1001646
comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Mascot:Decoy Search
annotated property: definition
annotated target: OBSOLETE Determines whether the Proteome Discoverer application searches an additional decoy database.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Error tolerant Search
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether to search error-tolerant.
has_obo_namespace: MS
id: MS:1001647

Axiom
annotated source: ProteomeDiscoverer:Mascot:Error tolerant Search
annotated property: definition
annotated target: Determines whether to search error-tolerant.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Max MGF File Size
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum size of the .mgf (Mascot Generic Format) file in MByte.
has_obo_namespace: MS
id: MS:1001648

Axiom
annotated source: ProteomeDiscoverer:Mascot:Max MGF File Size
annotated property: definition
annotated target: Maximum size of the .mgf (Mascot Generic Format) file in MByte.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Mascot Server URL
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: URL (Uniform resource Locator) of the Mascot server.
has_obo_namespace: MS
id: MS:1001649

Axiom
annotated source: ProteomeDiscoverer:Mascot:Mascot Server URL
annotated property: definition
annotated target: URL (Uniform resource Locator) of the Mascot server.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Number of attempts to submit the search
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Number of attempts to submit the Mascot search.
has_obo_namespace: MS
id: MS:1001650

Axiom
annotated source: ProteomeDiscoverer:Mascot:Number of attempts to submit the search
annotated property: definition
annotated target: Number of attempts to submit the Mascot search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:X Static Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Number of attempts to submit the Mascot search.
has_obo_namespace: MS
id: MS:1001651

Axiom
annotated source: ProteomeDiscoverer:Mascot:X Static Modification
annotated property: definition
annotated target: Number of attempts to submit the Mascot search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:User Name
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Name of the user submitting the Mascot search.
has_obo_namespace: MS
id: MS:1001652
comment: This term was made obsolete because it's recommended to use researcher (MS:1001271) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Mascot:User Name
annotated property: definition
annotated target: OBSOLETE Name of the user submitting the Mascot search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Time interval between attempts to submit a search in seconds.
has_obo_namespace: MS
id: MS:1001653

Axiom
annotated source: ProteomeDiscoverer:Mascot:Time interval between attempts to submit a search
annotated property: definition
annotated target: Time interval between attempts to submit a search in seconds.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Enzyme Name
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Specifies the enzyme reagent used for protein digestion.
has_obo_namespace: MS
id: MS:1001654
comment: This term was made obsolete because it's recommended to use cleavage agent name (MS:1001045) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Enzyme Name
annotated property: definition
annotated target: OBSOLETE Specifies the enzyme reagent used for protein digestion.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Fragment Mass Tolerance
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu.
has_obo_namespace: MS
id: MS:1001655
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.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Fragment Mass Tolerance
annotated property: definition
annotated target: OBSOLETE Mass tolerance used for matching fragment peaks in Da or mmu.
database_cross_reference: PSI:MS

Mascot:Instrument
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Type of instrument used to acquire the data in the raw file.
has_obo_namespace: MS
id: MS:1001656

Axiom
annotated source: Mascot:Instrument
annotated property: definition
annotated target: Type of instrument used to acquire the data in the raw file.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Maximum Missed Cleavage Sites
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum number of missed cleavage sites to consider during the digest.
has_obo_namespace: MS
id: MS:1001657

Axiom
annotated source: ProteomeDiscoverer:Maximum Missed Cleavage Sites
annotated property: definition
annotated target: Maximum number of missed cleavage sites to consider during the digest.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Peptide CutOff Score
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Minimum score in the IonScore column that each peptide must exceed in order to be reported.
has_obo_namespace: MS
id: MS:1001658

Axiom
annotated source: ProteomeDiscoverer:Mascot:Peptide CutOff Score
annotated property: definition
annotated target: Minimum score in the IonScore column that each peptide must exceed in order to be reported.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Precursor Mass Tolerance
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE Mass window for which precursor ions are considered to be the same species.
has_obo_namespace: MS
id: MS:1001659
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.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Precursor Mass Tolerance
annotated property: definition
annotated target: OBSOLETE Mass window for which precursor ions are considered to be the same species.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Protein CutOff Score
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Minimum protein score in the IonScore column that each protein must exceed in order to be reported.
has_obo_namespace: MS
id: MS:1001660

Axiom
annotated source: ProteomeDiscoverer:Mascot:Protein CutOff Score
annotated property: definition
annotated target: Minimum protein score in the IonScore column that each protein must exceed in order to be reported.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Protein Database
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Database to use in the search (configured on the Mascot server).
has_obo_namespace: MS
id: MS:1001661
comment: This term was made obsolete because it's recommended to use database name (MS:1001013) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Protein Database
annotated property: definition
annotated target: OBSOLETE Database to use in the search (configured on the Mascot server).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Protein Relevance Factor
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report.
has_obo_namespace: MS
id: MS:1001662

Axiom
annotated source: ProteomeDiscoverer:Mascot:Protein Relevance Factor
annotated property: definition
annotated target: Specifies a factor that is used in calculating a threshold that determines whether a protein appears in the results report.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Target FDR Relaxed
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence.
has_obo_namespace: MS
id: MS:1001663

Axiom
annotated source: ProteomeDiscoverer:Target FDR Relaxed
annotated property: definition
annotated target: Specifies the relaxed target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with moderate confidence.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Target FDR Strict
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence.
has_obo_namespace: MS
id: MS:1001664

Axiom
annotated source: ProteomeDiscoverer:Target FDR Strict
annotated property: definition
annotated target: Specifies the strict target false discovery rate (FDR, 0.0 - 1.0) for peptide hits with high confidence.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Taxonomy
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Limits searches to entries from a particular species or group of species.
has_obo_namespace: MS
id: MS:1001665
comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Mascot:Taxonomy
annotated property: definition
annotated target: OBSOLETE Limits searches to entries from a particular species or group of species.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Use Average Precursor Mass
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: OBSOLETE Use average mass for the precursor.
has_obo_namespace: MS
id: MS:1001666
comment: This term was made obsolete because it's recommended to use parent mass type average (MS:1001212) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Use Average Precursor Mass
annotated property: definition
annotated target: OBSOLETE Use average mass for the precursor.
database_cross_reference: PSI:MS

Mascot:use MudPIT scoring
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: OBSOLETE Determines whether to use MudPIT or normal scoring.
has_obo_namespace: MS
id: MS:1001667
comment: This term was made obsolete because it's recommended to use Mascot:ProteinScoringMethod (MS:1001318) instead.
deprecated: true

Axiom
annotated source: Mascot:use MudPIT scoring
annotated property: definition
annotated target: OBSOLETE Determines whether to use MudPIT or normal scoring.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Absolute XCorr Threshold
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported.
has_obo_namespace: MS
id: MS:1001668

Axiom
annotated source: ProteomeDiscoverer:Absolute XCorr Threshold
annotated property: definition
annotated target: Minimum cross-correlation threshold that determines whether peptides in an .srf file are imported.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Calculate Probability Score
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether to calculate a probability score for every peptide match.
has_obo_namespace: MS
id: MS:1001669

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Calculate Probability Score
annotated property: definition
annotated target: Determines whether to calculate a probability score for every peptide match.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:CTerminal Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Dynamic C-terminal modification that is used during the search.
has_obo_namespace: MS
id: MS:1001670

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:CTerminal Modification
annotated property: definition
annotated target: Dynamic C-terminal modification that is used during the search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained.
has_obo_namespace: MS
id: MS:1001671

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Fragment Ion Cutoff Percentage
annotated property: definition
annotated target: Percentage of the theoretical ions that must be found in order for a peptide to be scored and retained.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum number of identical modifications that a single peptide can have.
has_obo_namespace: MS
id: MS:1001672

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Max Identical Modifications Per Peptide
annotated property: definition
annotated target: Maximum number of identical modifications that a single peptide can have.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Max Modifications Per Peptide
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance.
has_obo_namespace: MS
id: MS:1001673

Axiom
annotated source: ProteomeDiscoverer:Max Modifications Per Peptide
annotated property: definition
annotated target: Maximum number of different modifications that a peptide can have, e.g. because of steric hindrance.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum number of peptides that are searched and scored per spectrum.
has_obo_namespace: MS
id: MS:1001674

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Maximum Peptides Considered
annotated property: definition
annotated target: Maximum number of peptides that are searched and scored per spectrum.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Maximum Peptides Output
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum number of peptide matches reported per spectrum.
has_obo_namespace: MS
id: MS:1001675

Axiom
annotated source: ProteomeDiscoverer:Maximum Peptides Output
annotated property: definition
annotated target: Maximum number of peptide matches reported per spectrum.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Maximum Protein References Per Peptide
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Maximum number of proteins that a single identified peptide can be associated with during protein assembly.
has_obo_namespace: MS
id: MS:1001676

Axiom
annotated source: ProteomeDiscoverer:Maximum Protein References Per Peptide
annotated property: definition
annotated target: Maximum number of proteins that a single identified peptide can be associated with during protein assembly.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:NTerminal Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Dynamic N-terminal modification that is used during the search.
has_obo_namespace: MS
id: MS:1001677

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:NTerminal Modification
annotated property: definition
annotated target: Dynamic N-terminal modification that is used during the search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Peptide CTerminus
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Static modification for the C terminal of the peptide used during the search.
has_obo_namespace: MS
id: MS:1001678

Axiom
annotated source: ProteomeDiscoverer:Peptide CTerminus
annotated property: definition
annotated target: Static modification for the C terminal of the peptide used during the search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Peptide NTerminus
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Static modification for the N terminal of the peptide used during the search.
has_obo_namespace: MS
id: MS:1001679

Axiom
annotated source: ProteomeDiscoverer:Peptide NTerminus
annotated property: definition
annotated target: Static modification for the N terminal of the peptide used during the search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Specifies a factor to apply to the protein score.
has_obo_namespace: MS
id: MS:1001680

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Peptide Relevance Factor
annotated property: definition
annotated target: Specifies a factor to apply to the protein score.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Protein Relevance Threshold
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report.
has_obo_namespace: MS
id: MS:1001681

Axiom
annotated source: ProteomeDiscoverer:Protein Relevance Threshold
annotated property: definition
annotated target: Specifies a peptide threshold that determines whether the protein that it is a part of is scored and retained in the report.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Search Against Decoy Database
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database.
has_obo_namespace: MS
id: MS:1001682
comment: This term was made obsolete because it's recommended to use quality estimation with decoy database (MS:1001194) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Search Against Decoy Database
annotated property: definition
annotated target: OBSOLETE Determines whether the Proteome Discoverer application searches against a decoy database.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Use average masses for the fragments.
has_obo_namespace: MS
id: MS:1001683

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Use Average Fragment Masses
annotated property: definition
annotated target: Use average masses for the fragments.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Use Neutral Loss a Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether a ions with neutral loss are used for spectrum matching.
has_obo_namespace: MS
id: MS:1001684

Axiom
annotated source: ProteomeDiscoverer:Use Neutral Loss a Ions
annotated property: definition
annotated target: Determines whether a ions with neutral loss are used for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Use Neutral Loss b Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether b ions with neutral loss are used for spectrum matching.
has_obo_namespace: MS
id: MS:1001685

Axiom
annotated source: ProteomeDiscoverer:Use Neutral Loss b Ions
annotated property: definition
annotated target: Determines whether b ions with neutral loss are used for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Use Neutral Loss y Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether y ions with neutral loss are used for spectrum matching.
has_obo_namespace: MS
id: MS:1001686

Axiom
annotated source: ProteomeDiscoverer:Use Neutral Loss y Ions
annotated property: definition
annotated target: Determines whether y ions with neutral loss are used for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Use Neutral Loss z Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines whether z ions with neutral loss are used for spectrum matching.
has_obo_namespace: MS
id: MS:1001687

Axiom
annotated source: ProteomeDiscoverer:Use Neutral Loss z Ions
annotated property: definition
annotated target: Determines whether z ions with neutral loss are used for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of a Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses a ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001688

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of a Ions
annotated property: definition
annotated target: Uses a ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of b Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses b ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001689

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of b Ions
annotated property: definition
annotated target: Uses b ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of c Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses c ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001690

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of c Ions
annotated property: definition
annotated target: Uses c ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of d Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses c ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001691

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of d Ions
annotated property: definition
annotated target: Uses c ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of v Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses c ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001692

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of v Ions
annotated property: definition
annotated target: Uses c ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of w Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses c ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001693

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of w Ions
annotated property: definition
annotated target: Uses c ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of x Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses x ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001694

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of x Ions
annotated property: definition
annotated target: Uses x ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of y Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses y ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001695

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of y Ions
annotated property: definition
annotated target: Uses y ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Weight of z Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Uses z ions for spectrum matching with this relative factor.
has_obo_namespace: MS
id: MS:1001696

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Weight of z Ions
annotated property: definition
annotated target: Uses z ions for spectrum matching with this relative factor.
database_cross_reference: PSI:MS

ProteomeDiscoverer:ZCore:Protein Score Cutoff
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Sets a minimum protein score that each protein must exceed in order to be reported.
has_obo_namespace: MS
id: MS:1001697

Axiom
annotated source: ProteomeDiscoverer:ZCore:Protein Score Cutoff
annotated property: definition
annotated target: Sets a minimum protein score that each protein must exceed in order to be reported.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specifies which peak to select if more than one peak is found inside the integration window.
has_obo_namespace: MS
id: MS:1001698

Axiom
annotated source: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Method
annotated property: definition
annotated target: Specifies which peak to select if more than one peak is found inside the integration window.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Specifies the mass-to-charge window that enables one to look for the reporter peaks.
has_obo_namespace: MS
id: MS:1001699

Axiom
annotated source: ProteomeDiscoverer:Reporter Ions Quantizer:Integration Window Tolerance
annotated property: definition
annotated target: Specifies the mass-to-charge window that enables one to look for the reporter peaks.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Quantitation method for isobarically labeled quantitation.
has_obo_namespace: MS
id: MS:1001700

Axiom
annotated source: ProteomeDiscoverer:Reporter Ions Quantizer:Quantitation Method
annotated property: definition
annotated target: Quantitation method for isobarically labeled quantitation.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Exporter:Export Format
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Format of the exported spectra (dta, mgf or mzData).
has_obo_namespace: MS
id: MS:1001701
comment: This term was made obsolete because it's recommended to use one of the 'mass spectrometer file format' terms (MS:1000560) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Spectrum Exporter:Export Format
annotated property: definition
annotated target: OBSOLETE Format of the exported spectra (dta, mgf or mzData).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Exporter:File name
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Name of the output file that contains the exported data.
has_obo_namespace: MS
id: MS:1001702

Axiom
annotated source: ProteomeDiscoverer:Spectrum Exporter:File name
annotated property: definition
annotated target: Name of the output file that contains the exported data.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Search Modifications Only For Identified Proteins
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Influences the modifications search.
has_obo_namespace: MS
id: MS:1001703

Axiom
annotated source: ProteomeDiscoverer:Search Modifications Only For Identified Proteins
annotated property: definition
annotated target: Influences the modifications search.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard high confidence XCorr parameter for charge = 1.
has_obo_namespace: MS
id: MS:1001704

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge1
annotated property: definition
annotated target: Standard high confidence XCorr parameter for charge = 1.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard high confidence XCorr parameter for charge = 2.
has_obo_namespace: MS
id: MS:1001705

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge2
annotated property: definition
annotated target: Standard high confidence XCorr parameter for charge = 2.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard high confidence XCorr parameter for charge = 3.
has_obo_namespace: MS
id: MS:1001706

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge3
annotated property: definition
annotated target: Standard high confidence XCorr parameter for charge = 3.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard high confidence XCorr parameter for charge >= 4.
has_obo_namespace: MS
id: MS:1001707

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std High Confidence XCorr Charge4
annotated property: definition
annotated target: Standard high confidence XCorr parameter for charge >= 4.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard medium confidence XCorr parameter for charge = 1.
has_obo_namespace: MS
id: MS:1001708

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge1
annotated property: definition
annotated target: Standard medium confidence XCorr parameter for charge = 1.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard medium confidence XCorr parameter for charge = 2.
has_obo_namespace: MS
id: MS:1001709

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge2
annotated property: definition
annotated target: Standard medium confidence XCorr parameter for charge = 2.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard medium confidence XCorr parameter for charge = 3.
has_obo_namespace: MS
id: MS:1001710

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge3
annotated property: definition
annotated target: Standard medium confidence XCorr parameter for charge = 3.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Standard medium confidence XCorr parameter for charge >= 4.
has_obo_namespace: MS
id: MS:1001711

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:Std Medium Confidence XCorr Charge4
annotated property: definition
annotated target: Standard medium confidence XCorr parameter for charge >= 4.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT high confidence XCorr parameter for charge = 1.
has_obo_namespace: MS
id: MS:1001712

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge1
annotated property: definition
annotated target: FT high confidence XCorr parameter for charge = 1.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT high confidence XCorr parameter for charge = 2.
has_obo_namespace: MS
id: MS:1001713

