format-version: 1.3
date: 16:10:2023 11:38
data-version: 2.1.1
saved-by: Yasset Perez-Riverol
auto-generated-by: OBO-Edit 2.3.1
default-namespace: PRIDE
remark: I would set treat-xrefs-as-equivalent but there are some weird xrefs that would break that behaviour (PRIDE:PRIDE, value-type:xsd\:string, ...)
import: http://purl.obolibrary.org/obo/chmo.owl


[Typedef]
id: part_of
name: part_of
is_transitive: true

[Term]
id: PRIDE:0000000
name: Reference additional parameter
comment: Root node for terms relating to Reference additional parameters, in the context of ExperimentCollection/Experiment/Reference/additional/CvParam

[Term]
id: PRIDE:0000001
name: Protocol step description additional parameter
comment: Root node for terms relating to the description of a protocol as ordered steps, in relation to the PRIDE.xml element ExperimentCollection/Experiment/Protocol/ProtocolSteps/StepDescription

[Term]
id: PRIDE:0000002
name: ModificationItem additional parameter
comment: Root node for terms relating to the description of a ModificationItem (post translational modification or artifactual modification) in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/ModificationItem/additional/cvParam

[Term]
id: PRIDE:0000003
name: Peptide item additional parameter
comment: Root node for terms relating to the description of a PeptideItem in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/PeptideItem/additional/cvParam

[Term]
id: PRIDE:0000004
name: Identification additional parameter
comment: Root node for terms relating to the description of an Identification in relation to the PRIDE.xml element ExperimentCollection/Experiment/Identification/additional/cvParam

[Term]
id: PRIDE:0000005
name: Gel additional parameter
comment: Root node for terms relating to the description of a Gel in relation to the PRIDE.xml element ExperimentCollection/Experiment/TwoDimensionalIdentification/Gel/additional/cvParam

[Term]
id: PRIDE:0000006
name: Experiment additional parameter
comment: Root node for terms relating to the description of an Experiment in relation to the PRIDE.xml element ExperimentCollection/Experiment/additional/cvParam

[Term]
id: PRIDE:0000007
name: SearchEngineVersion
comment: Version number / identifier for search engine.
is_obsolete: true

[Term]
id: PRIDE:0000008
name: Protein search engine output parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000009
name: Ion mass tolerance
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000010
name: PrecursorIon mass tolerance
is_a: PRIDE:0000009 ! Ion mass tolerance

[Term]
id: PRIDE:0000011
name: MS2 ion mass tolerance
is_a: PRIDE:0000009 ! Ion mass tolerance

[Term]
id: PRIDE:0000012
name: Delta Cn
def: "1.0 - normalized correlation score." [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000013
name: X correlation
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000014
name: X correlation (+1)
is_a: PRIDE:0000013 ! X correlation

[Term]
id: PRIDE:0000015
name: X correlation (+2)
is_a: PRIDE:0000013 ! X correlation

[Term]
id: PRIDE:0000016
name: X correlation (+3)
is_a: PRIDE:0000013 ! X correlation

[Term]
id: PRIDE:0000017
name: Sample description additional parameter
comment: Root term for parameters in the context of ExperimentCollection/Experiment/mzData/description/admin/sampleDescription/cvParam

[Term]
id: PRIDE:0000018
name: Disease free
comment: Term to describe the fact that the sample derives from an organism which has been positively shown to be free of disease, e.g. as the consequence of a broad-spectrum screen.  NOTE: A request has been made to have this concept added to MeSH.  Once this has been achieved, this term will be dropped from the PRIDE CV and all uses of the this term will be updated to the appropriate MeSH concept.
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000019
name: Solubilization
def: "To make something soluble or more soluble, especially in water, by the action of a detergent or other agent." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000020
name: Depletion
def: "The removal of specific components of a complex mixture of proteins or peptides on the basis of some specific property of those components." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000021
name: Fractionation
def: "Process of classification of an analyte or a group of analytes from a sample according to physical (e.g., size) or chemical (e.g., bonding, reactivity) properties. (from https://doi.org/10.1351/goldbook.FT06825)" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000022
name: Separation
def: "To separate a complex mixture of proteins or peptides based on molecular characteristics and interaction type over a given amount of time." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000023
name: Band excision
def: "The removal of a region of a gel which contains protein(s) of interest." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000024
name: Enzyme digestion
def: "The fragmentation of proteins into peptides through the use of an enzyme such as trypsin." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000025
name: Reduction
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000026
name: Alkylation
def: "The transfer of an alkyl group from one molecule to another." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000027
name: Mass spectrometry
def: "This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000028
name: Cv Label
comment: Valid values for cvLabel entries referencing external database / CV / ontology.

[Term]
id: PRIDE:0000029
name: PubMed
comment: Valid value for the cvLabel entry referencing PubMed.
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000030
name: PRIDE
comment: Valid value for the cvLabel entry referencing PRIDE
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000031
name: GO
comment: Valid value for the cvLabel entry referencing GO.
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000032
name: MeSH
comment: Valid value for the cvLabel entry referencing Medical Subject Headings (MeSH)
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000033
name: NEWT
comment: Valid value for the cvLabel entry referencing NEWT or the NCBI taxonomy.
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000034
name: PSI
comment: Valid value for the cvLabel entry referencing the PSI ontology
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000035
name: UNIMOD
comment: Valid value for the cvLabel entry referencing UNIMOD
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000036
name: RESID
comment: Valid value for the cvLabel entry referencing RESID.
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000037
name: Staining
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000038
name: ISBN
comment: Valid value for the cvLabel entry referencing ISBN
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000039
name: Organelle isolation
def: "Any technique which separates differentiated structures from the cell." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000040
name: Experiment description
comment: This CV term should be used in association with a value that is a free-text description of the experiment.
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000041
name: Search database protein sequence
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000042
name: DOI
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000043
name: FIX
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000044
name: Search algorithm

[Term]
id: PRIDE:0000045
name: Sequest
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000046
name: Mascot
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000571 ! Quantification Software
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000047
name: XTandem
comment: Really X
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000048
name: OutputParameter
is_obsolete: true

[Term]
id: PRIDE:0000049
name: Peptide search engine output parameter
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000050
name: Rank/Sp
def: "Final correlation score rank and preliminary score rank." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000051
name: (M+H)+
def: "m/z of the singly-charged precursor (precursor mass + mass of hydrogen atom)." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000052
name: Cn
def: "normalized correlation score." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000053
name: Sequest score
def: "raw correlation score (Sequest)." [PRIDE:PRIDE]
synonym: "C*10^4" RELATED []
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000054
name: Sp
def: "preliminary score." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000055
name: Ions
def: "the number of frament ions matched (in the preliminary scoring process) out of the total number of fragment masses for the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000056
name: Bioworks
is_a: PRIDE:0000045 ! Sequest
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000057
name: Molecular weight
def: "Molecular weight of a protein." [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000058
name: z
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000059
name: File
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000060
name: Scan
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000061
name: Coverage
is_a: PRIDE:0000008 ! Protein search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000062
name: rsp
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000063
name: Protein description line
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000064
name: Secondary accession
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000065
name: Upstream flanking sequence
def: "Any sequence reported before the start of the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000066
name: Downstream flanking seqeuence
def: "Any sequence reported after the end of the peptide sequence." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000067
name: Reference reporting this experiment
is_a: PRIDE:0000000 ! Reference additional parameter

[Term]
id: PRIDE:0000068
name: Reference describing sample preparation
is_a: PRIDE:0000000 ! Reference additional parameter

[Term]
id: PRIDE:0000069
name: Mascot score
def: "Score as defined for the Mascot search algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000046 ! Mascot