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge2
annotated property: definition
annotated target: FT high confidence XCorr parameter for charge = 2.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT high confidence XCorr parameter for charge = 3.
has_obo_namespace: MS
id: MS:1001714

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge3
annotated property: definition
annotated target: FT high confidence XCorr parameter for charge = 3.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT high confidence XCorr parameter for charge >= 4.
has_obo_namespace: MS
id: MS:1001715

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT High Confidence XCorr Charge4
annotated property: definition
annotated target: FT high confidence XCorr parameter for charge >= 4.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT medium confidence XCorr parameter for charge = 1.
has_obo_namespace: MS
id: MS:1001716

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge1
annotated property: definition
annotated target: FT medium confidence XCorr parameter for charge = 1.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT medium confidence XCorr parameter for charge = 2.
has_obo_namespace: MS
id: MS:1001717

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge2
annotated property: definition
annotated target: FT medium confidence XCorr parameter for charge = 2.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT medium confidence XCorr parameter for charge = 3.
has_obo_namespace: MS
id: MS:1001718

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge3
annotated property: definition
annotated target: FT medium confidence XCorr parameter for charge = 3.
database_cross_reference: PSI:MS

ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: FT medium confidence XCorr parameter for charge >= 4.
has_obo_namespace: MS
id: MS:1001719

Axiom
annotated source: ProteomeDiscoverer:SEQUEST:FT Medium Confidence XCorr Charge4
annotated property: definition
annotated target: FT medium confidence XCorr parameter for charge >= 4.
database_cross_reference: PSI:MS

ProteomeDiscoverer:1. Dynamic Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter.
has_obo_namespace: MS
id: MS:1001720
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:1. Dynamic Modification
annotated property: definition
annotated target: OBSOLETE ProteomeDiscoverer's 1st dynamic post-translational modification (PTM) input parameter.
database_cross_reference: PSI:PI

ProteomeDiscoverer:2. Dynamic Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter.
has_obo_namespace: MS
id: MS:1001721
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:2. Dynamic Modification
annotated property: definition
annotated target: OBSOLETE ProteomeDiscoverer's 2nd dynamic post-translational modification (PTM) input parameter.
database_cross_reference: PSI:PI

ProteomeDiscoverer:3. Dynamic Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter.
has_obo_namespace: MS
id: MS:1001722
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:3. Dynamic Modification
annotated property: definition
annotated target: OBSOLETE ProteomeDiscoverer's 3rd dynamic post-translational modification (PTM) input parameter.
database_cross_reference: PSI:PI

ProteomeDiscoverer:4. Dynamic Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter.
has_obo_namespace: MS
id: MS:1001723
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Dynamic Modification (MS:1001644) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:4. Dynamic Modification
annotated property: definition
annotated target: OBSOLETE ProteomeDiscoverer's 4th dynamic post-translational modification (PTM) input parameter.
database_cross_reference: PSI:PI

ProteomeDiscoverer:Static Modification for X
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Static Modification for X.
has_obo_namespace: MS
id: MS:1001724

Axiom
annotated source: ProteomeDiscoverer:Static Modification for X
annotated property: definition
annotated target: Static Modification for X.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Initial minimal peptide probability
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Minimal initial peptide probability to contribute to analysis.
has_obo_namespace: MS
id: MS:1001725

Axiom
annotated source: ProteomeDiscoverer:Initial minimal peptide probability
annotated property: definition
annotated target: Minimal initial peptide probability to contribute to analysis.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Minimal peptide probability
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Minimum adjusted peptide probability contributing to protein probability.
has_obo_namespace: MS
id: MS:1001726

Axiom
annotated source: ProteomeDiscoverer:Minimal peptide probability
annotated property: definition
annotated target: Minimum adjusted peptide probability contributing to protein probability.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Minimal peptide weight
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Minimum peptide weight contributing to protein probability.
has_obo_namespace: MS
id: MS:1001727

Axiom
annotated source: ProteomeDiscoverer:Minimal peptide weight
annotated property: definition
annotated target: Minimum peptide weight contributing to protein probability.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Number of input1 spectra
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Number of spectra from 1+ precursor ions.
has_obo_namespace: MS
id: MS:1001728

Axiom
annotated source: ProteomeDiscoverer:Number of input1 spectra
annotated property: definition
annotated target: Number of spectra from 1+ precursor ions.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Number of input2 spectra
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Number of spectra from 2+ precursor ions.
has_obo_namespace: MS
id: MS:1001729

Axiom
annotated source: ProteomeDiscoverer:Number of input2 spectra
annotated property: definition
annotated target: Number of spectra from 2+ precursor ions.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Number of input3 spectra
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Number of spectra from 3+ precursor ions.
has_obo_namespace: MS
id: MS:1001730

Axiom
annotated source: ProteomeDiscoverer:Number of input3 spectra
annotated property: definition
annotated target: Number of spectra from 3+ precursor ions.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Number of input4 spectra
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Number of spectra from 4+ precursor ions.
has_obo_namespace: MS
id: MS:1001731

Axiom
annotated source: ProteomeDiscoverer:Number of input4 spectra
annotated property: definition
annotated target: Number of spectra from 4+ precursor ions.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Number of input5 spectra
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: int
definition: Number of spectra from 5+ precursor ions.
has_obo_namespace: MS
id: MS:1001732

Axiom
annotated source: ProteomeDiscoverer:Number of input5 spectra
annotated property: definition
annotated target: Number of spectra from 5+ precursor ions.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Number of predicted correct proteins
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Total number of predicted correct protein ids (sum of probabilities).
has_obo_namespace: MS
id: MS:1001733

Axiom
annotated source: ProteomeDiscoverer:Number of predicted correct proteins
annotated property: definition
annotated target: Total number of predicted correct protein ids (sum of probabilities).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Organism
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Sample organism (used for annotation purposes).
has_obo_namespace: MS
id: MS:1001734
comment: This term was made obsolete because it's recommended to use taxonomy: scientific name (MS:1001469) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Organism
annotated property: definition
annotated target: OBSOLETE Sample organism (used for annotation purposes).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Reference Database
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Full path database name.
has_obo_namespace: MS
id: MS:1001735
comment: This term was made obsolete. Use attribute in mzIdentML / mzQuantML instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Reference Database
annotated property: definition
annotated target: OBSOLETE Full path database name.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Residue substitution list
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Residues considered equivalent when comparing peptides.
has_obo_namespace: MS
id: MS:1001736

Axiom
annotated source: ProteomeDiscoverer:Residue substitution list
annotated property: definition
annotated target: Residues considered equivalent when comparing peptides.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Source file extension
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE File type (if not pepXML).
has_obo_namespace: MS
id: MS:1001737
comment: This term was made obsolete because it's recommended to use mass spectrometer file format (MS:1000560) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Source file extension
annotated property: definition
annotated target: OBSOLETE File type (if not pepXML).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Source Files
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Input pepXML files.
has_obo_namespace: MS
id: MS:1001738
comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Source Files
annotated property: definition
annotated target: OBSOLETE Input pepXML files.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Source Files old
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE Input pepXML files (old).
has_obo_namespace: MS
id: MS:1001739
comment: This term was made obsolete because it's recommended to use pepXML file (MS:1001421) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:Source Files old
annotated property: definition
annotated target: OBSOLETE Input pepXML files (old).
database_cross_reference: PSI:MS

ProteomeDiscoverer:WinCyg reference database
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Windows full path for database.
has_obo_namespace: MS
id: MS:1001740

Axiom
annotated source: ProteomeDiscoverer:WinCyg reference database
annotated property: definition
annotated target: Windows full path for database.
database_cross_reference: PSI:MS

ProteomeDiscoverer:WinCyg source files
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Windows pepXML file names.
has_obo_namespace: MS
id: MS:1001741

Axiom
annotated source: ProteomeDiscoverer:WinCyg source files
annotated property: definition
annotated target: Windows pepXML file names.
database_cross_reference: PSI:MS

LTQ Orbitrap Velos
type: Class
subclass of: Thermo Scientific instrument model
definition: Finnigan LTQ Orbitrap Velos MS.
has_obo_namespace: MS
id: MS:1001742

Axiom
annotated source: LTQ Orbitrap Velos
annotated property: definition
annotated target: Finnigan LTQ Orbitrap Velos MS.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of A Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use A ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001743

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of A Ions
annotated property: definition
annotated target: Determines if to use A ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of B Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use B ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001744

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of B Ions
annotated property: definition
annotated target: Determines if to use B ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of C Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use C ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001745

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of C Ions
annotated property: definition
annotated target: Determines if to use C ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of D Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use D ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001746

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of D Ions
annotated property: definition
annotated target: Determines if to use D ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of V Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use V ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001747

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of V Ions
annotated property: definition
annotated target: Determines if to use V ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of W Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use W ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001748

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of W Ions
annotated property: definition
annotated target: Determines if to use W ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of X Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use X ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001749

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of X Ions
annotated property: definition
annotated target: Determines if to use X ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of Y Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use Y ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001750

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of Y Ions
annotated property: definition
annotated target: Determines if to use Y ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Weight of Z Ions
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use z ions for spectrum matching.
has_obo_namespace: MS
id: MS:1001751

Axiom
annotated source: ProteomeDiscoverer:Mascot:Weight of Z Ions
annotated property: definition
annotated target: Determines if to use z ions for spectrum matching.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Determines if to use precursor reevaluation.
has_obo_namespace: MS
id: MS:1001752

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Use New Precursor Reevaluation
annotated property: definition
annotated target: Determines if to use precursor reevaluation.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Signal-to-Noise ratio below which peaks are removed (in FT mode only).
has_obo_namespace: MS
id: MS:1001753

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:SN Threshold FTonly
annotated property: definition
annotated target: Signal-to-Noise ratio below which peaks are removed (in FT mode only).
database_cross_reference: PSI:MS

ProteomeDiscoverer:Mascot:Please Do not Touch this
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches.
has_obo_namespace: MS
id: MS:1001754

Axiom
annotated source: ProteomeDiscoverer:Mascot:Please Do not Touch this
annotated property: definition
annotated target: Unknown Mascot parameter which ProteomeDiscoverer uses for mascot searches.
database_cross_reference: PSI:MS

contact phone number
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Phone number of the contact person or organization.
has_obo_namespace: MS
id: MS:1001755

Axiom
annotated source: contact phone number
annotated property: definition
annotated target: Phone number of the contact person or organization.
database_cross_reference: PSI:MS

contact fax number
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Fax number for the contact person or organization.
has_obo_namespace: MS
id: MS:1001756

Axiom
annotated source: contact fax number
annotated property: definition
annotated target: Fax number for the contact person or organization.
database_cross_reference: PSI:MS

contact toll-free phone number
type: Class
subclass of: contact attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Toll-free phone number of the contact person or organization.
has_obo_namespace: MS
id: MS:1001757

Axiom
annotated source: contact toll-free phone number
annotated property: definition
annotated target: Toll-free phone number of the contact person or organization.
database_cross_reference: PSI:MS

Mascot:SigThresholdType
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Significance threshold type used in Mascot reporting (either 'identity' or 'homology').
has_obo_namespace: MS
id: MS:1001758

Axiom
annotated source: Mascot:SigThresholdType
annotated property: definition
annotated target: Significance threshold type used in Mascot reporting (either 'identity' or 'homology').
database_cross_reference: PSI:MS

Mascot:ProteinGrouping
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering').
has_obo_namespace: MS
id: MS:1001759

Axiom
annotated source: Mascot:ProteinGrouping
annotated property: definition
annotated target: Strategy used by Mascot to group proteins with same peptide matches (one of 'none', 'Occam's razor' or 'family clustering').
database_cross_reference: PSI:MS

Percolator:features
type: Class
subclass of: MS_1002107
subclass of: Restriction
  on property: has value type
  some values from: string
definition: List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'.
has_obo_namespace: MS
id: MS:1001760

Axiom
annotated source: Percolator:features
annotated property: definition
annotated target: List of Percolator features that were used in processing the peptide matches. Typical Percolator features are 'retentionTime', 'dM', 'mScore', 'lgDScore', 'mrCalc', 'charge' and 'dMppm'.
database_cross_reference: PSI:MS

ACQUITY UPLC
type: Class
subclass of: MS_1003591
subclass of: MS_1003606
definition: Waters LC-system ACQUITY UPLC.
has_obo_namespace: MS
id: MS:1001761

Axiom
annotated source: ACQUITY UPLC
annotated property: definition
annotated target: Waters LC-system ACQUITY UPLC.
database_cross_reference: PSI:MS

ACQUITY UPLC H-Class
type: Class
subclass of: MS_1003591
subclass of: MS_1003606
definition: Waters LC-system ACQUITY UPLC H-Class.
has_obo_namespace: MS
id: MS:1001762

Axiom
annotated source: ACQUITY UPLC H-Class
annotated property: definition
annotated target: Waters LC-system ACQUITY UPLC H-Class.
database_cross_reference: PSI:MS

ACQUITY UPLC H-Class Bio
type: Class
subclass of: MS_1003591
subclass of: MS_1003606
definition: Waters LC-system ACQUITY UPLC H-Class Bio.
has_obo_namespace: MS
id: MS:1001763

Axiom
annotated source: ACQUITY UPLC H-Class Bio
annotated property: definition
annotated target: Waters LC-system ACQUITY UPLC H-Class Bio.
database_cross_reference: PSI:MS

ACQUITY UPLC I-Class
type: Class
subclass of: MS_1003591
subclass of: MS_1003606
definition: Waters LC-system ACQUITY UPLC I-Class.
has_obo_namespace: MS
id: MS:1001764

Axiom
annotated source: ACQUITY UPLC I-Class
annotated property: definition
annotated target: Waters LC-system ACQUITY UPLC I-Class.
database_cross_reference: PSI:MS

ACQUITY UPLC Systems with 2D Technology
type: Class
subclass of: MS_1003591
subclass of: MS_1003606
definition: Waters LC-system ACQUITY UPLC Systems with 2D Technology.
has_obo_namespace: MS
id: MS:1001765

Axiom
annotated source: ACQUITY UPLC Systems with 2D Technology
annotated property: definition
annotated target: Waters LC-system ACQUITY UPLC Systems with 2D Technology.
database_cross_reference: PSI:MS

nanoACQUITY UPLC
type: Class
subclass of: MS_1003591
subclass of: MS_1003599
subclass of: MS_1003606
definition: Waters LC-system nanoACQUITY UPLC.
has_obo_namespace: MS
id: MS:1001766

Axiom
annotated source: nanoACQUITY UPLC
annotated property: definition
annotated target: Waters LC-system nanoACQUITY UPLC.
database_cross_reference: PSI:MS

nanoACQUITY UPLC System with 1D Technology
type: Class
subclass of: MS_1003591
subclass of: MS_1003599
subclass of: MS_1003606
definition: Waters LC-system nanoACQUITY UPLC System with 1D Technology.
has_obo_namespace: MS
id: MS:1001767

Axiom
annotated source: nanoACQUITY UPLC System with 1D Technology
annotated property: definition
annotated target: Waters LC-system nanoACQUITY UPLC System with 1D Technology.
database_cross_reference: PSI:MS

nanoACQUITY UPLC with HDX Technology
type: Class
subclass of: MS_1003591
subclass of: MS_1003599
subclass of: MS_1003606
definition: Waters LC-system nanoACQUITY UPLC with HDX Technology.
has_obo_namespace: MS
id: MS:1001768

Axiom
annotated source: nanoACQUITY UPLC with HDX Technology
annotated property: definition
annotated target: Waters LC-system nanoACQUITY UPLC with HDX Technology.
database_cross_reference: PSI:MS

TRIZAIC UPLC nanoTile
type: Class
subclass of: MS_1003591
subclass of: MS_1003606
definition: Waters LC-system TRIZAIC UPLC nanoTile.
has_obo_namespace: MS
id: MS:1001769

Axiom
annotated source: TRIZAIC UPLC nanoTile
annotated property: definition
annotated target: Waters LC-system TRIZAIC UPLC nanoTile.
database_cross_reference: PSI:MS

GCT Premier
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based GCT Premier.
has_obo_namespace: MS
id: MS:1001770

Axiom
annotated source: GCT Premier
annotated property: definition
annotated target: Waters oa-ToF based GCT Premier.
database_cross_reference: PSI:MS

MALDI Synapt G2 HDMS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI Synapt G2 HDMS.
has_obo_namespace: MS
id: MS:1001771

Axiom
annotated source: MALDI Synapt G2 HDMS
annotated property: definition
annotated target: Waters oa-ToF based MALDI Synapt G2 HDMS.
database_cross_reference: PSI:MS

MALDI Synapt G2 MS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI Synapt G2 MS.
has_obo_namespace: MS
id: MS:1001772

Axiom
annotated source: MALDI Synapt G2 MS
annotated property: definition
annotated target: Waters oa-ToF based MALDI Synapt G2 MS.
database_cross_reference: PSI:MS

MALDI Synapt G2-S HDMS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI Synapt G2 MS.
has_obo_namespace: MS
id: MS:1001773

Axiom
annotated source: MALDI Synapt G2-S HDMS
annotated property: definition
annotated target: Waters oa-ToF based MALDI Synapt G2 MS.
database_cross_reference: PSI:MS

MALDI Synapt G2-S MS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI Synapt G2-S MS.
has_obo_namespace: MS
id: MS:1001774

Axiom
annotated source: MALDI Synapt G2-S MS
annotated property: definition
annotated target: Waters oa-ToF based MALDI Synapt G2-S MS.
database_cross_reference: PSI:MS

MALDI Synapt HDMS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI Synapt HDMS.
has_obo_namespace: MS
id: MS:1001775

Axiom
annotated source: MALDI Synapt HDMS
annotated property: definition
annotated target: Waters oa-ToF based MALDI Synapt HDMS.
database_cross_reference: PSI:MS

MALDI Synapt MS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based MALDI Synapt MS.
has_obo_namespace: MS
id: MS:1001776

Axiom
annotated source: MALDI Synapt MS
annotated property: definition
annotated target: Waters oa-ToF based MALDI Synapt MS.
database_cross_reference: PSI:MS

Synapt G2 HDMS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Synapt G2 HDMS.
has_obo_namespace: MS
id: MS:1001777

Axiom
annotated source: Synapt G2 HDMS
annotated property: definition
annotated target: Waters oa-ToF based Synapt G2 HDMS.
database_cross_reference: PSI:MS

Synapt G2 MS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Synapt G2 MS.
has_obo_namespace: MS
id: MS:1001778

Axiom
annotated source: Synapt G2 MS
annotated property: definition
annotated target: Waters oa-ToF based Synapt G2 MS.
database_cross_reference: PSI:MS

Synapt G2-S HDMS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Synapt G2-S HDMS.
has_obo_namespace: MS
id: MS:1001779

Axiom
annotated source: Synapt G2-S HDMS
annotated property: definition
annotated target: Waters oa-ToF based Synapt G2-S HDMS.
database_cross_reference: PSI:MS

Synapt G2-S MS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Synapt G2-S MS.
has_obo_namespace: MS
id: MS:1001780

Axiom
annotated source: Synapt G2-S MS
annotated property: definition
annotated target: Waters oa-ToF based Synapt G2-S MS.
database_cross_reference: PSI:MS

Synapt HDMS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Synapt HDMS.
has_obo_namespace: MS
id: MS:1001781

Axiom
annotated source: Synapt HDMS
annotated property: definition
annotated target: Waters oa-ToF based Synapt HDMS.
database_cross_reference: PSI:MS

Synapt MS
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Synapt MS.
has_obo_namespace: MS
id: MS:1001782

Axiom
annotated source: Synapt MS
annotated property: definition
annotated target: Waters oa-ToF based Synapt MS.
database_cross_reference: PSI:MS

Xevo G2 Q-Tof
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Xevo G2 Q-Tof.
has_obo_namespace: MS
id: MS:1001783

Axiom
annotated source: Xevo G2 Q-Tof
annotated property: definition
annotated target: Waters oa-ToF based Xevo G2 Q-Tof.
database_cross_reference: PSI:MS

Xevo G2 Tof
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Xevo G2 Tof.
has_obo_namespace: MS
id: MS:1001784

Axiom
annotated source: Xevo G2 Tof
annotated property: definition
annotated target: Waters oa-ToF based Xevo G2 Tof.
database_cross_reference: PSI:MS

Xevo Q-Tof
type: Class
subclass of: Waters instrument model
definition: Waters oa-ToF based Xevo Q-Tof.
has_obo_namespace: MS
id: MS:1001785

Axiom
annotated source: Xevo Q-Tof
annotated property: definition
annotated target: Waters oa-ToF based Xevo Q-Tof.
database_cross_reference: PSI:MS

3100
type: Class
subclass of: Waters instrument model
definition: Waters quadrupole based 3100.
has_obo_namespace: MS
id: MS:1001786

Axiom
annotated source: 3100
annotated property: definition
annotated target: Waters quadrupole based 3100.
database_cross_reference: PSI:MS

Acquity SQD
type: Class
subclass of: Waters instrument model
definition: Waters quadrupole based Acquity SQD.
has_obo_namespace: MS
id: MS:1001787

Axiom
annotated source: Acquity SQD
annotated property: definition
annotated target: Waters quadrupole based Acquity SQD.
database_cross_reference: PSI:MS

Acquity TQD
type: Class
subclass of: Waters instrument model
definition: Waters quadrupole based Acquity TQD.
has_obo_namespace: MS
id: MS:1001788

Axiom
annotated source: Acquity TQD
annotated property: definition
annotated target: Waters quadrupole based Acquity TQD.
database_cross_reference: PSI:MS

Quattro micro GC
type: Class
subclass of: Waters instrument model
definition: Waters (triple) quadrupole based Quattro micro GC.
has_obo_namespace: MS
id: MS:1001789

Axiom
annotated source: Quattro micro GC
annotated property: definition
annotated target: Waters (triple) quadrupole based Quattro micro GC.
database_cross_reference: PSI:MS

Xevo TQ MS
type: Class
subclass of: Waters instrument model
subclass of: MS_1003762
definition: Waters quadrupole based Xevo TQ MS.
has_obo_namespace: MS
id: MS:1001790

Axiom
annotated source: Xevo TQ MS
annotated property: definition
annotated target: Waters quadrupole based Xevo TQ MS.
database_cross_reference: PSI:MS

Xevo TQD
type: Class
subclass of: Waters instrument model
definition: Waters quadrupole based Xevo TQD.
has_obo_namespace: MS
id: MS:1001791

Axiom
annotated source: Xevo TQD
annotated property: definition
annotated target: Waters quadrupole based Xevo TQD.
database_cross_reference: PSI:MS

Xevo TQ-S
type: Class
subclass of: Waters instrument model
definition: Waters quadrupole based Xevo TQ-S.
has_obo_namespace: MS
id: MS:1001792

Axiom
annotated source: Xevo TQ-S
annotated property: definition
annotated target: Waters quadrupole based Xevo TQ-S.
database_cross_reference: PSI:MS

Mascot:PreferredTaxonomy
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1001793

Axiom
annotated source: Mascot:PreferredTaxonomy
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

Empower
type: Class
subclass of: Waters software
subclass of: analysis software
subclass of: data processing software
definition: Waters Empower software for liquid chromatography and mass spectrometry acquisition.
has_obo_namespace: MS
id: MS:1001795

Axiom
annotated source: Empower
annotated property: definition
annotated target: Waters Empower software for liquid chromatography and mass spectrometry acquisition.
database_cross_reference: PSI:MS

UNIFY
type: Class
subclass of: Waters software
subclass of: analysis software
subclass of: data processing software
definition: Waters UNIFY software for liquid chromatography and mass spectrometry acquisition.
has_obo_namespace: MS
id: MS:1001796

Axiom
annotated source: UNIFY
annotated property: definition
annotated target: Waters UNIFY software for liquid chromatography and mass spectrometry acquisition.
database_cross_reference: PSI:MS

travelling wave ion mobility mass spectrometer
type: Class
definition: 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.
has_exact_synonym: TWIMS
has_obo_namespace: MS
id: MS:1001797
comment: This child of the former purgatory term ion mobility spectrometry was made obsolete.
deprecated: true

Axiom
annotated source: travelling wave ion mobility mass spectrometer
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

LECO software
type: Class
subclass of: software
definition: LECO software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1001798

Axiom
annotated source: LECO software
annotated property: definition
annotated target: LECO software for data acquisition and analysis.
database_cross_reference: PSI:MS

ChromaTOF software
type: Class
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
subclass of: LECO software
definition: Software for acquisition, processing and analysis of data for LECO instruments.
has_obo_namespace: MS
id: MS:1001799

Axiom
annotated source: ChromaTOF software
annotated property: definition
annotated target: Software for acquisition, processing and analysis of data for LECO instruments.
database_cross_reference: PSI:MS

LECO instrument model
type: Class
subclass of: instrument model
definition: LECO instrument model.
has_obo_namespace: MS
id: MS:1001800

Axiom
annotated source: LECO instrument model
annotated property: definition
annotated target: LECO instrument model.
database_cross_reference: PSI:MS

Pegasus HRT
type: Class
subclass of: LECO instrument model
definition: LECO high resolution time-of-flight GC mass spectrometer.
has_obo_namespace: MS
id: MS:1001801

Axiom
annotated source: Pegasus HRT
annotated property: definition
annotated target: LECO high resolution time-of-flight GC mass spectrometer.
database_cross_reference: PSI:MS

Citius HRT
type: Class
subclass of: LECO instrument model
definition: LECO high resolution time-of-flight LC mass spectrometer.
has_obo_namespace: MS
id: MS:1001802

Axiom
annotated source: Citius HRT
annotated property: definition
annotated target: LECO high resolution time-of-flight LC mass spectrometer.
database_cross_reference: PSI:MS

Pegasus
type: Class
subclass of: LECO instrument model
definition: LECO GC time-of-flight mass spectrometer.
has_obo_namespace: MS
id: MS:1001803

Axiom
annotated source: Pegasus
annotated property: definition
annotated target: LECO GC time-of-flight mass spectrometer.
database_cross_reference: PSI:MS

TruTOF
type: Class
subclass of: LECO instrument model
definition: LECO bench-top GC time-of-flight mass spectrometer.
has_obo_namespace: MS
id: MS:1001804

Axiom
annotated source: TruTOF
annotated property: definition
annotated target: LECO bench-top GC time-of-flight mass spectrometer.
database_cross_reference: PSI:MS

quantification datatype
type: Class
subclass of: quantification information
definition: The data type of the value reported in a QuantLayer.
has_obo_namespace: MS
id: MS:1001805

Axiom
annotated source: quantification datatype
annotated property: definition
annotated target: The data type of the value reported in a QuantLayer.
database_cross_reference: PSI:MS

quantification object attribute
type: Class
subclass of: quantification information
definition: Attributes describing the details of an object relevant for reporting quantification workflows or values.
has_obo_namespace: MS
id: MS:1001806

Axiom
annotated source: quantification object attribute
annotated property: definition
annotated target: Attributes describing the details of an object relevant for reporting quantification workflows or values.
database_cross_reference: PSI:MS

study variable attribute
type: Class
subclass of: quantification object attribute
definition: Attribute describing a study variable.
has_obo_namespace: MS
id: MS:1001807

Axiom
annotated source: study variable attribute
annotated property: definition
annotated target: Attribute describing a study variable.
database_cross_reference: PSI:MS

technical replicate
type: Class
subclass of: study variable attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'.
has_obo_namespace: MS
id: MS:1001808

Axiom
annotated source: technical replicate
annotated property: definition
annotated target: The study variable is 'technical replicate'. The string value denotes the category of technical replicate, e.g. 'run generated from same sample'.
database_cross_reference: PSI:MS

biological replicate
type: Class
subclass of: study variable attribute
definition: The study variable is 'biological replicate'. This means, the run was generated from another individual or sample.
has_obo_namespace: MS
id: MS:1001809

Axiom
annotated source: biological replicate
annotated property: definition
annotated target: The study variable is 'biological replicate'. This means, the run was generated from another individual or sample.
database_cross_reference: PSI:MS

experimental condition 'case'
type: Class
subclass of: study variable attribute
definition: The experimental condition is 'case' in contrast to 'control'.
has_obo_namespace: MS
id: MS:1001810

Axiom
annotated source: experimental condition 'case'
annotated property: definition
annotated target: The experimental condition is 'case' in contrast to 'control'.
database_cross_reference: PSI:MS

experimental condition 'control'
type: Class
subclass of: study variable attribute
definition: The experimental condition is 'control' in contrast to 'case'.
has_obo_namespace: MS
id: MS:1001811

Axiom
annotated source: experimental condition 'control'
annotated property: definition
annotated target: The experimental condition is 'control' in contrast to 'case'.
database_cross_reference: PSI:MS

experimental condition 'disease'
type: Class
subclass of: study variable attribute
definition: The experimental condition is 'disease' in contrast to 'healthy'.
has_obo_namespace: MS
id: MS:1001812

Axiom
annotated source: experimental condition 'disease'
annotated property: definition
annotated target: The experimental condition is 'disease' in contrast to 'healthy'.
database_cross_reference: PSI:MS

experimental condition 'healthy'
type: Class
subclass of: study variable attribute
definition: The experimental condition is 'healthy' in contrast to 'disease'.
has_obo_namespace: MS
id: MS:1001813

Axiom
annotated source: experimental condition 'healthy'
annotated property: definition
annotated target: The experimental condition is 'healthy' in contrast to 'disease'.
database_cross_reference: PSI:MS

generic experimental condition
type: Class
subclass of: study variable attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The experimental condition is given in the value of this term.
has_obo_namespace: MS
id: MS:1001814

Axiom
annotated source: generic experimental condition
annotated property: definition
annotated target: The experimental condition is given in the value of this term.
database_cross_reference: PSI:MS

time series, time point X
type: Class
subclass of: study variable attribute
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The experimental design followed a time series design. The time point of this run is given in the value of this term.
has_obo_namespace: MS
id: MS:1001815

Axiom
annotated source: time series, time point X
annotated property: definition
annotated target: The experimental design followed a time series design. The time point of this run is given in the value of this term.
database_cross_reference: PSI:MS

dilution series, concentration X
type: Class
subclass of: study variable attribute
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The experimental design followed a dilution series design. The concentration of this run is given in the value of this term.
has_obo_namespace: MS
id: MS:1001816

Axiom
annotated source: dilution series, concentration X
annotated property: definition
annotated target: The experimental design followed a dilution series design. The concentration of this run is given in the value of this term.
database_cross_reference: PSI:MS

raw file attribute
type: Class
subclass of: quantification object attribute
definition: Attribute describing a raw file.
has_obo_namespace: MS
id: MS:1001817

Axiom
annotated source: raw file attribute
annotated property: definition
annotated target: Attribute describing a raw file.
database_cross_reference: PSI:MS

one sample run
type: Class
subclass of: raw file attribute
definition: The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free).
has_obo_namespace: MS
id: MS:1001818

Axiom
annotated source: one sample run
annotated property: definition
annotated target: The raw file contains the run of one sample (e.g. spectral counting, LC-MS label-free).
database_cross_reference: PSI:MS

two sample run
type: Class
subclass of: raw file attribute
definition: The raw file contains the run of two samples (e.g. SILAC, metabolic labelling).
has_obo_namespace: MS
id: MS:1001819

Axiom
annotated source: two sample run
annotated property: definition
annotated target: The raw file contains the run of two samples (e.g. SILAC, metabolic labelling).
database_cross_reference: PSI:MS

three sample run
type: Class
subclass of: raw file attribute
definition: The raw file contains the run of three samples (e.g. 3-plex SILAC).
has_obo_namespace: MS
id: MS:1001820

Axiom
annotated source: three sample run
annotated property: definition
annotated target: The raw file contains the run of three samples (e.g. 3-plex SILAC).
database_cross_reference: PSI:MS

four sample run
type: Class
subclass of: raw file attribute
definition: The raw file contains the run of four samples (e.g. 4-plex iTraq).
has_obo_namespace: MS
id: MS:1001821

Axiom
annotated source: four sample run
annotated property: definition
annotated target: The raw file contains the run of four samples (e.g. 4-plex iTraq).
database_cross_reference: PSI:MS

eight sample run
type: Class
subclass of: raw file attribute
definition: The raw file contains the run of eight samples (e.g. 8-plex iTraq).
has_obo_namespace: MS
id: MS:1001822

Axiom
annotated source: eight sample run
annotated property: definition
annotated target: The raw file contains the run of eight samples (e.g. 8-plex iTraq).
database_cross_reference: PSI:MS

raw files group attribute
type: Class
subclass of: quantification object attribute
definition: Attribute describing, how raw files build a raw file group.
has_obo_namespace: MS
id: MS:1001823

Axiom
annotated source: raw files group attribute
annotated property: definition
annotated target: Attribute describing, how raw files build a raw file group.
database_cross_reference: PSI:MS

merge of runs of 1D gel bands
type: Class
subclass of: raw files group attribute
definition: Attribute describing, how raw files build a raw file group.
has_obo_namespace: MS
id: MS:1001824

Axiom
annotated source: merge of runs of 1D gel bands
annotated property: definition
annotated target: Attribute describing, how raw files build a raw file group.
database_cross_reference: PSI:MS

feature list attribute
type: Class
subclass of: quantification object attribute
definition: Attribute describing a feature list.
has_obo_namespace: MS
id: MS:1001825

Axiom
annotated source: feature list attribute
annotated property: definition
annotated target: Attribute describing a feature list.
database_cross_reference: PSI:MS

mass trace reporting: rectangles
type: Class
subclass of: feature list attribute
definition: 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.
has_obo_namespace: MS
id: MS:1001826

Axiom
annotated source: mass trace reporting: rectangles
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mass trace reporting: polygons
type: Class
subclass of: feature list attribute
definition: 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.
has_obo_namespace: MS
id: MS:1001827

Axiom
annotated source: mass trace reporting: polygons
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

feature attribute
type: Class
subclass of: quantification object attribute
definition: Attribute describing a feature.
has_obo_namespace: MS
id: MS:1001828