[Term]
id: PRIDE:0000070
name: Peptide cleavage
def: "Cleavage of the peptide bond." [PRIDE:PRIDE]
is_a: PRIDE:0000024 ! Enzyme digestion

[Term]
id: PRIDE:0000071
name: Search engine setting
is_a: PRIDE:0000001 ! Protocol step description additional parameter
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000072
name: Fixed modification setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000073
name: Variable modification setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000074
name: Maximum Missed Cleavages Setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000075
name: Mass value type setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000076
name: Mass value type setting monoisotopic
is_a: PRIDE:0000075 ! Mass value type setting

[Term]
id: PRIDE:0000077
name: Mass value type setting average
is_a: PRIDE:0000075 ! Mass value type setting

[Term]
id: PRIDE:0000078
name: Peptide mass tolerance setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000079
name: Accurate mass mode setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000080
name: Accurate mass mode setting true
is_a: PRIDE:0000079 ! Accurate mass mode setting

[Term]
id: PRIDE:0000081
name: Accurate mass mode setting false
is_a: PRIDE:0000079 ! Accurate mass mode setting

[Term]
id: PRIDE:0000082
name: Mass error type setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000083
name: mass error type setting ppm
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000084
name: mass error type setting mmu
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000085
name: mass error type setting percent
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000086
name: mass error type setting Daltons
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000087
name: Protonated setting
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000088
name: Protonated setting MH+
is_a: PRIDE:0000087 ! Protonated setting

[Term]
id: PRIDE:0000089
name: Protonated setting Mr
is_a: PRIDE:0000087 ! Protonated setting

[Term]
id: PRIDE:0000090
name: Protonated setting M-H-
is_a: PRIDE:0000087 ! Protonated setting

[Term]
id: PRIDE:0000091
name: Rank
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000092
name: All peptides matched
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000093
name: All peptides matched true
is_a: PRIDE:0000092 ! All peptides matched

[Term]
id: PRIDE:0000094
name: All peptides matched false
is_a: PRIDE:0000092 ! All peptides matched

[Term]
id: PRIDE:0000095
name: Masses matched
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000096
name: Reported Chromosome
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000097
name: Project
def: "Allows experiments to be grouped or organised under projects.  Experiments may be grouped under more than one project." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000098
name: Indistinguishable alternative protein accession
def: "A qualifier is mandatory when using this term.  The qualifier is an alternative protein accession that is indistinguishable from the primary protein accession based upon observed peptide sequences only." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000099
name: PeptideProphet probability score
def: "The probability score for this peptide assignment to be correct, as calculated by PeptideProphet." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000101 ! PeptideProphet

[Term]
id: PRIDE:0000100
name: ProteinProphet probability score
def: "The probability score for this protein identification to be correct, as calculated by ProteinProphet." [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
relationship: part_of PRIDE:0000102 ! ProteinProphet

[Term]
id: PRIDE:0000101
name: PeptideProphet
def: "The PeptideProphet algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000102
name: ProteinProphet
def: "The ProteinProphet algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000103
name: Gel run date
def: "The date upon which the gel was run.  A value is mandatory - must be formatted as xsd:dateTime." [PRIDE:PRIDE]
is_a: PRIDE:0000005 ! Gel additional parameter

[Term]
id: PRIDE:0000104
name: Sample volume loaded
def: "The volume of sample loaded on to the gel measured in micro litres.  Mandatory value must be formatted as xsd:Double." [PRIDE:PRIDE]
xref: PRIDE:PRIDE
is_a: PRIDE:0000005 ! Gel additional parameter

[Term]
id: PRIDE:0000105
name: Width in pixels
def: "The width of the referenced gel image in pixels.  Mandatory value of type xsd:int." [PRIDE:PRIDE]
is_a: PRIDE:0000005 ! Gel additional parameter

[Term]
id: PRIDE:0000106
name: Height in pixels
def: "The height of the referenced gel image in pixels.  Mandatory value of type xsd:int." [PRIDE:PRIDE]
is_a: PRIDE:0000005 ! Gel additional parameter

[Term]
id: PRIDE:0000107
name: Gel spot parameter
def: "Parameters describing the spot on a gel that has been analysed resulting in the annotated protein identification." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000108
name: Gel spot intensity
def: "The intensity of the spot on the gel.   Mandatory value of type xsd:double." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter

[Term]
id: PRIDE:0000109
name: Gel spot area 
def: "The area of the spot on the gel measured in millimetres squared.   Mandatory value of type xsd:double." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter

[Term]
id: PRIDE:0000110
name: Gel spot volume
def: "The volume of the spot on the gel measured in millimetres cubed.  Mandatory value of type xsd:double." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000131 ! Spot normalized volume

[Term]
id: PRIDE:0000111
name: Reference describing data analysis
def: "A reference annotated with this term describes analysis of the data presented in the enclosing PRIDE experiment." [PRIDE:PRIDE]
is_a: PRIDE:0000000 ! Reference additional parameter

[Term]
id: PRIDE:0000112
name: Identified by peptide mass fingerprint
def: "The annotated protein identification arises from peptide mass fingerprinting.  Peptide identifications may or may not be included." [PRIDE:PRIDE]
synonym: "PMF" EXACT []
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000113
name: Identified by peptide fragmentation
def: "The protein identification annotated with this term has been identified by peptide fragmentation and subsequent database searching." [PRIDE:PRIDE]
synonym: "PFF" EXACT []
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000114
name: iTRAQ reagent 114
comment: The name of the sample labelled with iTRAQ reagent 114.
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000115
name: iTRAQ reagent 115
comment: The name of the sample labelled with iTRAQ reagent 115.
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000116
name: iTRAQ reagent 116
comment: The name of the sample labelled with iTRAQ reagent 116.
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000117
name: iTRAQ reagent 117
comment: The name of the sample labelled with iTRAQ reagent 117.
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000118
name: iTRAQ intensity 114
comment: The intensity of the sample labelled with iTRAQ reagent 114.
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000119
name: iTRAQ intensity 115
comment: The intensity of the sample labelled with iTRAQ reagent 115.
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000120
name: iTRAQ intensity 116
comment: The intensity of the sample labelled with iTRAQ reagent 116.
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000121
name: iTRAQ intensity 117
comment: The intensity of the sample labelled with iTRAQ reagent 117.
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000122
name: Two Dimensional Polyacrylamide Gel Electrophoresis
def: "A type of gel electrophoresis in which proteins are first separated by charge and then by molecular weight, enabling the analysis of complex protein mixtures." [PRIDE:PRIDE]
is_a: PRIDE:0000022 ! Separation


[Term]
id: PRIDE:0000123
name: Immobilized pH Gradient Electrophoresis
def: "Electrophoresis using an gel  which has a  pH gradient along its length." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis
is_a: PRIDE:0000568 ! 2D PAGE

[Term]
id: PRIDE:0000124
name: Sodium dodecyl sulfate polyacrylamide gel electrophoresis
def: "A type of polyacrylamide gel electrophoresis in which the anionic detergent sodium dodecyl sulfate (SDS) is used to denature the sample proteins into linear monomers, rendering their charge proportional to their length so that migration is a function of size. Abbreviated SDS-polyacrylamide gel electrophoresis or SDS-PAGE." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000122 ! Two Dimensional Polyacrylamide Gel Electrophoresis
is_a: PRIDE:0000568 ! 2D PAGE


[Term]
id: PRIDE:0000125
name: pH low value
def: "The lowest pH of an immobilised pH gradient gel." [PRIDE:PRIDE]
is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term]
id: PRIDE:0000126
name: pH high value
def: "The highest pH of an immobilised pH gradient gel." [PRIDE:PRIDE]
is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term]
id: PRIDE:0000127
name: IPG strip length cm
def: "The length in centimeters of an immobilised pH gradient gel." [PRIDE:PRIDE]
comment: This value associated with this CV term should always be in centimeters.
is_a: PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term]
id: PRIDE:0000128
name: First dimension details
def: "Details of immobilised pH gradient gel electrophoresis which exclude the pH range of the gel and strip length parameters." [PRIDE:PRIDE]
comment: This CV term should be used in association with a value that is a free-text description of the first dimension details
relationship: part_of PRIDE:0000123 ! Immobilized pH Gradient Electrophoresis