Axiom
annotated source: feature attribute
annotated property: definition
annotated target: Attribute describing a feature.
database_cross_reference: PSI:MS

SRM transition ID
type: Class
subclass of: feature attribute
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Identifier for an SRM transition in an external document describing additional information about the transition.
has_obo_namespace: MS
id: MS:1001829

Axiom
annotated source: SRM transition ID
annotated property: definition
annotated target: Identifier for an SRM transition in an external document describing additional information about the transition.
database_cross_reference: PSI:MS

Progenesis LC-MS
type: Class
subclass of: quantitation software name
definition: Software from Nonlinear Dynamics for LC-MS label-free workflow.
has_obo_namespace: MS
id: MS:1001830

Axiom
annotated source: Progenesis LC-MS
annotated property: definition
annotated target: Software from Nonlinear Dynamics for LC-MS label-free workflow.
database_cross_reference: PSI:MS

SILACAnalyzer
type: Class
subclass of: TOPP software
subclass of: quantitation software name
definition: Software for SILAC workflow.
has_obo_namespace: MS
id: MS:1001831

Axiom
annotated source: SILACAnalyzer
annotated property: definition
annotated target: Software for SILAC workflow.
database_cross_reference: PSI:MS

quantitation software comment or customizations
type: Class
subclass of: quantification information
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Quantitation software comment or any customizations to the default setup of the software.
has_obo_namespace: MS
id: MS:1001832

Axiom
annotated source: quantitation software comment or customizations
annotated property: definition
annotated target: Quantitation software comment or any customizations to the default setup of the software.
database_cross_reference: PSI:PI

quantitation analysis summary
type: Class
subclass of: quantification information
definition: The overall workflow of this quantitation report.
has_obo_namespace: MS
id: MS:1001833

Axiom
annotated source: quantitation analysis summary
annotated property: definition
annotated target: The overall workflow of this quantitation report.
database_cross_reference: PSI:PI

LC-MS label-free quantitation analysis
type: Class
subclass of: quantitation analysis summary
definition: LC-MS label-free workflow (RT m/z map).
has_obo_namespace: MS
id: MS:1001834

Axiom
annotated source: LC-MS label-free quantitation analysis
annotated property: definition
annotated target: LC-MS label-free workflow (RT m/z map).
database_cross_reference: PSI:PI

SILAC quantitation analysis
type: Class
subclass of: quantitation analysis summary
definition: SILAC workflow (heavy, light, and sometimes medium peak).
has_obo_namespace: MS
id: MS:1001835

Axiom
annotated source: SILAC quantitation analysis
annotated property: definition
annotated target: SILAC workflow (heavy, light, and sometimes medium peak).
database_cross_reference: PSI:PI

spectral counting quantitation analysis
type: Class
subclass of: quantitation analysis summary
definition: Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant).
has_obo_namespace: MS
id: MS:1001836

Axiom
annotated source: spectral counting quantitation analysis
annotated property: definition
annotated target: Spectral counting workflow (number of identified MS2 spectra as approximation of peptide / protein quant).
database_cross_reference: PSI:PI

iTRAQ quantitation analysis
type: Class
subclass of: isobaric label quantitation analysis
definition: 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.
has_obo_namespace: MS
id: MS:1001837

Axiom
annotated source: iTRAQ quantitation analysis
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:15385600
database_cross_reference: PSI:PI

SRM quantitation analysis
type: Class
subclass of: quantitation analysis summary
definition: Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair).
has_obo_namespace: MS
id: MS:1001838

Axiom
annotated source: SRM quantitation analysis
annotated property: definition
annotated target: Selected Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair).
database_cross_reference: PSI:PI

metabolic labeling 14N / 15N quantitation analysis
type: Class
subclass of: quantitation analysis summary
definition: Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens).
has_obo_namespace: MS
id: MS:1001839

Axiom
annotated source: metabolic labeling 14N / 15N quantitation analysis
annotated property: definition
annotated target: Metabolic labeling workflow (heavy and light versions of peptides, depending on number of nitrogens).
database_cross_reference: PSI:PI

LC-MS feature intensity
type: Class
subclass of: MS_1002735
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Maximum peak intensity of the LC-MS feature.
has_obo_namespace: MS
id: MS:1001840

Axiom
annotated source: LC-MS feature intensity
annotated property: definition
annotated target: Maximum peak intensity of the LC-MS feature.
database_cross_reference: PSI:PI

LC-MS feature volume
type: Class
subclass of: MS_1002735
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Real (intensity times area) volume of the LC-MS feature.
has_obo_namespace: MS
id: MS:1001841

Axiom
annotated source: LC-MS feature volume
annotated property: definition
annotated target: Real (intensity times area) volume of the LC-MS feature.
database_cross_reference: PSI:PI

sequence-level spectral count
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting.
has_obo_namespace: MS
id: MS:1001842

Axiom
annotated source: sequence-level spectral count
annotated property: definition
annotated target: The number of MS2 spectra identified for a raw peptide sequence without PTMs and charge state in spectral counting.
database_cross_reference: PSI:PI

MS1 feature maximum intensity
type: Class
subclass of: MS_1002735
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Maximum intensity of MS1 feature.
has_obo_namespace: MS
id: MS:1001843

Axiom
annotated source: MS1 feature maximum intensity
annotated property: definition
annotated target: Maximum intensity of MS1 feature.
database_cross_reference: PSI:PI

MS1 feature area
type: Class
subclass of: MS_1002735
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Area of MS1 feature.
has_obo_namespace: MS
id: MS:1001844

Axiom
annotated source: MS1 feature area
annotated property: definition
annotated target: Area of MS1 feature.
database_cross_reference: PSI:PI

peak area
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OBSOLETE Area of MS1 peak (e.g. SILAC, 15N).
has_obo_namespace: MS
id: MS:1001845
comment: This term was made obsolete because it was a duplication of MS:1001844.
deprecated: true

Axiom
annotated source: peak area
annotated property: definition
annotated target: OBSOLETE Area of MS1 peak (e.g. SILAC, 15N).
database_cross_reference: PSI:PI

isotopic pattern area
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N).
has_obo_namespace: MS
id: MS:1001846

Axiom
annotated source: isotopic pattern area
annotated property: definition
annotated target: Area of all peaks belonging to the isotopic pattern of light or heavy peak (e.g. 15N).
database_cross_reference: PSI:PI

reporter ion intensity
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Intensity of MS2 reporter ion (e.g. iTraq).
has_obo_namespace: MS
id: MS:1001847

Axiom
annotated source: reporter ion intensity
annotated property: definition
annotated target: Intensity of MS2 reporter ion (e.g. iTraq).
database_cross_reference: PSI:PI

simple ratio of two values
type: Class
subclass of: ratio calculation method
definition: Simple ratio of two values (enumerator and denominator).
has_obo_namespace: MS
id: MS:1001848

Axiom
annotated source: simple ratio of two values
annotated property: definition
annotated target: Simple ratio of two values (enumerator and denominator).
database_cross_reference: PSI:PI

sum of MatchedFeature values
type: Class
subclass of: MS_1002735
subclass of: Restriction
  on property: has value type
  some values from: double
definition: OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values.
has_obo_namespace: MS
id: MS:1001849
comment: This term was made obsolete because the concept MatchedFeature was dropped.
deprecated: true

Axiom
annotated source: sum of MatchedFeature values
annotated property: definition
annotated target: OBSOLETE Peptide quantification value calculated as sum of MatchedFeature quantification values.
database_cross_reference: PSI:PI

normalized peptide value
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Normalized peptide value.
has_obo_namespace: MS
id: MS:1001850

Axiom
annotated source: normalized peptide value
annotated property: definition
annotated target: Normalized peptide value.
database_cross_reference: PSI:PI

protein value: sum of peptide values
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Protein quantification value calculated as sum of peptide values.
has_obo_namespace: MS
id: MS:1001851

Axiom
annotated source: protein value: sum of peptide values
annotated property: definition
annotated target: Protein quantification value calculated as sum of peptide values.
database_cross_reference: PSI:PI

normalized protein value
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Normalized protein value.
has_obo_namespace: MS
id: MS:1001852

Axiom
annotated source: normalized protein value
annotated property: definition
annotated target: Normalized protein value.
database_cross_reference: PSI:PI

max fold change
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis).
has_obo_namespace: MS
id: MS:1001853

Axiom
annotated source: max fold change
annotated property: definition
annotated target: Global datatype: Maximum of all pair-wise fold changes of group means (e.g. Progenesis).
database_cross_reference: PSI:PI

ANOVA p-value
type: Class
subclass of: p-value
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Global datatype: p-value of ANOVA of group means (e.g. Progenesis).
has_obo_namespace: MS
id: MS:1001854

Axiom
annotated source: ANOVA p-value
annotated property: definition
annotated target: Global datatype: p-value of ANOVA of group means (e.g. Progenesis).
database_cross_reference: PSI:PI

t-test p-value
type: Class
subclass of: p-value
subclass of: Restriction
  on property: has value type
  some values from: double
definition: P-value of t-Test of two groups.
has_obo_namespace: MS
id: MS:1001855

Axiom
annotated source: t-test p-value
annotated property: definition
annotated target: P-value of t-Test of two groups.
database_cross_reference: PSI:PI

reporter ion raw value
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Intensity (or area) of MS2 reporter ion (e.g. iTraq).
has_obo_namespace: MS
id: MS:1001856

Axiom
annotated source: reporter ion raw value
annotated property: definition
annotated target: Intensity (or area) of MS2 reporter ion (e.g. iTraq).
database_cross_reference: PSI:PI

reporter ion normalized value
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Normalized value of MS2 reporter ion (e.g. iTraq).
has_obo_namespace: MS
id: MS:1001857

Axiom
annotated source: reporter ion normalized value
annotated property: definition
annotated target: Normalized value of MS2 reporter ion (e.g. iTraq).
database_cross_reference: PSI:PI

XIC area
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Area of the extracted ion chromatogram (e.g. of a transition in SRM).
has_obo_namespace: MS
id: MS:1001858

Axiom
annotated source: XIC area
annotated property: definition
annotated target: Area of the extracted ion chromatogram (e.g. of a transition in SRM).
database_cross_reference: PSI:PI

normalized XIC area
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM).
has_obo_namespace: MS
id: MS:1001859

Axiom
annotated source: normalized XIC area
annotated property: definition
annotated target: Normalized area of the extracted ion chromatogram (e.g. of a transition in SRM).
database_cross_reference: PSI:PI

protein value: mean of peptide ratios
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Protein quantification value calculated as mean of peptide ratios.
has_obo_namespace: MS
id: MS:1001860

Axiom
annotated source: protein value: mean of peptide ratios
annotated property: definition
annotated target: Protein quantification value calculated as mean of peptide ratios.
database_cross_reference: PSI:PI

quantification data processing
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum interpretation
definition: Terms used to describe types of quantification data processing.
has_obo_namespace: MS
id: MS:1001861

Axiom
annotated source: quantification data processing
annotated property: definition
annotated target: Terms used to describe types of quantification data processing.
database_cross_reference: PSI:MS

normalization to mean of sum of all proteins
type: Class
subclass of: quantification data processing
definition: Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting).
has_obo_namespace: MS
id: MS:1001862

Axiom
annotated source: normalization to mean of sum of all proteins
annotated property: definition
annotated target: Normalization of protein values to the mean of the sum of all protein PSM counts (e.g. spectral counting).
database_cross_reference: PSI:MS

quantile normalization, proteins
type: Class
subclass of: quantification data processing
definition: Normalization of protein values to approach the same distribution.
has_obo_namespace: MS
id: MS:1001863

Axiom
annotated source: quantile normalization, proteins
annotated property: definition
annotated target: Normalization of protein values to approach the same distribution.
database_cross_reference: PSI:MS

quantile normalization, peptides
type: Class
subclass of: quantification data processing
definition: Normalization of peptide values to approach the same distribution.
has_obo_namespace: MS
id: MS:1001864

Axiom
annotated source: quantile normalization, peptides
annotated property: definition
annotated target: Normalization of peptide values to approach the same distribution.
database_cross_reference: PSI:MS

Progenesis automatic alignment
type: Class
subclass of: quantification data processing
definition: Automatic RT alignment of Progenesis software.
has_obo_namespace: MS
id: MS:1001865

Axiom
annotated source: Progenesis automatic alignment
annotated property: definition
annotated target: Automatic RT alignment of Progenesis software.
database_cross_reference: PSI:MS

Progenesis manual alignment
type: Class
subclass of: quantification data processing
definition: RT alignment of Progenesis software using automatic and manual vectors.
has_obo_namespace: MS
id: MS:1001866

Axiom
annotated source: Progenesis manual alignment
annotated property: definition
annotated target: RT alignment of Progenesis software using automatic and manual vectors.
database_cross_reference: PSI:MS

Progenesis normalization
type: Class
subclass of: quantification data processing
definition: Normalization as performed by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001867

Axiom
annotated source: Progenesis normalization
annotated property: definition
annotated target: Normalization as performed by Progenesis LC-MS.
database_cross_reference: PSI:MS

distinct peptide-level q-value
type: Class
subclass of: MS_1002484
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002305
subclass of: Restriction
  on property: has value type
  some values from: double
definition: 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).
has_obo_namespace: MS
id: MS:1001868

Axiom
annotated source: distinct peptide-level q-value
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:PI

protein-level q-value
type: Class
subclass of: single protein identification statistic
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002305
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Estimation of the q-value for proteins.
has_obo_namespace: MS
id: MS:1001869

Axiom
annotated source: protein-level q-value
annotated property: definition
annotated target: Estimation of the q-value for proteins.
database_cross_reference: PSI:PI

peptide sequence-level p-value
type: Class
subclass of: peptide sequence-level identification statistic
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002305
subclass of: Restriction
  on property: has value type
  some values from: double
definition: 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).
has_obo_namespace: MS
id: MS:1001870

Axiom
annotated source: peptide sequence-level p-value
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:PI

protein-level p-value
type: Class
subclass of: single protein identification statistic
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002305
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Estimation of the p-value for proteins.
has_obo_namespace: MS
id: MS:1001871

Axiom
annotated source: protein-level p-value
annotated property: definition
annotated target: Estimation of the p-value for proteins.
database_cross_reference: PSI:PI

peptide sequence-level e-value
type: Class
subclass of: peptide sequence-level identification statistic
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002306
subclass of: Restriction
  on property: has value type
  some values from: double
definition: 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).
has_obo_namespace: MS
id: MS:1001872

Axiom
annotated source: peptide sequence-level e-value
annotated property: definition
annotated target: 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).
database_cross_reference: PSI:PI

protein-level e-value
type: Class
subclass of: single protein identification statistic
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002306
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Estimation of the e-value for proteins.
has_obo_namespace: MS
id: MS:1001873

Axiom
annotated source: protein-level e-value
annotated property: definition
annotated target: Estimation of the e-value for proteins.
database_cross_reference: PSI:PI

FDRScore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: search engine specific score
subclass of: Restriction
  on property: has value type
  some values from: double
definition: 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.
has_obo_namespace: MS
id: MS:1001874
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).
deprecated: true

Axiom
annotated source: FDRScore
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:19253293

modification motif
type: Class
subclass of: modification specificity rule
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The regular expression describing the sequence motif for a modification.
has_obo_namespace: MS
id: MS:1001875

Axiom
annotated source: modification motif
annotated property: definition
annotated target: The regular expression describing the sequence motif for a modification.
database_cross_reference: PSI:PI

modification probability
type: Class
subclass of: modification specificity rule
definition: The a priori probability of a modification.
has_obo_namespace: MS
id: MS:1001876

Axiom
annotated source: modification probability
annotated property: definition
annotated target: The a priori probability of a modification.
database_cross_reference: PSI:PI

ChromaTOF HRT software
type: Class
subclass of: acquisition software
subclass of: analysis software
subclass of: data processing software
subclass of: LECO software
definition: Software for acquisition, processing and analysis of data for LECO instruments.
has_obo_namespace: MS
id: MS:1001877

Axiom
annotated source: ChromaTOF HRT software
annotated property: definition
annotated target: Software for acquisition, processing and analysis of data for LECO instruments.
database_cross_reference: PSI:MS

MALDI Solutions Microbial Identification
type: Class
subclass of: MALDI Solutions
definition: Shimadzu Biotech software for data acquisition, processing, and analysis.
has_obo_namespace: MS
id: MS:1001878

Axiom
annotated source: MALDI Solutions Microbial Identification
annotated property: definition
annotated target: Shimadzu Biotech software for data acquisition, processing, and analysis.
database_cross_reference: PSI:MS

source offset voltage
type: Class
subclass of: source attribute
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation.
has_exact_synonym: offset voltage
has_obo_namespace: MS
id: MS:1001879

Axiom
annotated source: source offset voltage
annotated property: definition
annotated target: The potential difference between two adjacent interface voltages affecting in-source collision induced dissociation.
database_cross_reference: PSI:MS

in-source collision-induced dissociation
type: Class
subclass of: dissociation method
definition: 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.
has_obo_namespace: MS
id: MS:1001880