[Term]
id: PRIDE:0000129
name: Second dimension details
def: "Details of sodium dodecyl sulfate polyacrylamide gel electrophoresis." [PRIDE:PRIDE]
comment: This CV term should be used in association with a value that is a free-text description of the second dimension details
is_a: PRIDE:0000124 ! Sodium dodecyl sulfate polyacrylamide gel electrophoresis

[Term]
id: PRIDE:0000130
name: Obsoleted parameters
def: "Obsoleted terms." [Curator:Rc]
is_obsolete: true

[Term]
id: PRIDE:0000131
name: Spot normalized volume
def: "A value for spot volume which is standardized across gels and is derived from the individual gel spot volume values." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter

[Term]
id: PRIDE:0000132
name: Spot normalized volume method
def: "The method by which the normalized value for spot volume is derived from the individual gel spot volume values." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter

[Term]
id: PRIDE:0000133
name: Isobaric residue K/Q
def: "The amino acids glutamine (Q) (mol wt = 146) cannot be distinguished from lysine (K) (mol wt = 146)." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000134
name: Anticoagulant
def: "A substance that prevents coagulation; that is, it stops blood from clotting." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000135
name: Mapping date
def: "Date of last mapping of given identifier to current UniProt accession number." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000136
name: Mapping status
def: "Status of last mapping of given identifier to current UniProt accession number. Valid values are 'mappingAllOK', 'not mapped peptide mismatch', 'not mapped accession not found' and 'not mapped taxon not found' ." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000137
name: Mapping history
def: "Status of last mapping of given identifier to current UniProt accession number. Valid values are 'unchanged since last mapping', 'changed accession' and 'changed version of accession' ." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000138
name: Discriminant score
def: "PeptideProphet discriminant score fval." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000101 ! PeptideProphet

[Term]
id: PRIDE:0000139
name: Not Mapped SOAP Error
def: "Error message: SOAP protocol failed." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000140
name: Not Mapped Database Error
def: "Error message: Error with queried database." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000141
name: Not Mapped No Mapping Found
def: "Error message: Unable to match given identifier." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000142
name: Not Mapped Peptide Mismatch
def: "Error message: One or more peptide sequences did not match query sequence." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000143
name: Mapped Taxon Not Found
def: "Error message: No mapping to proteins from defined taxon." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000144
name: Mapped All Ok
def: "Sucessful completion of operation message." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000145
name: PepSplice
def: "The PepSplice algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000146
name: PepSplice precision
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000147
name: PepSplice False Discovery Rate
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000148
name: PepSplice P-value
def: "A Score based on the hypergeometric model." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000149
name: PepSplice Deltascore
def: "The Difference between the pvalues of the 1st and the 2nd best peptide; if two peptides have the same pvalue, they are taken together." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000150
name: PepSplice Score Count
def: "The score count." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000151
name: PepSplice Penalty
def: "The Sum of all penalties for the peptide assignment." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000152
name: PepSplice Read Direction
def: "The reading direction on the DNA." [PRIDE:PRIDE]
relationship: part_of PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000153
name: PepSplice Forward Read Direction
def: "The reading direction on the DNA is 5' to 3'." [PRIDE:PRIDE]
is_a: PRIDE:0000152 ! PepSplice Read Direction

[Term]
id: PRIDE:0000154
name: PepSplice Reverse Read Direction
def: "The reading direction on the DNA 3' to 5'." [PRIDE:PRIDE]
is_a: PRIDE:0000152 ! PepSplice Read Direction
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000155
name: Unmappable
def: "unsucessful mapping." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000156
name: Project identifier
def: "unique identifier of project." [PRIDE:PRIDE]
synonym: "Project ID" EXACT []
relationship: part_of PRIDE:0000097 ! Project

[Term]
id: PRIDE:0000157
name: Search type
def: "type of search." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000158
name: MS search
is_a: PRIDE:0000157 ! Search type

[Term]
id: PRIDE:0000159
name: MS/MS search
is_a: PRIDE:0000157 ! Search type

[Term]
id: PRIDE:0000160
name: Enzyme
def: "type of enzyme used to fragment the protein. The value will equal the name of the enxzyme used e.g. ." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000161
name: Fragment mass tolerance setting
def: "range of acceptable fragment masses accepted by instrument." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000162
name: Allowed missed cleavages
def: "number of missed cleavage sites taken into account." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000163
name: Instrument type
def: "name of instrument used in analysis." [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000164
name: Mapped Without Supporting Peptides
def: "Sucessful mapping without supporting evidence from peptides." [PRIDE:PRIDE]
is_a: PRIDE:0000136 ! Mapping status

[Term]
id: PRIDE:0000165
name: Automatic allocation
def: "PICR tool has allocated the accession number." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000166
name: Ambiguous modification
def: "Modification with a MonoDeltaMass, which can not unambiguously be  assigned to only one modification and for which several possibilities exist." [PRIDE:PRIDE]
is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term]
id: PRIDE:0000167
name: Novel locus information
def: "Detailed information about a genomic locus identified by whole genome searches." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000168
name: Nucleic acid sequence
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000169
name: Start position of the nucleic acid sequence on the chromosome
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000170
name: Stop position of the nucleic acid sequence on the chromosome
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000171
name: funding reference
is_a: PRIDE:0000000 ! Reference additional parameter

[Term]
id: PRIDE:0000172
name: Search database protein sequence length
def: "Value of average of all individual peptide identifications for this protein." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000173
name: MeanOfPeptideScores
def: "Value of average of all individual peptide scores." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000174
name: Isoelectric point
def: "Isoelectric point of a protein." [PRIDE:PRIDE]
synonym: "pI" EXACT []
is_a: PRIDE:0000008 ! Protein search engine output parameter
relationship: part_of PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000175
name: XML generation software
def: "The software which was used to generate the PRIDE XML file." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000176
name: X\!Tandem Hyperscore
def: "The X!Tandem hyperscore for the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000177
name: Spectrum Mill peptide score
def: "The Spectrum Mill score for the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000178
name: Peptide selection
def: "A protocol step to select for a particular type of peptides." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000179
name: dotproduct
def: "X|Tandem dot product score." [PRIDE:PRIDE]
is_a: PRIDE:0000047 ! X|Tandem

[Term]
id: PRIDE:0000180
name: delta
def: "X|Tandem delta score." [PRIDE:PRIDE]
is_a: PRIDE:0000047 ! X|Tandem

[Term]
id: PRIDE:0000181
name: deltastar
def: "X|Tandem delta star score." [PRIDE:PRIDE]
is_a: PRIDE:0000047 ! X|Tandem

[Term]
id: PRIDE:0000182
name: zscore
def: "X|Tandem Z score." [PRIDE:PRIDE]
is_a: PRIDE:0000047 ! X|Tandem

[Term]
id: PRIDE:0000183
name: expect
def: "X|Tandem expectancy score." [PRIDE:PRIDE]
is_a: PRIDE:0000047 ! X|Tandem

[Term]
id: PRIDE:0000184
name: Query number
def: "Search parameter that allows users to find query results from old data." [PRIDE:PRIDE]
is_a: PRIDE:0000046 ! Mascot