Axiom
annotated source: in-source collision-induced dissociation
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

mz5 format
type: Class
subclass of: mass spectrometer file format
definition: mz5 file format, modelled after mzML.
has_obo_namespace: MS
id: MS:1001881

Axiom
annotated source: mz5 format
annotated property: definition
annotated target: mz5 file format, modelled after mzML.
database_cross_reference: PSI:MS

transition validation attribute
type: Class
subclass of: Restriction
  on property: part_of
  some values from: transition
definition: Attributes of the quality of a transition that affect its selection as appropriate.
has_obo_namespace: MS
id: MS:1001882

Axiom
annotated source: transition validation attribute
annotated property: definition
annotated target: Attributes of the quality of a transition that affect its selection as appropriate.
database_cross_reference: PSI:MS

coefficient of variation
type: Class
subclass of: transition validation attribute
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Variation of a set of signal measurements calculated as the standard deviation relative to the mean.
has_obo_namespace: MS
id: MS:1001883

Axiom
annotated source: coefficient of variation
annotated property: definition
annotated target: Variation of a set of signal measurements calculated as the standard deviation relative to the mean.
database_cross_reference: PSI:MS

signal-to-noise ratio
type: Class
subclass of: transition validation attribute
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal.
has_obo_namespace: MS
id: MS:1001884

Axiom
annotated source: signal-to-noise ratio
annotated property: definition
annotated target: Unitless number providing the ratio of the total measured intensity of a signal relative to the estimated noise level for that signal.
database_cross_reference: PSI:MS

command-line parameters
type: Class
subclass of: data processing parameter
subclass of: MS_1003201
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Parameters string passed to a command-line interface software application, omitting the executable name.
has_obo_namespace: MS
id: MS:1001885

Axiom
annotated source: command-line parameters
annotated property: definition
annotated target: Parameters string passed to a command-line interface software application, omitting the executable name.
database_cross_reference: PSI:MS

SQID
type: Class
subclass of: analysis software
subclass of: data processing software
definition: Software for data analysis of peptides and proteins.
has_obo_namespace: MS
id: MS:1001886

Axiom
annotated source: SQID
annotated property: definition
annotated target: Software for data analysis of peptides and proteins.
database_cross_reference: PSI:MS

SQID:score
type: Class
subclass of: PSM-level search engine specific statistic
definition: The SQID result 'Score'.
has_obo_namespace: MS
id: MS:1001887

Axiom
annotated source: SQID:score
annotated property: definition
annotated target: The SQID result 'Score'.
database_cross_reference: PSI:PI

SQID:deltaScore
type: Class
subclass of: PSM-level search engine specific statistic
definition: The SQID result 'deltaScore'.
has_obo_namespace: MS
id: MS:1001888

Axiom
annotated source: SQID:deltaScore
annotated property: definition
annotated target: The SQID result 'deltaScore'.
database_cross_reference: PSI:PI

SQID:protein score
type: Class
subclass of: MS_1002363
definition: The SQID result 'protein score'.
has_obo_namespace: MS
id: MS:1001889

Axiom
annotated source: SQID:protein score
annotated property: definition
annotated target: The SQID result 'protein score'.
database_cross_reference: PSI:PI

Progenesis:protein normalised abundance
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type normalised abundance for proteins produced by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001890

Axiom
annotated source: Progenesis:protein normalised abundance
annotated property: definition
annotated target: The data type normalised abundance for proteins produced by Progenesis LC-MS.
database_cross_reference: PSI:MS

Progenesis:peptide normalised abundance
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type normalised abundance for peptides produced by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001891

Axiom
annotated source: Progenesis:peptide normalised abundance
annotated property: definition
annotated target: The data type normalised abundance for peptides produced by Progenesis LC-MS.
database_cross_reference: PSI:MS

Progenesis:protein raw abundance
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type raw abundance for proteins produced by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001892

Axiom
annotated source: Progenesis:protein raw abundance
annotated property: definition
annotated target: The data type raw abundance for proteins produced by Progenesis LC-MS.
database_cross_reference: PSI:MS

Progenesis:peptide raw abundance
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type raw abundance for peptide produced by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001893

Axiom
annotated source: Progenesis:peptide raw abundance
annotated property: definition
annotated target: The data type raw abundance for peptide produced by Progenesis LC-MS.
database_cross_reference: PSI:MS

Progenesis:confidence score
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type confidence score produced by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001894

Axiom
annotated source: Progenesis:confidence score
annotated property: definition
annotated target: The data type confidence score produced by Progenesis LC-MS.
database_cross_reference: PSI:MS

Progenesis:peptide count
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The data type peptide count produced by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001895

Axiom
annotated source: Progenesis:peptide count
annotated property: definition
annotated target: The data type peptide count produced by Progenesis LC-MS.
database_cross_reference: PSI:MS

Progenesis:feature intensity
type: Class
subclass of: MS_1002735
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type feature intensity produced by Progenesis LC-MS.
has_obo_namespace: MS
id: MS:1001896

Axiom
annotated source: Progenesis:feature intensity
annotated property: definition
annotated target: The data type feature intensity produced by Progenesis LC-MS.
database_cross_reference: PSI:MS

MaxQuant:peptide counts (unique)
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The data type peptide counts (unique) produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001897

Axiom
annotated source: MaxQuant:peptide counts (unique)
annotated property: definition
annotated target: The data type peptide counts (unique) produced by MaxQuant.
database_cross_reference: PSI:MS

MaxQuant:peptide counts (all)
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The data type peptide counts (all) produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001898

Axiom
annotated source: MaxQuant:peptide counts (all)
annotated property: definition
annotated target: The data type peptide counts (all) produced by MaxQuant.
database_cross_reference: PSI:MS

MaxQuant:peptide counts (razor+unique)
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The data type peptide counts (razor+unique) produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001899

Axiom
annotated source: MaxQuant:peptide counts (razor+unique)
annotated property: definition
annotated target: The data type peptide counts (razor+unique) produced by MaxQuant.
database_cross_reference: PSI:MS

MaxQuant:sequence length
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The data type sequence length produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001900

Axiom
annotated source: MaxQuant:sequence length
annotated property: definition
annotated target: The data type sequence length produced by MaxQuant.
database_cross_reference: PSI:MS

MaxQuant:PEP
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type PEP (posterior error probability) produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001901

Axiom
annotated source: MaxQuant:PEP
annotated property: definition
annotated target: The data type PEP (posterior error probability) produced by MaxQuant.
database_cross_reference: PSI:MS

MaxQuant:LFQ intensity
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type LFQ intensity produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001902

Axiom
annotated source: MaxQuant:LFQ intensity
annotated property: definition
annotated target: The data type LFQ intensity produced by MaxQuant.
database_cross_reference: PSI:MS

MaxQuant:feature intensity
type: Class
subclass of: MS_1002735
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The data type feature intensity produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001903

Axiom
annotated source: MaxQuant:feature intensity
annotated property: definition
annotated target: The data type feature intensity produced by MaxQuant.
database_cross_reference: PSI:MS

MaxQuant:MS/MS count
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: int
definition: The data type MS2 count produced by MaxQuant.
has_obo_namespace: MS
id: MS:1001904

Axiom
annotated source: MaxQuant:MS/MS count
annotated property: definition
annotated target: The data type MS2 count produced by MaxQuant.
database_cross_reference: PSI:MS

emPAI value
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The emPAI value of protein abundance, produced from the emPAI algorithm.
has_obo_namespace: MS
id: MS:1001905

Axiom
annotated source: emPAI value
annotated property: definition
annotated target: The emPAI value of protein abundance, produced from the emPAI algorithm.
database_cross_reference: PSI:MS

APEX value
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The APEX value of protein abundance, produced from the APEX software.
has_obo_namespace: MS
id: MS:1001906

Axiom
annotated source: APEX value
annotated property: definition
annotated target: The APEX value of protein abundance, produced from the APEX software.
database_cross_reference: PSI:MS

retention time window width
type: Class
subclass of: retention time window attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The full width of a retention time window for a chromatographic peak.
has_obo_namespace: MS
id: MS:1001907

Axiom
annotated source: retention time window width
annotated property: definition
annotated target: The full width of a retention time window for a chromatographic peak.
database_cross_reference: PSI:MS

ISQ
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source.
has_obo_namespace: MS
id: MS:1001908

Axiom
annotated source: ISQ
annotated property: definition
annotated target: Thermo Scientific ISQ single quadrupole MS with the ExtractraBrite source.
database_cross_reference: PSI:MS

Velos Plus
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific second generation Velos.
has_obo_namespace: MS
id: MS:1001909

Axiom
annotated source: Velos Plus
annotated property: definition
annotated target: Thermo Scientific second generation Velos.
database_cross_reference: PSI:MS

Orbitrap Elite
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific Orbitrap Elite, sometimes referred to as the LTQ Orbitrap Elite.
has_exact_synonym: LTQ Orbitrap Elite
has_obo_namespace: MS
id: MS:1001910

Axiom
annotated source: Orbitrap Elite
annotated property: definition
annotated target: Thermo Scientific Orbitrap Elite, sometimes referred to as the LTQ Orbitrap Elite.
database_cross_reference: PSI:MS

Q Exactive
type: Class
subclass of: Thermo Scientific instrument model
definition: Thermo Scientific Q Exactive.
has_obo_namespace: MS
id: MS:1001911

Axiom
annotated source: Q Exactive
annotated property: definition
annotated target: Thermo Scientific Q Exactive.
database_cross_reference: PSI:MS

PinPoint
type: Class
subclass of: Thermo Finnigan software
subclass of: analysis software
subclass of: data processing software
definition: Thermo Scientific PinPoint SRM analysis software.
has_obo_namespace: MS
id: MS:1001912

Axiom
annotated source: PinPoint
annotated property: definition
annotated target: Thermo Scientific PinPoint SRM analysis software.
database_cross_reference: PSI:MS

S-lens voltage
type: Class
subclass of: source attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts.
has_obo_namespace: MS
id: MS:1001913

Axiom
annotated source: S-lens voltage
annotated property: definition
annotated target: Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts.
database_cross_reference: PSI:MS

pymzML
type: Class
subclass of: data processing software
definition: Python module to interface mzML Data.
has_obo_namespace: MS
id: MS:1001914

Axiom
annotated source: pymzML
annotated property: definition
annotated target: Python module to interface mzML Data.
database_cross_reference: PSI:MS

leukocyte elastase
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[ALIV])(?
definition: Enzyme leukocyte elastase (EC 3.4.21.37).
has_obo_namespace: MS
id: MS:1001915

Axiom
annotated source: leukocyte elastase
annotated property: definition
annotated target: Enzyme leukocyte elastase (EC 3.4.21.37).
database_cross_reference: BRENDA:3.4.21.37

proline endopeptidase
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[HKR]P)(?
definition: Enzyme proline endopeptidase (EC 3.4.21.26).
has_obo_namespace: MS
id: MS:1001916

Axiom
annotated source: proline endopeptidase
annotated property: definition
annotated target: Enzyme proline endopeptidase (EC 3.4.21.26).
database_cross_reference: BRENDA:3.4.21.26

glutamyl endopeptidase
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=[^E]E)
definition: Enzyme glutamyl endopeptidase (EC 3.4.21.19).
has_exact_synonym: Glu-C
has_exact_synonym: staphylococcal protease
has_obo_namespace: MS
id: MS:1001917

Axiom
annotated source: glutamyl endopeptidase
annotated property: definition
annotated target: Enzyme glutamyl endopeptidase (EC 3.4.21.19).
database_cross_reference: BRENDA:3.4.21.19

2-iodobenzoate
type: Class
subclass of: cleavage agent name
subclass of: Restriction
  on property: has regexp
  some values from: (?<=W)
definition: Chemical iodobenzoate. Cleaves after W.
has_obo_namespace: MS
id: MS:1001918

Axiom
annotated source: 2-iodobenzoate
annotated property: definition
annotated target: Chemical iodobenzoate. Cleaves after W.
database_cross_reference: PubChem_Compound:4739928

ProteomeXchange accession number
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Main identifier of a ProteomeXchange dataset.
has_obo_namespace: MS
id: MS:1001919

Axiom
annotated source: ProteomeXchange accession number
annotated property: definition
annotated target: Main identifier of a ProteomeXchange dataset.
database_cross_reference: PSI:PI

ProteomeXchange accession number version number
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: Version number of a ProteomeXchange accession number.
has_obo_namespace: MS
id: MS:1001921

Axiom
annotated source: ProteomeXchange accession number version number
annotated property: definition
annotated target: Version number of a ProteomeXchange accession number.
database_cross_reference: PSI:PI

Digital Object Identifier (DOI)
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002480
subclass of: Restriction
  on property: has value type
  some values from: string
definition: DOI unique identifier of a publication.
has_exact_synonym: doi
has_obo_namespace: MS
id: MS:1001922

Axiom
annotated source: Digital Object Identifier (DOI)
annotated property: definition
annotated target: DOI unique identifier of a publication.
database_cross_reference: PSI:PI
database_cross_reference: http://dx.doi.org

external reference keyword
type: Class
subclass of: MS_1002840
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Free text attribute that can enrich the information about an entity.
has_obo_namespace: MS
id: MS:1001923

Axiom
annotated source: external reference keyword
annotated property: definition
annotated target: Free text attribute that can enrich the information about an entity.
database_cross_reference: PSI:PI

journal article keyword
type: Class
subclass of: external reference keyword
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Keyword present in a scientific publication.
has_obo_namespace: MS
id: MS:1001924

Axiom
annotated source: journal article keyword
annotated property: definition
annotated target: Keyword present in a scientific publication.
database_cross_reference: PSI:PI

submitter keyword
type: Class
subclass of: external reference keyword
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Keyword assigned by the data submitter.
has_obo_namespace: MS
id: MS:1001925

Axiom
annotated source: submitter keyword
annotated property: definition
annotated target: Keyword assigned by the data submitter.
database_cross_reference: PSI:PI

curator keyword
type: Class
subclass of: external reference keyword
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Keyword assigned by a data curator.
has_obo_namespace: MS
id: MS:1001926

Axiom
annotated source: curator keyword
annotated property: definition
annotated target: Keyword assigned by a data curator.
database_cross_reference: PSI:PI

Tranche file hash
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Hash assigned by the Tranche resource to an individual file.
has_obo_namespace: MS
id: MS:1001927

Axiom
annotated source: Tranche file hash
annotated property: definition
annotated target: Hash assigned by the Tranche resource to an individual file.
database_cross_reference: PSI:PI

Tranche project hash
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Hash assigned by the Tranche resource to a whole project.
has_obo_namespace: MS
id: MS:1001928

Axiom
annotated source: Tranche project hash
annotated property: definition
annotated target: Hash assigned by the Tranche resource to a whole project.
database_cross_reference: PSI:PI

PRIDE experiment URI
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: anyURI
definition: URI that allows the access to one experiment in the PRIDE database.
has_obo_namespace: MS
id: MS:1001929

Axiom
annotated source: PRIDE experiment URI
annotated property: definition
annotated target: URI that allows the access to one experiment in the PRIDE database.
database_cross_reference: PSI:PI

PRIDE project URI
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: anyURI
definition: URI that allows the access to one project in the PRIDE database.
has_obo_namespace: MS
id: MS:1001930

Axiom
annotated source: PRIDE project URI
annotated property: definition
annotated target: URI that allows the access to one project in the PRIDE database.
database_cross_reference: PSI:PI

source interface
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source
definition: The source interface.
has_obo_namespace: MS
id: MS:1001931

Axiom
annotated source: source interface
annotated property: definition
annotated target: The source interface.
database_cross_reference: PSI:MS

source interface model
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source interface
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The source interface model.
has_obo_namespace: MS
id: MS:1001932

Axiom
annotated source: source interface model
annotated property: definition
annotated target: The source interface model.
database_cross_reference: PSI:MS

source sprayer
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The source sprayer.
has_obo_namespace: MS
id: MS:1001933

Axiom
annotated source: source sprayer
annotated property: definition
annotated target: The source sprayer.
database_cross_reference: PSI:MS

source sprayer type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source sprayer
definition: The source sprayer type.
has_obo_namespace: MS
id: MS:1001934

Axiom
annotated source: source sprayer type
annotated property: definition
annotated target: The source sprayer type.
database_cross_reference: PSI:MS

source sprayer manufacturer
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source sprayer
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The source sprayer manufacturer.
has_obo_namespace: MS
id: MS:1001935

Axiom
annotated source: source sprayer manufacturer
annotated property: definition
annotated target: The source sprayer manufacturer.
database_cross_reference: PSI:MS

source sprayer model
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source sprayer
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The source sprayer model.
has_obo_namespace: MS
id: MS:1001936

Axiom
annotated source: source sprayer model
annotated property: definition
annotated target: The source sprayer model.
database_cross_reference: PSI:MS

sample plate
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source
definition: Plate where the sample solution is spotted in a MALDI or similar instrument.
has_obo_namespace: MS
id: MS:1001937