[Term]
id: PRIDE:0000185
name: OMSSA E-value
def: "E-value parameter from OMSSA." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000186
name: OMSSA P-value
def: "P-value parameter from OMSSA." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000187
name: Fragment Ion Annotation
def: "Fragment ion annotation of the peptide." [PRIDE:PRIDE]
synonym: "product ion property" EXACT []
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000188
name: product ion m/z
def: "Mass." [PRIDE:PRIDE]
synonym: "fragment ion mass" EXACT []
is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term]
id: PRIDE:0000189
name: product ion intensity
def: "Intensity." [PRIDE:PRIDE]
synonym: "fragment ion intensity" EXACT []
is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term]
id: PRIDE:0000190
name: product ion mass error
def: "Mass error." [PRIDE:PRIDE]
synonym: "fragment ion mass error" EXACT []
is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term]
id: PRIDE:0000191
name: product ion retention time error
def: "Retention time error in minutes." [PRIDE:PRIDE]
synonym: "fragment ion retention time error" EXACT []
is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term]
id: PRIDE:0000192
name: product ion type
def: "Product ion type." [PRIDE:PRIDE]
synonym: "fragment ion type" EXACT []
is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term]
id: PRIDE:0000193
name: y ion
def: "Y ion type." [PRIDE:PRIDE]
synonym: "y fragment ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000194
name: b ion
def: "B ion type." [PRIDE:PRIDE]
synonym: "b fragment ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000195
name: b ion -NH3
def: "B ion type with a neutral loss of an ammonia group." [PRIDE:PRIDE]
synonym: "b fragment ion -NH3" EXACT []
is_a: PRIDE:0000194 ! b ion

[Term]
id: PRIDE:0000196
name: b ion -H2O
def: "B ion type with a neutral loss of a water molecule." [PRIDE:PRIDE]
synonym: "b fragment ion -H2O" EXACT []
is_a: PRIDE:0000194 ! b ion

[Term]
id: PRIDE:0000197
name: y ion -H2O
def: "Y ion type with the neutral loss of a molecule water." [PRIDE:PRIDE]
synonym: "y fragment ion -H2O" EXACT []
is_a: PRIDE:0000193 ! y ion

[Term]
id: PRIDE:0000198
name: y ion -NH3
def: "Y ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE]
synonym: "y fragment ion -NH3" EXACT []
is_a: PRIDE:0000193 ! y ion

[Term]
id: PRIDE:0000199
name: in source ion
def: "Ion resulting from in-source fragmentation." [PRIDE:PRIDE]
synonym: "in source fragment ion" EXACT []
synonym: "in-source ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000200
name: non-identified ion
def: "Fragment ion that could not be assigned to a predicted fragment ion mass." [PRIDE:PRIDE]
synonym: "unidentified ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000201
name: co-eluting ion
def: "Fragment ion that was matched to another, co-eluting peptide precursor." [PRIDE:PRIDE]
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000202
name: Parent Ion Annotation
def: "Parent ion annotation of the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000203
name: parent ion retention time
def: "Retention time in minutes." [PRIDE:PRIDE]
is_a: PRIDE:0000202 ! Parent Ion Annotation

[Term]
id: PRIDE:0000204
name: product ion charge
def: "Charge state." [PRIDE:PRIDE]
synonym: "fragment ion charge" EXACT []
is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term]
id: PRIDE:0000205
name: Heavy stable isotope label
def: "A general term for any stable isotope method." [PRIDE:PRIDE]
is_obsolete: true

[Term]
id: PRIDE:0000206
name: Heavy stable isotope label residue
def: "The precise amino acid that has been modified." [PRIDE:PRIDE]
is_obsolete: true

[Term]
id: PRIDE:0000207
name: Light stable isotope label
def: "A general term for any stable isotope method." [PRIDE:PRIDE]
is_obsolete: true

[Term]
id: PRIDE:0000208
name: Light stable isotope label residue
def: "The precise amino acid that has been modified." [PRIDE:PRIDE]
is_obsolete: true

[Term]
id: PRIDE:0000209
name: Peptide pair id
def: "Facilitate mapping between peptide pairs (usually heavy/light) to which the stable isotope ratio below relates." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000210
name: Stable isotope ratio
def: "Ratio of peptide pair the sequence/sample is the numerator in the ratio." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000211
name: Quantitative sample reference
def: "This links back to the value given to the heavy/light stable isotope label to relate the peptide ratio back to the sample." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000212
name: Mascot expect value
def: "Expect value as defined for the Mascot search algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000046 ! Mascot

[Term]
id: PRIDE:0000213
name: Inspect
def: "The Inspect search algorithm." [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000214
name: Inspect MQScore
def: "Quality score of a match." [PRIDE:PRIDE]
is_a: PRIDE:0000213 ! Inspect

[Term]
id: PRIDE:0000215
name: Inspect p-value
def: "Probability that the top match is correct." [PRIDE:PRIDE]
is_a: PRIDE:0000213 ! Inspect

[Term]
id: PRIDE:0000216
name: ProteomExchange project accession number
def: "ProteomExchange accession number of the project where the PRIDE experiment is included." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000217
name: ProteomExchange project hash
def: "Hash in Tranche of the whole ProteomExchange project where the PRIDE experiment is included." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000218
name: Original MS data file format
def: "Original format of the file containing MS data." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000219
name: Date of search
def: "Date when the search was performed." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000220
name: Calculated Mass To Charge Ratio
def: "m/z value converted from the MH+ value, according to this formula: CalculatedMZ = (precursorMH+ - HYDROGEN_MASS + (precursorCharge * HYDROGEN_MASS))/ precursorCharge." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000221
name: parent ion retention time error
def: "Retention time error in minutes." [PRIDE:PRIDE]
is_a: PRIDE:0000202 ! Parent Ion Annotation

[Term]
id: PRIDE:0000222
name: spectrum iTRAQ ratio
def: "average iTRAQ ratio sample over control." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_obsolete: true

[Term]
id: PRIDE:0000223
name: peptide iTRAQ ratio average
def: "Average spectrum iTRAQ ratio (=geometric mean) for the peptide." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_obsolete: true

[Term]
id: PRIDE:0000224
name: protein iTRAQ ratio average
def: "Average spectrum iTRAQ ratio (=geometric mean) for the protein." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
is_obsolete: true

[Term]
id: PRIDE:0000225
name: protein iTRAQ ratio number of contributing spectra
def: "Number of quantified spectra contributing to the protein iTRAQ ratio." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
is_obsolete: true

[Term]
id: PRIDE:0000226
name: protein iTRAQ ratio standard deviation
def: "Geometric sample standard deviation of the protein iTRAQ ratio." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
is_obsolete: true

[Term]
id: PRIDE:0000227
name: x ion
def: "X ion type." [PRIDE:PRIDE]
synonym: "x fragment ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000228
name: x ion -H2O
def: "X ion type with the neutral loss of a molecule water." [PRIDE:PRIDE]
synonym: "x fragment ion -H2O" EXACT []
is_a: PRIDE:0000227 ! x ion

[Term]
id: PRIDE:0000229
name: x ion -NH3
def: "X ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE]
synonym: "x fragment ion -NH3" EXACT []
is_a: PRIDE:0000227 ! x ion

[Term]
id: PRIDE:0000230
name: z ion
def: "Z ion type." [PRIDE:PRIDE]
synonym: "z fragment ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000231
name: z ion -H2O
def: "Z ion type with the neutral loss of a molecule water." [PRIDE:PRIDE]
synonym: "z fragment ion -H2O" EXACT []
is_a: PRIDE:0000230 ! z ion

[Term]
id: PRIDE:0000232
name: z ion -NH3
def: "Z ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE]
synonym: "z fragment ion -NH3" EXACT []
is_a: PRIDE:0000230 ! z ion

[Term]
id: PRIDE:0000233
name: a ion
def: "A ion type." [PRIDE:PRIDE]
synonym: "a fragment ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000234
name: a ion -H2O
def: "A ion type with the neutral loss of a molecule water." [PRIDE:PRIDE]
synonym: "a fragment ion -H2O" EXACT []
is_a: PRIDE:0000233 ! a ion

[Term]
id: PRIDE:0000235
name: a ion -NH3
def: "A ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE]
synonym: "a fragment ion -NH3" EXACT []
is_a: PRIDE:0000233 ! a ion

[Term]
id: PRIDE:0000236
name: c ion
def: "C ion type." [PRIDE:PRIDE]
synonym: "c fragment ion" EXACT []
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000237
name: c ion -H2O
def: "C ion type with the neutral loss of a molecule water." [PRIDE:PRIDE]
synonym: "c fragment ion -H2O" EXACT []
is_a: PRIDE:0000236 ! c ion

[Term]
id: PRIDE:0000238
name: c ion -NH3
def: "C ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE]
synonym: "c fragment ion -NH3" EXACT []
is_a: PRIDE:0000236 ! c ion

[Term]
id: PRIDE:0000239
name: immonium ion
def: "Immonium ion type." [PRIDE:PRIDE]
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000240
name: immonium A
def: "Immonium ion type for alanine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000241
name: immonium C
def: "Immonium ion type for cysteine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000242
name: immonium D
def: "Immonium ion type for aspartic acid." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000243
name: immonium E
def: "Immonium ion type for glutamic acid." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000244
name: immonium F
def: "Immonium ion type for phenylalanine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000245
name: immonium G
def: "Immonium ion type for glycine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000246
name: immonium H
def: "Immonium ion type for histidine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000247
name: immonium I
def: "Immonium ion type for isoleucine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000248
name: immonium K
def: "Immonium ion type for lysine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000249
name: immonium L
def: "Immonium ion type for leucine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000250
name: immonium M
def: "Immonium ion type for methionine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000251
name: immonium N
def: "Immonium ion type for asparagine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000252
name: immonium P
def: "Immonium ion type for proline." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000253
name: immonium Q
def: "Immonium ion type for glutamine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000254
name: immonium R
def: "Immonium ion type for arginine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000255
name: immonium S
def: "Immonium ion type for serine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000256
name: immonium T
def: "Immonium ion type for threnine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000257
name: immonium V
def: "Immonium ion type for valine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000258
name: immonium W
def: "Immonium ion type for tryptophan." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000259
name: immonium Y
def: "Immonium ion type for tyrosine." [PRIDE:PRIDE]
is_a: PRIDE:0000239 ! immonium ion

[Term]
id: PRIDE:0000260
name: precursor ion type
def: "precursor ion type." [PRIDE:PRIDE]
synonym: "parent ion type" EXACT []
is_a: PRIDE:0000202 ! Parent Ion Annotation

[Term]
id: PRIDE:0000261
name: precursor ion -H2O
def: "Precursor ion type with the neutral loss of a molecule water." [PRIDE:PRIDE]
synonym: "parent ion -H2O" EXACT []
is_a: PRIDE:0000263 ! precursor ion

[Term]
id: PRIDE:0000262
name: precursor ion -NH3
def: "Precursor ion type with the neutral loss of an ammonia group." [PRIDE:PRIDE]
synonym: "parent ion -NH3" EXACT []
is_a: PRIDE:0000263 ! precursor ion

[Term]
id: PRIDE:0000263
name: precursor ion
def: "Precursor ion." [PRIDE:PRIDE]
synonym: "parent ion" EXACT []
is_a: PRIDE:0000260 ! precursor ion type

[Term]
id: PRIDE:0000264
name: iTRAQ reagent 113
comment: The name of the sample labelled with iTRAQ reagent 113
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000265
name: iTRAQ reagent 118
comment: The name of the sample labelled with iTRAQ reagent 118
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000266
name: iTRAQ reagent 119
comment: The name of the sample labelled with iTRAQ reagent 119
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000267
name: iTRAQ reagent 121
comment: The name of the sample labelled with iTRAQ reagent 121
is_a: PRIDE:0000329 ! iTRAQ reagent

[Term]
id: PRIDE:0000268
name: iTRAQ intensity 113
comment: The intensity of the sample labelled with iTRAQ reagent 113
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000269
name: iTRAQ intensity 118
comment: The intensity of the sample labelled with iTRAQ reagent 118
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000270
name: iTRAQ intensity 119
comment: The intensity of the sample labelled with iTRAQ reagent 119
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000271
name: iTRAQ intensity 121
comment: The intensity of the sample labelled with iTRAQ reagent 121
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000272
name: Project secondary name
def: "Allows experiments inside the same project to be grouped or organised as subprojects. This will not be displayed in the PRIDE web page." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000273
name: SloMo score threshold for valid modification location
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000274
name: MaxQuant percentage threshold for valid modification location
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000275
name: SloMo score
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000276
name: MaxQuant percentage
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000277
name: Valid location
is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term]
id: PRIDE:0000278
name: Processing method additional parameter

[Term]
id: PRIDE:0000279
name: In silico enzyme digestion
def: "Enzyme that is selected as a parameter of the search engine." [PRIDE:PRIDE]
is_a: PRIDE:0000278 ! Processing method additional parameter

[Term]
id: PRIDE:0000280
name: zH ion
def: "Z ion type with one extra proton" [PRIDE:PRIDE]
synonym: "zH fragment ion" EXACT []
is_a: PRIDE:0000230 ! z ion

[Term]
id: PRIDE:0000281
name: zHH ion
def: "Z ion type with two extra protons" [PRIDE:PRIDE]
synonym: "zHH fragment ion" EXACT []
is_a: PRIDE:0000230 ! z ion

[Term]
id: PRIDE:0000282
name: Fixed modification
def: "Fixed type of post-translational modification." [PRIDE:PRIDE]
is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term]
id: PRIDE:0000283
name: Variable modification
def: "Variable type of post-translational modification." [PRIDE:PRIDE]
is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term]
id: PRIDE:0000284
name: Sf
def: "The Sf score for each peptide is calculated by a neural network algorithm that incorporates teh Xcorr, DeltaCn, Sp, RSp, peptide mass, charge state, and the number of matched peptides for the search. The protein Sf score is the sum of peptide Sf scores for all the peptides associated with that protein." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
relationship: part_of PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000285
name: TMT reagent 126
comment: The name of the sample labelled with TMT reagent 126
is_a: PRIDE:0000337 ! TMT reagent

[Term]
id: PRIDE:0000286
name: TMT reagent 127
comment: The name of the sample labelled with TMT reagent 127
is_a: PRIDE:0000337 ! TMT reagent

[Term]
id: PRIDE:0000287
name: TMT reagent 128
comment: The name of the sample labelled with TMT reagent 128
is_a: PRIDE:0000337 ! TMT reagent

[Term]
id: PRIDE:0000288
name: TMT reagent 129
comment: The name of the sample labelled with TMT reagent 129
is_a: PRIDE:0000337 ! TMT reagent

[Term]
id: PRIDE:0000289
name: TMT reagent 130
comment: The name of the sample labelled with TMT reagent 130
is_a: PRIDE:0000337 ! TMT reagent

[Term]
id: PRIDE:0000290
name: TMT reagent 131
comment: The name of the sample labelled with TMT reagent 131
is_a: PRIDE:0000337 ! TMT reagent