Axiom
annotated source: sample plate
annotated property: definition
annotated target: Plate where the sample solution is spotted in a MALDI or similar instrument.
database_cross_reference: PSI:MS

sample plate type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sample plate
definition: The sample plate type.
has_obo_namespace: MS
id: MS:1001938

Axiom
annotated source: sample plate type
annotated property: definition
annotated target: The sample plate type.
database_cross_reference: PSI:MS

stainless steel plate
type: Class
subclass of: sample plate type
definition: Stainless steel plate.
has_obo_namespace: MS
id: MS:1001939

Axiom
annotated source: stainless steel plate
annotated property: definition
annotated target: Stainless steel plate.
database_cross_reference: PSI:MS

coated glass plate
type: Class
subclass of: sample plate type
definition: Coated glass plate.
has_obo_namespace: MS
id: MS:1001940

Axiom
annotated source: coated glass plate
annotated property: definition
annotated target: Coated glass plate.
database_cross_reference: PSI:MS

electrospray supply type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source
definition: Whether the sprayer is fed or is loaded with sample once.
has_obo_namespace: MS
id: MS:1001941

Axiom
annotated source: electrospray supply type
annotated property: definition
annotated target: Whether the sprayer is fed or is loaded with sample once.
database_cross_reference: PSI:MS

static supply electrospray
type: Class
subclass of: electrospray supply type
definition: The sprayer is loaded with sample once.
has_obo_namespace: MS
id: MS:1001942

Axiom
annotated source: static supply electrospray
annotated property: definition
annotated target: The sprayer is loaded with sample once.
database_cross_reference: PSI:MS

fed supply electrospray
type: Class
subclass of: electrospray supply type
definition: The sprayer is continuously fed with sample.
has_obo_namespace: MS
id: MS:1001943

Axiom
annotated source: fed supply electrospray
annotated property: definition
annotated target: The sprayer is continuously fed with sample.
database_cross_reference: PSI:MS

Collision cell exit potential
type: Class
subclass of: precursor activation attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000218
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts.
has_exact_synonym: CXP
has_obo_namespace: MS
id: MS:1001944

Axiom
annotated source: Collision cell exit potential
annotated property: definition
annotated target: Potential difference between Q2 and Q3 in a triple quadrupole instrument in volts.
database_cross_reference: PSI:MS

Pegasus 4D
type: Class
subclass of: LECO instrument model
definition: LECO nominal mass resolution time-of-flight GCxGC mass spectrometer.
has_obo_namespace: MS
id: MS:1001945

Axiom
annotated source: Pegasus 4D
annotated property: definition
annotated target: LECO nominal mass resolution time-of-flight GCxGC mass spectrometer.
database_cross_reference: PSI:MS

PEAKS Studio
type: Class
subclass of: quantitation software name
subclass of: analysis software
subclass of: data processing software
definition: PEAKS Studio software for data analysis.
has_obo_namespace: MS
id: MS:1001946

Axiom
annotated source: PEAKS Studio
annotated property: definition
annotated target: PEAKS Studio software for data analysis.
database_cross_reference: PSI:MS

PEAKS Online
type: Class
subclass of: quantitation software name
subclass of: analysis software
subclass of: data processing software
definition: PEAKS Online software for high throughput data analysis.
has_obo_namespace: MS
id: MS:1001947

Axiom
annotated source: PEAKS Online
annotated property: definition
annotated target: PEAKS Online software for high throughput data analysis.
database_cross_reference: PSI:MS

PEAKS Node
type: Class
subclass of: quantitation software name
subclass of: analysis software
subclass of: data processing software
definition: PEAKS Node software for high throughput data analysis.
has_obo_namespace: MS
id: MS:1001948

Axiom
annotated source: PEAKS Node
annotated property: definition
annotated target: PEAKS Node software for high throughput data analysis.
database_cross_reference: PSI:MS

BSI software
type: Class
subclass of: software
definition: Bioinformatics Solutions Inc. Software for data processing and analysis.
has_obo_namespace: MS
id: MS:1001949

Axiom
annotated source: BSI software
annotated property: definition
annotated target: Bioinformatics Solutions Inc. Software for data processing and analysis.
database_cross_reference: PSI:MS

PEAKS:peptideScore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The PEAKS peptide '-10lgP Score'.
has_obo_namespace: MS
id: MS:1001950

Axiom
annotated source: PEAKS:peptideScore
annotated property: definition
annotated target: The PEAKS peptide '-10lgP Score'.
database_cross_reference: PSI:MS

PEAKS:proteinScore
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The PEAKS protein '-10lgP Score'.
has_obo_namespace: MS
id: MS:1001951

Axiom
annotated source: PEAKS:proteinScore
annotated property: definition
annotated target: The PEAKS protein '-10lgP Score'.
database_cross_reference: PSI:MS

ZCore:probScore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The ZCore probability score.
has_obo_namespace: MS
id: MS:1001952

Axiom
annotated source: ZCore:probScore
annotated property: definition
annotated target: The ZCore probability score.
database_cross_reference: PSI:MS

source interface manufacturer
type: Class
subclass of: Restriction
  on property: part_of
  some values from: source interface
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The source interface manufacturer.
has_obo_namespace: MS
id: MS:1001953

Axiom
annotated source: source interface manufacturer
annotated property: definition
annotated target: The source interface manufacturer.
database_cross_reference: PSI:MS

acquisition parameter
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Parameters used in the mass spectrometry acquisition.
has_obo_namespace: MS
id: MS:1001954

Axiom
annotated source: acquisition parameter
annotated property: definition
annotated target: Parameters used in the mass spectrometry acquisition.
database_cross_reference: PSI:MS

no cleavage
type: Class
subclass of: cleavage agent name
definition: No cleavage.
has_obo_namespace: MS
id: MS:1001955

Axiom
annotated source: no cleavage
annotated property: definition
annotated target: No cleavage.
database_cross_reference: PSI:MS

unspecific cleavage
type: Class
subclass of: cleavage agent name
definition: Unspecific cleavage.
has_obo_namespace: MS
id: MS:1001956

Axiom
annotated source: unspecific cleavage
annotated property: definition
annotated target: Unspecific cleavage.
database_cross_reference: PSI:MS

(?<=[ALIV])(?
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for leukocyte elastase.
has_obo_namespace: MS
id: MS:1001957

Axiom
annotated source: (?<=[ALIV])(?
annotated property: definition
annotated target: Regular expression for leukocyte elastase.
database_cross_reference: PSI:PI

(?<=[HKR]P)(?
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for proline endopeptidase.
has_obo_namespace: MS
id: MS:1001958

Axiom
annotated source: (?<=[HKR]P)(?
annotated property: definition
annotated target: Regular expression for proline endopeptidase.
database_cross_reference: PSI:PI

(?<=[^E]E)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for glutamyl endopeptidase.
has_obo_namespace: MS
id: MS:1001959

Axiom
annotated source: (?<=[^E]E)
annotated property: definition
annotated target: Regular expression for glutamyl endopeptidase.
database_cross_reference: PSI:PI

(?<=W)
type: Class
subclass of: Cleavage agent regular expression
definition: Regular expression for 2-iodobenzoate.
has_obo_namespace: MS
id: MS:1001960

Axiom
annotated source: (?<=W)
annotated property: definition
annotated target: Regular expression for 2-iodobenzoate.
database_cross_reference: PSI:PI

peptide spectrum match scoring algorithm
type: Class
subclass of: Restriction
  on property: part_of
  some values from: spectrum generation information
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Algorithm used to score the match between a spectrum and a peptide ion.
has_obo_namespace: MS
id: MS:1001961

Axiom
annotated source: peptide spectrum match scoring algorithm
annotated property: definition
annotated target: Algorithm used to score the match between a spectrum and a peptide ion.
database_cross_reference: PSI:MS

Mascot:C13 counts
type: Class
subclass of: MS_1002095
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: C13 peaks to use in peak detection.
has_obo_namespace: MS
id: MS:1001962

Axiom
annotated source: Mascot:C13 counts
annotated property: definition
annotated target: C13 peaks to use in peak detection.
database_cross_reference: PSI:MS

ProteinExtractor:Weighting
type: Class
subclass of: MS_1002098
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Weighting factor for protein list compilation by ProteinExtractor.
has_obo_namespace: MS
id: MS:1001963

Axiom
annotated source: ProteinExtractor:Weighting
annotated property: definition
annotated target: Weighting factor for protein list compilation by ProteinExtractor.
database_cross_reference: PSI:MS

ProteinScape:second round Mascot
type: Class
subclass of: MS_1002100
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating a second round search with Mascot.
has_obo_namespace: MS
id: MS:1001964

Axiom
annotated source: ProteinScape:second round Mascot
annotated property: definition
annotated target: Flag indicating a second round search with Mascot.
database_cross_reference: PSI:MS

ProteinScape:second round Phenyx
type: Class
subclass of: MS_1002100
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Flag indicating a second round search with Phenyx.
has_obo_namespace: MS
id: MS:1001965

Axiom
annotated source: ProteinScape:second round Phenyx
annotated property: definition
annotated target: Flag indicating a second round search with Phenyx.
database_cross_reference: PSI:MS

product ion mobility
type: Class
subclass of: product ion attribute
definition: The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry.
has_obo_namespace: MS
id: MS:1001966

Axiom
annotated source: product ion mobility
annotated property: definition
annotated target: The mobility of an MS2 product ion, as measured by ion mobility mass spectrometry.
database_cross_reference: PSI:MS

product ion drift time
type: Class
subclass of: MS_1002222
subclass of: Restriction
  on property: has_units
  some values from: UO_0000028
subclass of: Restriction
  on property: has value type
  some values from: float
definition: OBSOLETE The ion drift time of an MS2 product ion.
has_obo_namespace: MS
id: MS:1001967
comment: This term was made obsolete because it was replaced by ion mobility drift time (MS:1002476).
deprecated: true

Axiom
annotated source: product ion drift time
annotated property: definition
annotated target: OBSOLETE The ion drift time of an MS2 product ion.
database_cross_reference: PSI:MS

PTM localization PSM-level statistic
type: Class
subclass of: MS_1002689
definition: Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level.
has_obo_namespace: MS
id: MS:1001968

Axiom
annotated source: PTM localization PSM-level statistic
annotated property: definition
annotated target: Statistic to convey the confidence of the localization of an amino acid modification on a peptide sequence at the PSM-level.
database_cross_reference: PSI:MS

phosphoRS score
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: phosphoRS score for PTM site location at the PSM-level.
has_obo_namespace: MS
id: MS:1001969

Axiom
annotated source: phosphoRS score
annotated property: definition
annotated target: phosphoRS score for PTM site location at the PSM-level.
database_cross_reference: DOI:10.1021/pr200611n
database_cross_reference: PMID:22073976

phosphoRS sequence probability
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Probability that the respective isoform is correct.
has_obo_namespace: MS
id: MS:1001970

Axiom
annotated source: phosphoRS sequence probability
annotated property: definition
annotated target: Probability that the respective isoform is correct.
database_cross_reference: DOI:10.1021/pr200611n
database_cross_reference: PMID:22073976

phosphoRS site probability
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Estimate of the probability that the respective site is truly phosphorylated.
has_obo_namespace: MS
id: MS:1001971

Axiom
annotated source: phosphoRS site probability
annotated property: definition
annotated target: Estimate of the probability that the respective site is truly phosphorylated.
database_cross_reference: DOI:10.1021/pr200611n
database_cross_reference: PMID:22073976

PTM scoring algorithm version
type: Class
subclass of: peptide modification details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Version of the post-translational modification scoring algorithm.
has_obo_namespace: MS
id: MS:1001972

Axiom
annotated source: PTM scoring algorithm version
annotated property: definition
annotated target: Version of the post-translational modification scoring algorithm.
database_cross_reference: PSI:MS

DeBunker
type: Class
subclass of: analysis software
definition: DeBunker software.
has_obo_namespace: MS
id: MS:1001973

Axiom
annotated source: DeBunker
annotated property: definition
annotated target: DeBunker software.
database_cross_reference: PSI:MS

DeBunker:score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Score specific to DeBunker.
has_obo_namespace: MS
id: MS:1001974

Axiom
annotated source: DeBunker:score
annotated property: definition
annotated target: Score specific to DeBunker.
database_cross_reference: PSI:MS

delta m/z
type: Class
subclass of: spectrum identification result details
subclass of: Restriction
  on property: has_units
  some values from: UO_0000166
subclass of: Restriction
  on property: has_units
  some values from: UO_0000169
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value.
has_exact_synonym: m/z difference
has_obo_namespace: MS
id: MS:1001975

Axiom
annotated source: delta m/z
annotated property: definition
annotated target: The difference between a theoretically calculated m/z and the corresponding experimentally measured m/z. It can be expressed as absolute or relative value.
database_cross_reference: PSI:MS

delta M
type: Class
subclass of: spectrum identification result details
subclass of: Restriction
  on property: has_units
  some values from: UO_0000166
subclass of: Restriction
  on property: has_units
  some values from: UO_0000169
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value.
has_exact_synonym: mass difference
has_obo_namespace: MS
id: MS:1001976

Axiom
annotated source: delta M
annotated property: definition
annotated target: The difference between a theoretically calculated molecular mass M and the corresponding experimentally measured M. It can be expressed as absolute or relative value.
database_cross_reference: PSI:MS

MSQuant
type: Class
subclass of: analysis software
definition: MSQuant software.
has_obo_namespace: MS
id: MS:1001977

Axiom
annotated source: MSQuant
annotated property: definition
annotated target: MSQuant software.
database_cross_reference: PSI:MS

MSQuant:PTM-score
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The PTM score from MSQuant software.
has_obo_namespace: MS
id: MS:1001978

Axiom
annotated source: MSQuant:PTM-score
annotated property: definition
annotated target: The PTM score from MSQuant software.
database_cross_reference: DOI:10.1021/pr900721e
database_cross_reference: PMID:19888749

MaxQuant:PTM Score
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The PTM score from MaxQuant software.
has_obo_namespace: MS
id: MS:1001979

Axiom
annotated source: MaxQuant:PTM Score
annotated property: definition
annotated target: The PTM score from MaxQuant software.
database_cross_reference: PSI:MS

MaxQuant:Phospho (STY) Probabilities
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The Phospho (STY) Probabilities from MaxQuant software.
has_obo_namespace: MS
id: MS:1001980

Axiom
annotated source: MaxQuant:Phospho (STY) Probabilities
annotated property: definition
annotated target: The Phospho (STY) Probabilities from MaxQuant software.
database_cross_reference: PSI:MS

MaxQuant:Phospho (STY) Score Diffs
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The Phospho (STY) Score Diffs from MaxQuant software.
has_obo_namespace: MS
id: MS:1001981

Axiom
annotated source: MaxQuant:Phospho (STY) Score Diffs
annotated property: definition
annotated target: The Phospho (STY) Score Diffs from MaxQuant software.
database_cross_reference: PSI:MS

MaxQuant:P-site localization probability
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The P-site localization probability value from MaxQuant software.
has_obo_namespace: MS
id: MS:1001982

Axiom
annotated source: MaxQuant:P-site localization probability
annotated property: definition
annotated target: The P-site localization probability value from MaxQuant software.
database_cross_reference: PSI:MS

MaxQuant:PTM Delta Score
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest).
has_obo_namespace: MS
id: MS:1001983

Axiom
annotated source: MaxQuant:PTM Delta Score
annotated property: definition
annotated target: The PTM Delta Score value from MaxQuant software (Difference between highest scoring site and second highest).
database_cross_reference: PSI:MS

Ascore software
type: Class
subclass of: analysis software
definition: Ascore software.
has_obo_namespace: MS
id: MS:1001984

Axiom
annotated source: Ascore software
annotated property: definition
annotated target: Ascore software.
database_cross_reference: PSI:MS

Ascore
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: A-score for PTM site location at the PSM-level.
has_obo_namespace: MS
id: MS:1001985

Axiom
annotated source: Ascore
annotated property: definition
annotated target: A-score for PTM site location at the PSM-level.
database_cross_reference: DOI:10.1038/nbt1240
database_cross_reference: PMID:16964243

H-Score
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has regexp
  some values from: MS_1002505
subclass of: Restriction
  on property: has value type
  some values from: string
definition: H-Score for peptide phosphorylation site location.
has_obo_namespace: MS
id: MS:1001986

Axiom
annotated source: H-Score
annotated property: definition
annotated target: H-Score for peptide phosphorylation site location.
database_cross_reference: DOI:10.1021/pr1006813
database_cross_reference: PMID:20836569

vacuum drying MALDI sample preparation
type: Class
subclass of: matrix application type
definition: Vacuum-drying MALDI sample preparation crystallization method.
has_obo_namespace: MS
id: MS:1001987

Axiom
annotated source: vacuum drying MALDI sample preparation
annotated property: definition
annotated target: Vacuum-drying MALDI sample preparation crystallization method.
database_cross_reference: PSI:MS

crushed crystal MALDI sample preparation
type: Class
subclass of: matrix application type
definition: Crushed-crystal MALDI sample preparation method.
has_obo_namespace: MS
id: MS:1001988