[Term]
id: PRIDE:0000291
name: TMT intensity 126
comment: The intensity value of the sample labelled with TMT reagent 126 [Curator:ACSORDAS]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000292
name: TMT intensity 127
comment: The intensity value of the sample labelled with TMT reagent 127 [Curator:ACSORDAS]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000293
name: TMT intensity 128
comment: The intensity value of the sample labelled with TMT reagent 128 [Curator:ACSORDAS]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000294
name: TMT intensity 129
comment: The intensity value of the sample labelled with TMT reagent 129 [Curator:ACSORDAS]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000295
name: TMT intensity 130
comment: The intensity value of the sample labelled with TMT reagent 130 [Curator:ACSORDAS]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000296
name: TMT intensity 131
comment: The intensity value of the sample labelled with TMT reagent 131 [Curator:ACSORDAS]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000297
name: Gene name
comment: Name of the gene that has been identified (if a nucleotide database was used to perform the search)
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000298
name: Modification Position in Protein Sequence
comment: Position of the modification in the protein sequence
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000299
name: Submitted Protein Accession
comment: The original submitted protein accession for this identification. This might have been curated as part of the submission process.
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000300
name: Gel spot identifier
def: "The gel spot's identifier. This identifier should resemble the one used in, for example, the associated publication." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter
created_by: jg
creation_date: 2011-05-12T11:32:07Z

[Term]
id: PRIDE:0000301
name: Non-significant protein identification
def: "Identifies a protein identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value)." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
created_by: jg
creation_date: 2011-05-12T11:39:59Z

[Term]
id: PRIDE:0000302
name: Non-significant peptide identification
def: "Identifies a peptide identification that is not significant as defined by the search engine input parameters (for example the set threshold or the set required expect value)." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
created_by: jg
creation_date: 2011-05-12T11:50:00Z

[Term]
id: PRIDE:0000303
name: Decoy hit
def: "Indicates that this protein identification comes from the used decoy database." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
created_by: jg
creation_date: 2011-05-12T11:58:52Z
is_obsolete: true

[Term]
id: PRIDE:0000304
name: Gel identifier
def: "The gel's identifier. This identifier should resemble the one used in, for example, the associated publication." [PRIDE:PRIDE]
is_a: PRIDE:0000107 ! Gel spot parameter
created_by: jg
creation_date: 2011-05-25T11:22:05Z

[Term]
id: PRIDE:0000305
name: Gel-based experiment
def: "Defines a gel-based proteomics experiment." [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: jg
creation_date: 2011-05-25T05:44:24Z

[Term]
id: PRIDE:0000306
name: Imported from NCBI Peptidome
comment: Experiment.[Curator:ACSORDAS]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000307
name: Quantification method
comment: Defines various quantification methods
is_a: PRIDE:0000391 ! Quantification parameter
created_by: jg
creation_date: 2011-07-22T09:15:33Z

[Term]
id: PRIDE:0000308
name: Gel-based quantification method
comment: Describes gel-based quantification methods
is_a: PRIDE:0000307 ! Quantification method
created_by: jg
creation_date: 2011-07-22T09:16:24Z

[Term]
id: PRIDE:0000309
name: Gel-free quantification method
comment: Describes gel-free quantification methods
is_a: PRIDE:0000307 ! Quantification method
created_by: jg
creation_date: 2011-07-22T09:17:03Z

[Term]
id: PRIDE:0000310
name: Isotope labeling
comment: Describes quantification techniques using isotope labeling
is_a: PRIDE:0000309 ! Gel-free quantification method
created_by: jg
creation_date: 2011-07-22T09:17:34Z

[Term]
id: PRIDE:0000311
name: Selected Reaction Monitoring
comment: Describes quantification techniques based on selected / multiple reaction monitoring
is_a: PRIDE:0000309 ! Gel-free quantification method
created_by: jg
creation_date: 2011-07-22T09:18:39Z

[Term]
id: PRIDE:0000312
name: Label free
comment: Describes label free quantification techniques.
is_a: PRIDE:0000309 ! Gel-free quantification method
created_by: jg
creation_date: 2011-07-22T09:19:54Z

[Term]
id: PRIDE:0000313
name: iTRAQ
comment: Quantification technique developed by Applied Biosystems using various reporter ions that can be detected at MS2 level
is_a: PRIDE:0000317 ! MS2 based isotope labeling
created_by: jg
creation_date: 2011-07-22T09:20:23Z

[Term]
id: PRIDE:0000314
name: TMT
comment: Tandem Mass Tag is a MS2 based isotope labeling quantification technique
synonym: "Tandem Mass Tag" EXACT []
is_a: PRIDE:0000317 ! MS2 based isotope labeling
created_by: jg
creation_date: 2011-07-22T09:23:12Z

[Term]
id: PRIDE:0000315
name: SILAC
comment: Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification
synonym: "Stable isotope labeling with amino acids in cell culture" EXACT []
is_a: PRIDE:0000316 ! MS1 based isotope labeling
created_by: jg
creation_date: 2011-07-22T09:25:50Z

[Term]
id: PRIDE:0000316
name: MS1 based isotope labeling
comment: Describes isotope labeling quantification techniques detectable at MS1 level.
is_a: PRIDE:0000310 ! Isotope labeling
created_by: jg
creation_date: 2011-07-22T09:28:05Z

[Term]
id: PRIDE:0000317
name: MS2 based isotope labeling
comment: Describes isotope labeling quantification techniques detectable at MS1 level.
is_a: PRIDE:0000310 ! Isotope labeling
created_by: jg
creation_date: 2011-07-22T09:29:15Z

[Term]
id: PRIDE:0000318
name: 18O
comment: The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen.
is_a: PRIDE:0000316 ! MS1 based isotope labeling
created_by: jg
creation_date: 2011-07-22T09:30:12Z

[Term]
id: PRIDE:0000319
name: ICAT
comment: Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements.
synonym: "Isotope-Coded Affinity Tags" EXACT []
is_a: PRIDE:0000316 ! MS1 based isotope labeling
created_by: jg
creation_date: 2011-07-22T09:31:24Z

[Term]
id: PRIDE:0000320
name: AQUA
comment: AQUA is an isotope labeling based quantification technique that uses known peptides.
is_a: PRIDE:0000316 ! MS1 based isotope labeling
created_by: jg
creation_date: 2011-07-22T09:32:46Z

[Term]
id: PRIDE:0000321
name: ICPL
comment: Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses.
synonym: "Isotope-coded protein label" EXACT []
is_a: PRIDE:0000316 ! MS1 based isotope labeling
created_by: jg
creation_date: 2011-07-22T09:34:37Z

[Term]
id: PRIDE:0000322
name: emPAI
comment: The Exponentially Modified Protein Abundance Index (emPAI) offers approximate, label-free, relative quantification of the proteins in a mixture based on protein coverage by the peptide matches in a database search result.
synonym: "Exponentially Modified Protein Abundance Index" EXACT []
is_a: PRIDE:0000312 ! Label free
created_by: jg
creation_date: 2011-07-22T09:36:57Z

[Term]
id: PRIDE:0000323
name: TIC
comment: The Total Ion Current (TIC) can be measured or calculated in order to target specific ions.
synonym: "Total Ion Current" EXACT []
is_a: PRIDE:0000312 ! Label free
created_by: jg
creation_date: 2011-07-22T09:38:17Z

[Term]
id: PRIDE:0000324
name: Quantification reagent
comment: A reagent used for quantification.
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000391 ! Quantification parameter
created_by: jg
creation_date: 2011-07-22T09:43:30Z

[Term]
id: PRIDE:0000325
name: SILAC heavy
comment: The heavy label used in SILAC experiments.
is_a: PRIDE:0000328 ! SILAC reagent
is_a: PRIDE:0000539 ! SILAC channel label
created_by: jg
creation_date: 2011-07-22T09:44:18Z