Axiom
annotated source: crushed crystal MALDI sample preparation
annotated property: definition
annotated target: Crushed-crystal MALDI sample preparation method.
database_cross_reference: PSI:MS

fast evaporation MALDI sample preparation
type: Class
subclass of: matrix application type
definition: Fast-evaporation MALDI sample preparation method.
has_obo_namespace: MS
id: MS:1001989

Axiom
annotated source: fast evaporation MALDI sample preparation
annotated property: definition
annotated target: Fast-evaporation MALDI sample preparation method.
database_cross_reference: DOI:10.1021/ac00091a044

overlayer MALDI sample preparation
type: Class
subclass of: matrix application type
definition: Overlayer method combining features of the crushed-crystal method and the fast-evaporation method.
has_obo_namespace: MS
id: MS:1001990

Axiom
annotated source: overlayer MALDI sample preparation
annotated property: definition
annotated target: Overlayer method combining features of the crushed-crystal method and the fast-evaporation method.
database_cross_reference: PSI:MS

sandwich MALDI sample preparation
type: Class
subclass of: matrix application type
definition: Sandwich MALDI sample preparation method.
has_obo_namespace: MS
id: MS:1001991

Axiom
annotated source: sandwich MALDI sample preparation
annotated property: definition
annotated target: Sandwich MALDI sample preparation method.
database_cross_reference: DOI:10.1002/(SICI)1096-9888(199706)32:6<593::AID-JMS511>3.3.CO;2-4

spin coating MALDI sample preparation
type: Class
subclass of: matrix application type
definition: Spin coating MALDI sample preparation method.
has_obo_namespace: MS
id: MS:1001992

Axiom
annotated source: spin coating MALDI sample preparation
annotated property: definition
annotated target: Spin coating MALDI sample preparation method.
database_cross_reference: DOI:10.1021/cc0500710
database_cross_reference: PMID:16283807

quick and dirty MALDI sample preparation
type: Class
subclass of: matrix application type
definition: Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling.
has_obo_namespace: MS
id: MS:1001993

Axiom
annotated source: quick and dirty MALDI sample preparation
annotated property: definition
annotated target: Quick & dirty (Q&D) sample preparation separating matrix handling from sample handling.
database_cross_reference: PSI:MS

top hat baseline reduction
type: Class
subclass of: baseline reduction
definition: Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'.
has_obo_namespace: MS
id: MS:1001994

Axiom
annotated source: top hat baseline reduction
annotated property: definition
annotated target: Top-hat morphological filter based on the basic morphological operations 'erosion' and 'dilatation'.
database_cross_reference: PSI:MS

convex hull baseline reduction
type: Class
subclass of: baseline reduction
definition: Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures.
has_obo_namespace: MS
id: MS:1001995

Axiom
annotated source: convex hull baseline reduction
annotated property: definition
annotated target: Constructs the baseline by fitting multiple parabolas to the spectrum starting with the large scale structures.
database_cross_reference: PSI:MS

median baseline reduction
type: Class
subclass of: baseline reduction
definition: The spectrum that will be baseline subtracted is divided into a number of segments.
has_obo_namespace: MS
id: MS:1001996

Axiom
annotated source: median baseline reduction
annotated property: definition
annotated target: The spectrum that will be baseline subtracted is divided into a number of segments.
database_cross_reference: PSI:MS

wavelet transformation smoothing
type: Class
subclass of: smoothing
definition: The random noise is removed by using the undecimated wavelet transform.
has_obo_namespace: MS
id: MS:1001997

Axiom
annotated source: wavelet transformation smoothing
annotated property: definition
annotated target: The random noise is removed by using the undecimated wavelet transform.
database_cross_reference: DOI:10.1093/bioinformatics/btl355
database_cross_reference: PMID:16820428

sophisticated numerical annotation procedure
type: Class
subclass of: area peak picking
definition: It searches for known patterns in the measured spectrum.
has_exact_synonym: SNAP
has_obo_namespace: MS
id: MS:1001998

Axiom
annotated source: sophisticated numerical annotation procedure
annotated property: definition
annotated target: It searches for known patterns in the measured spectrum.
database_cross_reference: DOI:10.1021/ac951158i
database_cross_reference: PMID:21619291

area normalization
type: Class
subclass of: intensity normalization
definition: Normalization of areas below the curves.
has_obo_namespace: MS
id: MS:1001999

Axiom
annotated source: area normalization
annotated property: definition
annotated target: Normalization of areas below the curves.
database_cross_reference: PSI:MS

LIFT
type: Class
subclass of: dissociation method
definition: 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.
has_obo_namespace: MS
id: MS:1002000

Axiom
annotated source: LIFT
annotated property: definition
annotated target: 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.
database_cross_reference: DOI:10.1007/s00216-003-2057-0
database_cross_reference: PMID:12830354

MS1 label-based raw feature quantitation
type: Class
subclass of: MS1 label-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS1 label-based raw feature quantitation.
has_obo_namespace: MS
id: MS:1002001

Axiom
annotated source: MS1 label-based raw feature quantitation
annotated property: definition
annotated target: MS1 label-based raw feature quantitation.
database_cross_reference: PSI:PI

MS1 label-based peptide level quantitation
type: Class
subclass of: MS1 label-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS1 label-based peptide level quantitation.
has_obo_namespace: MS
id: MS:1002002

Axiom
annotated source: MS1 label-based peptide level quantitation
annotated property: definition
annotated target: MS1 label-based peptide level quantitation.
database_cross_reference: PSI:PI

MS1 label-based protein level quantitation
type: Class
subclass of: MS1 label-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS1 label-based protein level quantitation.
has_obo_namespace: MS
id: MS:1002003

Axiom
annotated source: MS1 label-based protein level quantitation
annotated property: definition
annotated target: MS1 label-based protein level quantitation.
database_cross_reference: PSI:PI

MS1 label-based proteingroup level quantitation
type: Class
subclass of: MS1 label-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS1 label-based proteingroup level quantitation.
has_obo_namespace: MS
id: MS:1002004

Axiom
annotated source: MS1 label-based proteingroup level quantitation
annotated property: definition
annotated target: MS1 label-based proteingroup level quantitation.
database_cross_reference: PSI:PI

iRT retention time normalization standard
type: Class
subclass of: retention time normalization standard
definition: 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.
has_obo_namespace: MS
id: MS:1002005

Axiom
annotated source: iRT retention time normalization standard
annotated property: definition
annotated target: 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.
database_cross_reference: DOI:10.1002/pmic.201100463
database_cross_reference: http://www.biognosys.ch/products/rt-kit.html

SRM transition type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: transition
definition: The type of the transitions, e.g. target or decoy.
has_exact_synonym: MRM transition type
has_obo_namespace: MS
id: MS:1002006

Axiom
annotated source: SRM transition type
annotated property: definition
annotated target: The type of the transitions, e.g. target or decoy.
database_cross_reference: PSI:MS

target SRM transition
type: Class
subclass of: SRM transition type
definition: A transition used to target a specific compound that may be in the sample.
has_exact_synonym: target MRM transition
has_obo_namespace: MS
id: MS:1002007

Axiom
annotated source: target SRM transition
annotated property: definition
annotated target: A transition used to target a specific compound that may be in the sample.
database_cross_reference: PSI:MS

decoy SRM transition
type: Class
subclass of: SRM transition type
definition: A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows.
has_exact_synonym: decoy MRM transition
has_obo_namespace: MS
id: MS:1002008

Axiom
annotated source: decoy SRM transition
annotated property: definition
annotated target: A transition not expected to be present in the sample and used to calculate statistical confidence of target transition detections in some workflows.
database_cross_reference: PSI:MS

isobaric label quantitation analysis
type: Class
subclass of: quantitation analysis summary
definition: Quantitation analysis using an isobaric labelling workflow.
has_obo_namespace: MS
id: MS:1002009

Axiom
annotated source: isobaric label quantitation analysis
annotated property: definition
annotated target: Quantitation analysis using an isobaric labelling workflow.
database_cross_reference: PSI:PI

TMT quantitation analysis
type: Class
subclass of: isobaric label quantitation analysis
definition: 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.
has_obo_namespace: MS
id: MS:1002010

Axiom
annotated source: TMT quantitation analysis
annotated property: definition
annotated target: 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.
database_cross_reference: PMID:12713048
database_cross_reference: PSI:PI

desorption electrospray ionization
type: Class
subclass of: atmospheric pressure ionization
definition: Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure.
has_exact_synonym: DESI
has_obo_namespace: MS
id: MS:1002011

Axiom
annotated source: desorption electrospray ionization
annotated property: definition
annotated target: Combination of electrospray and desorption ionization method that ionizes gases, liquids and solids in open air under atmospheric pressure.
database_cross_reference: DOI:10.1126/science.1104404
database_cross_reference: PMID:15486296

Mascot:PTM site assignment confidence
type: Class
subclass of: PTM localization PSM-level statistic
subclass of: Restriction
  on property: has_units
  some values from: UO_0000187
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score).
has_obo_namespace: MS
id: MS:1002012

Axiom
annotated source: Mascot:PTM site assignment confidence
annotated property: definition
annotated target: Relative probability that PTM site assignment is correct, derived from the Mascot score difference between matches to the same spectrum (Mascot Delta Score).
database_cross_reference: http://www.matrixscience.com/help/pt_mods_help.html#SITE

collision energy ramp start
type: Class
subclass of: collision energy
subclass of: Restriction
  on property: has_units
  some values from: UO_0000266
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Collision energy at the start of the collision energy ramp.
has_obo_namespace: MS
id: MS:1002013

Axiom
annotated source: collision energy ramp start
annotated property: definition
annotated target: Collision energy at the start of the collision energy ramp.
database_cross_reference: PSI:PI

collision energy ramp end
type: Class
subclass of: collision energy
subclass of: Restriction
  on property: has_units
  some values from: UO_0000266
subclass of: Restriction
  on property: has value type
  some values from: float
definition: Collision energy at the end of the collision energy ramp.
has_obo_namespace: MS
id: MS:1002014

Axiom
annotated source: collision energy ramp end
annotated property: definition
annotated target: Collision energy at the end of the collision energy ramp.
database_cross_reference: PSI:PI

spectral count peptide level quantitation
type: Class
subclass of: spectral counting quantitation analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Spectral count peptide level quantitation.
has_obo_namespace: MS
id: MS:1002015

Axiom
annotated source: spectral count peptide level quantitation
annotated property: definition
annotated target: Spectral count peptide level quantitation.
database_cross_reference: PSI:PI

spectral count protein level quantitation
type: Class
subclass of: spectral counting quantitation analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Spectral count protein level quantitation.
has_obo_namespace: MS
id: MS:1002016

Axiom
annotated source: spectral count protein level quantitation
annotated property: definition
annotated target: Spectral count protein level quantitation.
database_cross_reference: PSI:PI

spectral count proteingroup level quantitation
type: Class
subclass of: spectral counting quantitation analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Spectral count proteingroup level quantitation.
has_obo_namespace: MS
id: MS:1002017

Axiom
annotated source: spectral count proteingroup level quantitation
annotated property: definition
annotated target: Spectral count proteingroup level quantitation.
database_cross_reference: PSI:PI

MS1 label-based analysis
type: Class
subclass of: quantitation analysis summary
definition: MS1 label-based analysis.
has_obo_namespace: MS
id: MS:1002018

Axiom
annotated source: MS1 label-based analysis
annotated property: definition
annotated target: MS1 label-based analysis.
database_cross_reference: PSI:PI

label-free raw feature quantitation
type: Class
subclass of: LC-MS label-free quantitation analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Label-free raw feature quantitation.
has_obo_namespace: MS
id: MS:1002019

Axiom
annotated source: label-free raw feature quantitation
annotated property: definition
annotated target: Label-free raw feature quantitation.
database_cross_reference: PSI:PI

label-free peptide level quantitation
type: Class
subclass of: LC-MS label-free quantitation analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Label-free peptide level quantitation.
has_obo_namespace: MS
id: MS:1002020

Axiom
annotated source: label-free peptide level quantitation
annotated property: definition
annotated target: Label-free peptide level quantitation.
database_cross_reference: PSI:PI

label-free protein level quantitation
type: Class
subclass of: LC-MS label-free quantitation analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Label-free protein level quantitation.
has_obo_namespace: MS
id: MS:1002021

Axiom
annotated source: label-free protein level quantitation
annotated property: definition
annotated target: Label-free protein level quantitation.
database_cross_reference: PSI:PI

label-free proteingroup level quantitation
type: Class
subclass of: LC-MS label-free quantitation analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: Label-free proteingroup level quantitation.
has_obo_namespace: MS
id: MS:1002022

Axiom
annotated source: label-free proteingroup level quantitation
annotated property: definition
annotated target: Label-free proteingroup level quantitation.
database_cross_reference: PSI:PI

MS2 tag-based analysis
type: Class
subclass of: quantitation analysis summary
definition: MS2 tag-based analysis.
has_obo_namespace: MS
id: MS:1002023

Axiom
annotated source: MS2 tag-based analysis
annotated property: definition
annotated target: MS2 tag-based analysis.
database_cross_reference: PSI:PI

MS2 tag-based feature level quantitation
type: Class
subclass of: MS2 tag-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS2 tag-based feature level quantitation.
has_obo_namespace: MS
id: MS:1002024

Axiom
annotated source: MS2 tag-based feature level quantitation
annotated property: definition
annotated target: MS2 tag-based feature level quantitation.
database_cross_reference: PSI:PI

MS2 tag-based peptide level quantitation
type: Class
subclass of: MS2 tag-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS2 tag-based peptide level quantitation.
has_obo_namespace: MS
id: MS:1002025

Axiom
annotated source: MS2 tag-based peptide level quantitation
annotated property: definition
annotated target: MS2 tag-based peptide level quantitation.
database_cross_reference: PSI:PI

MS2 tag-based protein level quantitation
type: Class
subclass of: MS2 tag-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS2 tag-based protein level quantitation.
has_obo_namespace: MS
id: MS:1002026

Axiom
annotated source: MS2 tag-based protein level quantitation
annotated property: definition
annotated target: MS2 tag-based protein level quantitation.
database_cross_reference: PSI:PI

MS2 tag-based proteingroup level quantitation
type: Class
subclass of: MS2 tag-based analysis
subclass of: Restriction
  on property: has value type
  some values from: boolean
definition: MS2 tag-based proteingroup level quantitation.
has_obo_namespace: MS
id: MS:1002027

Axiom
annotated source: MS2 tag-based proteingroup level quantitation
annotated property: definition
annotated target: MS2 tag-based proteingroup level quantitation.
database_cross_reference: PSI:PI

nucleic acid base modification
type: Class
subclass of: peptide modification details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Nucleic acid base modification (substitution, insertion or deletion).
has_obo_namespace: MS
id: MS:1002028

Axiom
annotated source: nucleic acid base modification
annotated property: definition
annotated target: Nucleic acid base modification (substitution, insertion or deletion).
database_cross_reference: PSI:PI

original nucleic acid sequence
type: Class
subclass of: peptide modification details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence.
has_obo_namespace: MS
id: MS:1002029

Axiom
annotated source: original nucleic acid sequence
annotated property: definition
annotated target: Specification of the original nucleic acid sequence, prior to a modification. The value slot should hold the DNA or RNA sequence.
database_cross_reference: PSI:PI

modified nucleic acid sequence
type: Class
subclass of: peptide modification details
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence.
has_obo_namespace: MS
id: MS:1002030

Axiom
annotated source: modified nucleic acid sequence
annotated property: definition
annotated target: Specification of the modified nucleic acid sequence. The value slot should hold the DNA or RNA sequence.
database_cross_reference: PSI:PI

PASSEL transition group browser URI
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: anyURI
definition: URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment.
has_obo_namespace: MS
id: MS:1002031

Axiom
annotated source: PASSEL transition group browser URI
annotated property: definition
annotated target: URI to retrieve transition group data for a PASSEL (PeptideAtlas SRM Experiment Library) experiment.
database_cross_reference: PSI:PI

PeptideAtlas dataset URI
type: Class
subclass of: external reference identifier
subclass of: Restriction
  on property: has value type
  some values from: anyURI
definition: URI that allows access to a PeptideAtlas dataset.
has_obo_namespace: MS
id: MS:1002032

Axiom
annotated source: PeptideAtlas dataset URI
annotated property: definition
annotated target: URI that allows access to a PeptideAtlas dataset.
database_cross_reference: PSI:PI

contact role
type: Class
subclass of: contact attribute
definition: Role of the contact person.
has_obo_namespace: MS
id: MS:1002033

Axiom
annotated source: contact role
annotated property: definition
annotated target: Role of the contact person.
database_cross_reference: PSI:PI

first author
type: Class
subclass of: contact role
definition: 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.
has_obo_namespace: MS
id: MS:1002034

Axiom
annotated source: first author
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

senior author
type: Class
subclass of: contact role
definition: 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.
has_obo_namespace: MS
id: MS:1002035

Axiom
annotated source: senior author
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

co-author
type: Class
subclass of: contact role
definition: One of a set of authors associated with a publication or release.
has_obo_namespace: MS
id: MS:1002036