[Term]
id: PRIDE:0000326
name: SILAC light
comment: The light reagent used in SILAC experiments.
is_a: PRIDE:0000328 ! SILAC reagent
is_a: PRIDE:0000539 ! SILAC channel label
created_by: jg
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000327
name: SILAC medium
comment: The medium weight reagent used in SILAC experiments.
is_a: PRIDE:0000328 ! SILAC reagent
is_a: PRIDE:0000539 ! SILAC channel label
created_by: jg
creation_date: 2011-07-22T09:47:09Z

[Term]
id: PRIDE:0000328
name: SILAC reagent
comment: Reagent used in SILAC labeling.
is_a: PRIDE:0000433 ! Reagents used in Labeled Method
created_by: jg
creation_date: 2011-07-22T09:48:42Z

[Term]
id: PRIDE:0000329
name: iTRAQ reagent
comment: Reagent used in iTRAQ experiments.
is_a: PRIDE:0000433 ! Reagents used in Labeled Method
created_by: jg
creation_date: 2011-07-22T09:49:46Z

[Term]
id: PRIDE:0000330
name: Arbitrary quantification unit
comment: A unit describing values that can only be interpreted within the same spectrum but cannot be compared to values found in other spectra and or experiments.
is_a: PRIDE:0000392 ! Quantification unit
created_by: jg
creation_date: 2012-03-06T11:32:24Z

[Term]
id: PRIDE:0000331
name: Counts
comment: Quantification values reported as arbitrary counts (most often ion counts).
is_a: PRIDE:0000330 ! Arbitrary quantification unit
created_by: jg
creation_date: 2012-03-06T11:33:13Z

[Term]
id: PRIDE:0000337
name: TMT reagent
comment: Reagent used in TMT experiments.
is_a: PRIDE:0000433 ! Reagents used in Labeled Method
created_by: jg
creation_date: 2011-07-22T10:08:04Z

[Term]
id: PRIDE:0000344
name: ICAT reagent
comment: Reagent used in ICAT experiments.
is_a: PRIDE:0000433 ! Reagents used in Labeled Method
created_by: jg
creation_date: 2011-07-22T10:19:04Z

[Term]
id: PRIDE:0000345
name: ICAT light reagent
is_a: PRIDE:0000344 ! ICAT reagent
created_by: jg
creation_date: 2011-07-22T10:19:38Z

[Term]
id: PRIDE:0000346
name: ICAT heavy reagent
is_a: PRIDE:0000344 ! ICAT reagent
created_by: jg
creation_date: 2011-07-22T10:19:38Z

[Term]
id: PRIDE:0000347
name: ICPL reagent
comment: Reagent used in ICPL experiments.
is_a: PRIDE:0000433 ! Reagents used in Labeled Method
created_by: jg
creation_date: 2011-07-22T10:22:42Z

[Term]
id: PRIDE:0000348
name: ICPL 0 reagent
is_a: PRIDE:0000347 ! ICPL reagent
created_by: jg
creation_date: 2011-07-22T10:24:42Z

[Term]
id: PRIDE:0000349
name: ICPL 4 reagent
is_a: PRIDE:0000347 ! ICPL reagent
created_by: jg
creation_date: 2011-07-22T10:24:42Z

[Term]
id: PRIDE:0000350
name: ICPL 6 reagent
is_a: PRIDE:0000347 ! ICPL reagent
created_by: jg
creation_date: 2011-07-22T10:24:42Z

[Term]
id: PRIDE:0000351
name: ICPL 10 reagent
is_a: PRIDE:0000347 ! ICPL reagent
created_by: jg
creation_date: 2011-07-22T10:24:42Z

[Term]
id: PRIDE:0000352
name: Quantification value
comment: Parameters to report quantification values.
is_a: PRIDE:0000391 ! Quantification parameter
created_by: jg
creation_date: 2011-07-22T10:26:08Z

[Term]
id: PRIDE:0000353
name: Multiplexed quantification value
comment: Parameters describing quantification values for multiplexed samples.
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000352 ! Quantification value
created_by: jg
creation_date: 2011-07-22T10:26:33Z

[Term]
id: PRIDE:0000354
name: Intensity subsample 1
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000355
name: Intensity subsample 2
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000356
name: Intensity subsample 3
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000357
name: Intensity subsample 4
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000358
name: Intensity subsample 5
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000359
name: Intensity subsample 6
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000360
name: Intensity subsample 7
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000361
name: Intensity subsample 8
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T10:27:30Z

[Term]
id: PRIDE:0000362
name: Other quantification value
comment: Values from other quantification techniques.
is_a: PRIDE:0000352 ! Quantification value
created_by: jg
creation_date: 2011-07-22T10:55:31Z

[Term]
id: PRIDE:0000363
name: emPAI value
comment: The emPAI for the protein.
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000362 ! Other quantification value
created_by: jg
creation_date: 2011-07-22T10:55:56Z

[Term]
id: PRIDE:0000364
name: TIC value
comment: The Total Ion Count for the given entity.
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000362 ! Other quantification value
created_by: jg
creation_date: 2011-07-22T10:57:36Z

[Term]
id: PRIDE:0000365
name: Multiplexed sample description
comment: Describes multiples subsamples.
is_a: PRIDE:0000017 ! Sample description additional parameter
created_by: jg
creation_date: 2011-07-22T10:59:57Z

[Term]
id: PRIDE:0000366
name: Contains multiple subsamples
comment: Identifies samples that are made up of multiplexed subsamples.
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:00:32Z

[Term]
id: PRIDE:0000367
name: Subsample 1 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000368
name: Subsample 2 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000369
name: Subsample 3 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000370
name: Subsample 4 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000371
name: Subsample 5 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000372
name: Subsample 6 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000373
name: Subsample 7 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000374
name: Subsample 8 description
is_a: PRIDE:0000365 ! Multiplexed sample description
created_by: jg
creation_date: 2011-07-22T11:02:56Z

[Term]
id: PRIDE:0000375
name: Standard deviation subsample 1
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000376
name: Standard deviation subsample 2
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000377
name: Standard deviation subsample 3
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000378
name: Standard deviation subsample 4
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000379
name: Standard deviation subsample 5
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000380
name: Standard deviation subsample 6
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000381
name: Standard deviation subsample 7
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000382
name: Standard deviation subsample 8
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000383
name: Standard error subsample 1
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000384
name: Standard error subsample 2
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000385
name: Standard error subsample 3
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000386
name: Standard error subsample 4
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000387
name: Standard error subsample 5
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000388
name: Standard error subsample 6
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000389
name: Standard error subsample 7
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000390
name: Standard error subsample 8
is_a: PRIDE:0000353 ! Multiplexed quantification value
created_by: jg
creation_date: 2011-07-22T11:04:09Z

[Term]
id: PRIDE:0000391
name: Quantification parameter
comment: Quantification related parameter.
created_by: jg
creation_date: 2011-07-26T03:59:31Z

[Term]
id: PRIDE:0000392
name: Quantification unit
comment: Unit used to report quantification results.
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000391 ! Quantification parameter
created_by: jg
creation_date: 2011-07-26T04:00:17Z

[Term]
id: PRIDE:0000393
name: Relative quantification unit
comment: Unit to report relative quantification results.
is_a: PRIDE:0000392 ! Quantification unit
created_by: jg
creation_date: 2011-07-26T04:01:53Z

[Term]
id: PRIDE:0000394
name: Absolute quantification unit
comment: Unit used to describe absolute quantification results.
is_a: PRIDE:0000392 ! Quantification unit
created_by: jg
creation_date: 2011-07-26T04:02:29Z

[Term]
id: PRIDE:0000395
name: Ratio
comment: Quantification results represent ratios.
is_a: PRIDE:0000393 ! Relative quantification unit
created_by: jg
creation_date: 2011-07-26T04:12:44Z

[Term]
id: PRIDE:0000396
name: Copies per cell
comment: Quantification results are reported as copies per cell.
is_a: PRIDE:0000394 ! Absolute quantification unit
created_by: jg
creation_date: 2011-07-26T04:13:32Z