Axiom
annotated source: co-author
annotated property: definition
annotated target: One of a set of authors associated with a publication or release.
database_cross_reference: PSI:MS

dataset submitter
type: Class
subclass of: contact role
definition: A person who submits a dataset to a repository.
has_obo_namespace: MS
id: MS:1002037

Axiom
annotated source: dataset submitter
annotated property: definition
annotated target: A person who submits a dataset to a repository.
database_cross_reference: PSI:MS

label free sample
type: Class
subclass of: sample attribute
definition: A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy".
has_exact_synonym: light sample
has_obo_namespace: MS
id: MS:1002038

Axiom
annotated source: label free sample
annotated property: definition
annotated target: A sample that has not been labelled or modified. This is often referred to as "light" to distinguish from "heavy".
database_cross_reference: PSI:PI

inlet attribute
type: Class
subclass of: object attribute
subclass of: Restriction
  on property: part_of
  some values from: source
definition: Inlet properties that are associated with a value.
has_obo_namespace: MS
id: MS:1002039

Axiom
annotated source: inlet attribute
annotated property: definition
annotated target: Inlet properties that are associated with a value.
database_cross_reference: PSI:MS

inlet temperature
type: Class
subclass of: source attribute
subclass of: inlet attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000012
subclass of: Restriction
  on property: has_units
  some values from: UO_0000027
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The temperature of the inlet of a mass spectrometer.
has_obo_namespace: MS
id: MS:1002040

Axiom
annotated source: inlet temperature
annotated property: definition
annotated target: The temperature of the inlet of a mass spectrometer.
database_cross_reference: PSI:MS

source temperature
type: Class
subclass of: source attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000012
subclass of: Restriction
  on property: has_units
  some values from: UO_0000027
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The temperature of the source of a mass spectrometer.
has_obo_namespace: MS
id: MS:1002041

Axiom
annotated source: source temperature
annotated property: definition
annotated target: The temperature of the source of a mass spectrometer.
database_cross_reference: PSI:MS

modulation time
type: Class
subclass of: run attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1002042

Axiom
annotated source: modulation time
annotated property: definition
annotated target: 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.
database_cross_reference: http://chromatographyonline.findanalytichem.com/lcgc/Column:+Coupling+Matters/Nomenclature-and-Conventions-in-Comprehensive-Mult/ArticleStandard/Article/detail/58429

ProteinProspector
type: Class
subclass of: analysis software
definition: ProteinProspector software for data acquisition and analysis.
has_obo_namespace: MS
id: MS:1002043

Axiom
annotated source: ProteinProspector
annotated property: definition
annotated target: ProteinProspector software for data acquisition and analysis.
database_cross_reference: PSI:PI

ProteinProspector:score
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The ProteinProspector result 'Score'.
has_obo_namespace: MS
id: MS:1002044

Axiom
annotated source: ProteinProspector:score
annotated property: definition
annotated target: The ProteinProspector result 'Score'.
database_cross_reference: PSI:PI

ProteinProspector:expectation value
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: The ProteinProspector result 'Expectation value'.
has_obo_namespace: MS
id: MS:1002045

Axiom
annotated source: ProteinProspector:expectation value
annotated property: definition
annotated target: The ProteinProspector result 'Expectation value'.
database_cross_reference: PSI:PI

native source path
type: Class
subclass of: spectrum generation information
subclass of: Restriction
  on property: has value type
  some values from: string
definition: The original source path used for directory-based sources.
has_obo_namespace: MS
id: MS:1002046

Axiom
annotated source: native source path
annotated property: definition
annotated target: The original source path used for directory-based sources.
database_cross_reference: PSI:MS

MS-GF
type: Class
subclass of: analysis software
definition: MS-GF software used to re-score the peptide-spectrum matches.
has_obo_namespace: MS
id: MS:1002047

Axiom
annotated source: MS-GF
annotated property: definition
annotated target: MS-GF software used to re-score the peptide-spectrum matches.
database_cross_reference: DOI:10.1074/mcp.M110.003731
database_cross_reference: PMID:20829449

MS-GF+
type: Class
subclass of: analysis software
definition: MS-GF+ software used to analyze the spectra.
has_exact_synonym: MS-GFDB
has_obo_namespace: MS
id: MS:1002048

Axiom
annotated source: MS-GF+
annotated property: definition
annotated target: MS-GF+ software used to analyze the spectra.
database_cross_reference: PSI:PI

MS-GF:RawScore
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: int
definition: MS-GF raw score.
has_obo_namespace: MS
id: MS:1002049

Axiom
annotated source: MS-GF:RawScore
annotated property: definition
annotated target: MS-GF raw score.
database_cross_reference: PSI:PI

MS-GF:DeNovoScore
type: Class
subclass of: MS_1002363
subclass of: Restriction
  on property: has value type
  some values from: int
definition: MS-GF de novo score.
has_obo_namespace: MS
id: MS:1002050

Axiom
annotated source: MS-GF:DeNovoScore
annotated property: definition
annotated target: MS-GF de novo score.
database_cross_reference: PSI:PI

MS-GF:Energy
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: nonNegativeInteger
definition: MS-GF energy score.
has_obo_namespace: MS
id: MS:1002051

Axiom
annotated source: MS-GF:Energy
annotated property: definition
annotated target: MS-GF energy score.
database_cross_reference: PSI:PI

MS-GF:SpecEValue
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: MS_1002353
subclass of: Restriction
  on property: has_order
  some values from: MS_1002109
subclass of: Restriction
  on property: has value type
  some values from: double
definition: MS-GF spectral E-value.
has_obo_namespace: MS
id: MS:1002052

Axiom
annotated source: MS-GF:SpecEValue
annotated property: definition
annotated target: MS-GF spectral E-value.
database_cross_reference: PSI:PI

MS-GF:EValue
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: MS_1002353
subclass of: Restriction
  on property: has_order
  some values from: MS_1002109
subclass of: Restriction
  on property: has value type
  some values from: double
definition: MS-GF E-value.
has_obo_namespace: MS
id: MS:1002053

Axiom
annotated source: MS-GF:EValue
annotated property: definition
annotated target: MS-GF E-value.
database_cross_reference: PSI:PI

MS-GF:QValue
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: MS_1002354
subclass of: Restriction
  on property: has value type
  some values from: double
definition: MS-GF Q-value.
has_obo_namespace: MS
id: MS:1002054

Axiom
annotated source: MS-GF:QValue
annotated property: definition
annotated target: MS-GF Q-value.
database_cross_reference: PSI:PI

MS-GF:PepQValue
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: MS-GF peptide-level Q-value.
has_obo_namespace: MS
id: MS:1002055

Axiom
annotated source: MS-GF:PepQValue
annotated property: definition
annotated target: MS-GF peptide-level Q-value.
database_cross_reference: PSI:PI

MS-GF:PEP
type: Class
subclass of: PSM-level search engine specific statistic
subclass of: Restriction
  on property: has value type
  some values from: double
definition: MS-GF posterior error probability.
has_obo_namespace: MS
id: MS:1002056

Axiom
annotated source: MS-GF:PEP
annotated property: definition
annotated target: MS-GF posterior error probability.
database_cross_reference: PSI:PI

modification specificity protein N-term
type: Class
subclass of: modification specificity rule
definition: As parameter for search engine: apply the modification only at the N-terminus of a protein.
has_obo_namespace: MS
id: MS:1002057

Axiom
annotated source: modification specificity protein N-term
annotated property: definition
annotated target: As parameter for search engine: apply the modification only at the N-terminus of a protein.
database_cross_reference: PSI:PI

modification specificity protein C-term
type: Class
subclass of: modification specificity rule
definition: As parameter for search engine: apply the modification only at the C-terminus of a protein.
has_obo_namespace: MS
id: MS:1002058

Axiom
annotated source: modification specificity protein C-term
annotated property: definition
annotated target: As parameter for search engine: apply the modification only at the C-terminus of a protein.
database_cross_reference: PSI:PI

Microsoft Excel
type: Class
subclass of: quantitation software name
definition: Microsoft Excel (can be used for spectral counting).
has_obo_namespace: MS
id: MS:1002059

Axiom
annotated source: Microsoft Excel
annotated property: definition
annotated target: Microsoft Excel (can be used for spectral counting).
database_cross_reference: PSI:PI

database UniProtKB/TrEMBL
type: Class
subclass of: MS_1002126
definition: The name of the UniProtKB/TrEMBL database.
has_obo_namespace: MS
id: MS:1002060

Axiom
annotated source: database UniProtKB/TrEMBL
annotated property: definition
annotated target: The name of the UniProtKB/TrEMBL database.
database_cross_reference: PSI:PI

decoy DB from UniProtKB/TrEMBL
type: Class
definition: OBSOLETE Decoy database from a TrEMBL protein sequence database.
has_obo_namespace: MS
id: MS:1002061
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.
deprecated: true

Axiom
annotated source: decoy DB from UniProtKB/TrEMBL
annotated property: definition
annotated target: OBSOLETE Decoy database from a TrEMBL protein sequence database.
database_cross_reference: PSI:PI

metabolic labelling: natural N (mainly 14N)
type: Class
subclass of: modification parameters
definition: Metabolic labelling: natural N (mainly 14N).
has_obo_namespace: MS
id: MS:1002062

Axiom
annotated source: metabolic labelling: natural N (mainly 14N)
annotated property: definition
annotated target: Metabolic labelling: natural N (mainly 14N).
database_cross_reference: PSI:PI

FindPairs
type: Class
subclass of: quantitation software name
definition: Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite.
has_obo_namespace: MS
id: MS:1002063

Axiom
annotated source: FindPairs
annotated property: definition
annotated target: Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite.
database_cross_reference: http://www.medizinisches-proteom-center.de/software

peptide consensus RT
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Peptide consensus retention time.
has_obo_namespace: MS
id: MS:1002064

Axiom
annotated source: peptide consensus RT
annotated property: definition
annotated target: Peptide consensus retention time.
database_cross_reference: PSI:PI

peptide consensus m/z
type: Class
subclass of: MS_1002737
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Peptide consensus mass/charge ratio.
has_obo_namespace: MS
id: MS:1002065

Axiom
annotated source: peptide consensus m/z
annotated property: definition
annotated target: Peptide consensus mass/charge ratio.
database_cross_reference: PSI:PI

ratio calculation method
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Method used to calculate the ratio.
has_obo_namespace: MS
id: MS:1002066

Axiom
annotated source: ratio calculation method
annotated property: definition
annotated target: Method used to calculate the ratio.
database_cross_reference: PSI:PI

protein value: median of peptide ratios
type: Class
subclass of: MS_1002738
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Protein quantification value calculated as median of peptide ratios.
has_obo_namespace: MS
id: MS:1002067

Axiom
annotated source: protein value: median of peptide ratios
annotated property: definition
annotated target: Protein quantification value calculated as median of peptide ratios.
database_cross_reference: PSI:PI

metabolic labelling: heavy N (mainly 15N)
type: Class
subclass of: modification parameters
definition: Metabolic labelling: heavy N (mainly 15N).
has_obo_namespace: MS
id: MS:1002068

Axiom
annotated source: metabolic labelling: heavy N (mainly 15N)
annotated property: definition
annotated target: Metabolic labelling: heavy N (mainly 15N).
database_cross_reference: PSI:PI

metabolic labelling purity
type: Class
subclass of: modification parameters
subclass of: Restriction
  on property: has value type
  some values from: string
definition: 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.
has_obo_namespace: MS
id: MS:1002069

Axiom
annotated source: metabolic labelling purity
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:PI

t-test
type: Class
subclass of: quantification data processing
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed.
has_obo_namespace: MS
id: MS:1002070

Axiom
annotated source: t-test
annotated property: definition
annotated target: Perform a t-test (two groups). Specify in string value, whether paired / unpaired, variance equal / different, one- / two-sided version is performed.
database_cross_reference: PSI:PI

ANOVA-test
type: Class
subclass of: quantification data processing
subclass of: Restriction
  on property: has value type
  some values from: string
definition: Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed.
has_obo_namespace: MS
id: MS:1002071

Axiom
annotated source: ANOVA-test
annotated property: definition
annotated target: Perform an ANOVA-test (more than two groups). Specify in string value, which version is performed.
database_cross_reference: PSI:PI

p-value
type: Class
subclass of: quantification datatype
subclass of: Restriction
  on property: has_domain
  some values from: MS_1002305
subclass of: Restriction
  on property: has value type
  some values from: double
definition: P-value as result of one of the processing steps described. Specify in the description, which processing step it was.
has_obo_namespace: MS
id: MS:1002072

Axiom
annotated source: p-value
annotated property: definition
annotated target: P-value as result of one of the processing steps described. Specify in the description, which processing step it was.
database_cross_reference: PSI:PI

mzIdentML format
type: Class
subclass of: intermediate analysis format
definition: The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'.
has_obo_namespace: MS
id: MS:1002073

Axiom
annotated source: mzIdentML format
annotated property: definition
annotated target: The mzIdentML format for peptide and protein identification data from the PSI. File extension '.mzid'.
database_cross_reference: PSI:PI
database_cross_reference: http://www.psidev.info/mzidentml

quantification file format
type: Class
subclass of: file format
definition: File format containing quantification results.
has_obo_namespace: MS
id: MS:1002074

Axiom
annotated source: quantification file format
annotated property: definition
annotated target: File format containing quantification results.
database_cross_reference: PSI:PI

mzQuantML format
type: Class
subclass of: quantification file format
definition: The mzQuantML format for quantification data from the PSI. File extension '.mzq'.
has_obo_namespace: MS
id: MS:1002075

Axiom
annotated source: mzQuantML format
annotated property: definition
annotated target: The mzQuantML format for quantification data from the PSI. File extension '.mzq'.
database_cross_reference: PSI:PI
database_cross_reference: http://www.psidev.info/mzquantml

PAnalyzer
type: Class
subclass of: analysis software
definition: PAnalyzer software for getting protein evidence categories.
has_obo_namespace: MS
id: MS:1002076

Axiom
annotated source: PAnalyzer
annotated property: definition
annotated target: PAnalyzer software for getting protein evidence categories.
database_cross_reference: http://code.google.com/p/ehu-bio/wiki/PAnalyzer

impact
type: Class
subclass of: Bruker Daltonics micrOTOF series
definition: Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray.
has_obo_namespace: MS
id: MS:1002077

Axiom
annotated source: impact
annotated property: definition
annotated target: Bruker Daltonics' impact: ESI Q-TOF, Nanospray, APCI, APPI, GC-APCI, CaptiveSpray.
database_cross_reference: PSI:MS

ProteomeDiscoverer:1. Static Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter.
has_obo_namespace: MS
id: MS:1002078
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:1. Static Modification
annotated property: definition
annotated target: OBSOLETE ProteomeDiscoverer's 1st static post-translational modification (PTM) input parameter.
database_cross_reference: PSI:PI

ProteomeDiscoverer:2. Static Modification
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has value type
  some values from: string
definition: OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter.
has_obo_namespace: MS
id: MS:1002079
comment: This term was made obsolete because it's recommended to use ProteomeDiscoverer:Static Modification (MS:1001645) instead.
deprecated: true

Axiom
annotated source: ProteomeDiscoverer:2. Static Modification
annotated property: definition
annotated target: OBSOLETE ProteomeDiscoverer's 2nd static post-translational modification (PTM) input parameter.
database_cross_reference: PSI:PI

ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Precursor clipping range before.
has_obo_namespace: MS
id: MS:1002080

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range Before
annotated property: definition
annotated target: Precursor clipping range before.
database_cross_reference: PSI:MS

ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After
type: Class
subclass of: MS_1002101
subclass of: Restriction
  on property: has_units
  some values from: UO_0000221
subclass of: Restriction
  on property: has value type
  some values from: double
definition: Precursor clipping range after.
has_obo_namespace: MS
id: MS:1002081

Axiom
annotated source: ProteomeDiscoverer:Spectrum Selector:Precursor Clipping Range After
annotated property: definition
annotated target: Precursor clipping range after.
database_cross_reference: PSI:MS

first column elution time
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column.
has_obo_namespace: MS
id: MS:1002082

Axiom
annotated source: first column elution time
annotated property: definition
annotated target: The time of elution from the first chromatographic column in the chromatographic separation step, relative to the start of chromatography on the first column.
database_cross_reference: PSI:MS

second column elution time
type: Class
subclass of: scan attribute
subclass of: Restriction
  on property: has_units
  some values from: UO_0000010
subclass of: Restriction
  on property: has_units
  some values from: UO_0000031
subclass of: Restriction
  on property: has value type
  some values from: float
definition: 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.
has_obo_namespace: MS
id: MS:1002083

Axiom
annotated source: second column elution time
annotated property: definition
annotated target: 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.
database_cross_reference: PSI:MS

multidimensional chromatography modulation description
type: Class
subclass of: run attribute
definition: Multidimensional chromatography modulation description.
has_obo_namespace: MS
id: MS:1002084

Axiom
annotated source: multidimensional chromatography modulation description
annotated property: definition
annotated target: Multidimensional chromatography modulation description.
database_cross_reference: PSI:MS