[Term]
id: PRIDE:0000397
name: Data derived from previous dataset
comment: One dataset is a reanalysis of previously published data
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000398
name: No PTMs are included in the dataset
comment: No post-translational-modifications are been included in the identified peptides of one dataset
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000399
name: Accepted manuscript
comment: A dataset has one associated manuscript, which has been accepted but no PubMedID is available yet.
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000400
name: Reference
xref: value-type:xsd\:string "The allowed value-type for this CV term."
comment: Literature reference associated with one dataset (including the authors, title, year and journal details). The value field can be used for the PubMedID, or to specify if one manuscript is just submitted or accepted, but it does not have a PubMedID yet.
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000401
name: Experimental information has been refined since this experiment was originally made publicly available
comment: This means that the experimental information available has been improved, for instance precursor charges were added.
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000402
name: Original data
comment: One dataset is not a reanalysis of previously published data
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000403
name: Associated file URI
comment: URI of one external file associated to the PRIDE experiment (maybe through a PX submission).
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000404
name: Associated raw file URI
comment: URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission).
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: jav

[Term]
id: PRIDE:0000405
name: Submit PRIDE Experiment to IntAct 
comment: Indicates that this PRIDE experiment contains interaction data and should be submitted to IntAct (maybe through a PX submission).
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: rc

[Term]
id: PRIDE:0000406
name: ProteomeCentral dataset URI
def: "URI associated to one PX submission in ProteomeCentral." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000407
name: Result file URI
def: "URI of one file labeled as 'Result', associated to one PX submission." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: jav

[Term]
id: PRIDE:0000408
name: Search engine output file URI
def: "URI of one search engine output file associated to one PX submission." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: jav

[Term]
id: PRIDE:0000409
name: Peak list file URI
def: "URI of one of one search engine output file associated to one PX submission." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: jav

[Term]
id: PRIDE:0000410
name: 'Other' type file URI
def: "URI of one file labeled as 'Other', associated to one PX submission." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: jav

[Term]
id: PRIDE:0000411
name: Dataset FTP location
def: "FTP location of one entire PX data set." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000412
name: Dataset with no associated published manuscript
def: "A dataset which does not have an associated published manuscript." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000413
name: Instrument name
def: "The value of this term (related to one PRIDE experiment) can be used to provide the name of instruments that are not included in any other CV yet." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000414
name: Peer-reviewed dataset
def: "Dataset has been peer-reviewed somehow." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000415
name: Non peer-reviewed dataset
def: "Dataset that has not been peer-reviewed by any means." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000416
name: Supported dataset by repository
def: "The PX dataset is supported by and is available through the submission repository." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000417
name: Unsupported dataset by repository
def: "The PX dataset is not fully supported by the submission repository." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000418
name: Other member of protein ambiguity group
def: "Accession of another protein that was assigned to the same protein ambiguity group. This term must be repeated to include all protein group members, except for itself." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
created_by: jav

[Term]
id: PRIDE:0000419
name: b ion -H3PO4
def: "B ion type with a neutral loss of a phosphate molecule." [PRIDE:PRIDE]
synonym: "b fragment ion -H3PO4" EXACT []
is_a: PRIDE:0000194 ! b ion

[Term]
id: PRIDE:0000420
name: b ion -2H3PO4
def: "B ion type with a neutral loss of 2 phosphate molecules." [PRIDE:PRIDE]
synonym: "b fragment ion -2H3PO4" EXACT []
is_a: PRIDE:0000194 ! b ion

[Term]
id: PRIDE:0000421
name: b ion -3H3PO4
def: "B ion type with a neutral loss of 3 phosphate molecules." [PRIDE:PRIDE]
synonym: "b fragment ion -3H3PO4" EXACT []
is_a: PRIDE:0000194 ! b ion

[Term]
id: PRIDE:0000422
name: y ion -H3PO4
def: "Y ion type with a neutral loss of a phosphate molecule." [PRIDE:PRIDE]
synonym: "y fragment ion -H3PO4" EXACT []
is_a: PRIDE:0000193 ! y ion

[Term]
id: PRIDE:0000423
name: y ion -2H3PO4
def: "Y ion type with a neutral loss of 2 phosphate molecules." [PRIDE:PRIDE]
synonym: "y fragment ion -2H3PO4" EXACT []
is_a: PRIDE:0000193 ! y ion

[Term]
id: PRIDE:0000424
name: y ion -3H3PO4
def: "Y ion type with a neutral loss of 3 phosphate molecules." [PRIDE:PRIDE]
synonym: "y fragment ion -3H3PO4" EXACT []
is_a: PRIDE:0000193 ! y ion

[Term]
id: PRIDE:0000425
name: MS1 intensity based label-free quantification method
is_a: PRIDE:0000309 ! Gel-free quantification method
created_by: rw

[Term]
id: PRIDE:0000426
name: Mass spectrometry proteomics experimental strategy
comment: The basic mass spectrometry strategy used in the experiment.
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: acsordas

[Term]
id: PRIDE:0000427
name: Top-down proteomics
comment: Proteins enter directly the mass spectrometer.
is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy
is_a: PRIDE:0000457 ! Experiment Type
created_by: acsordas

[Term]
id: PRIDE:0000428
name: Bottom-up proteomics
comment: Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer.
is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy
is_a: PRIDE:0000457 ! Experiment Type
created_by: acsordas

[Term]
id: PRIDE:0000429
name: MS/MS shotgun proteomics
comment: Bottom-up MS/MS shotgun experiment with data-dependent acquisition, using nomenclature in PMID 20622845, the method of choice for the a priori identification of the protein components of complex samples.
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: acsordas

[Term]
id: PRIDE:0000430
name: Chemical cross-linking coupled with mass spectrometry proteomics
comment: Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) to provide information about protein folding and protein-protein interaction.
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: acsordas

[Term]
id: PRIDE:0000431
name: Affinity purification coupled with mass spectrometry proteomics
comment: Affinity purification combined with mass spectrometry (AP-MS) has been used to understand protein-complex composition and protein-protein interaction.
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: acsordas

[Term]
id: PRIDE:0000432
name: Dataset with its publication pending
comment: A dataset which has an associated manuscript pending for publication.
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: rw

[Term]
id: PRIDE:0000433
name: Reagents used in Labeled Methods
comment: Labeled reagents used for quantification.
is_a: PRIDE:0000324 ! Quantification reagent
created_by: acsordas

[Term]
id: PRIDE:0000434
name: Unlabeled sample
comment: An unlabeled sample used for quantification.
is_a: PRIDE:0000324 ! Quantification reagent
created_by: acsordas

[Term]
id: PRIDE:0000435
name: Peptide counting
comment: Use of the number of peptides for an identified protein as a measure of abundance. Method reviewed in PMID 22772140.
is_a: PRIDE:0000312 ! Label free
created_by: acsordas

[Term]
id: PRIDE:0000436
name: Spectrum counting
comment: Use of the number of PSMs for an identified protein as a measure of abundance. Method reviewed in PMID 22772140
is_a: PRIDE:0000312 ! Label free
created_by: acsordas

[Term]
id: PRIDE:0000437
name: PAI
comment: Protein Abundance Index (PAI) is the number of identified peptides divided by the number of observable peptides. Method reviewed in PMID 22772140
is_a: PRIDE:0000312 ! Label free
created_by: acsordas

[Term]
id: PRIDE:0000438
name: Spectrum count/molecular weight
comment: Spectrum count is divided by the molecular weight of a protein. Method reviewed in PMID 22772140
is_a: PRIDE:0000312 ! Label free
created_by: acsordas

[Term]
id: PRIDE:0000439
name: SAF
comment: The spectrum count is normalized for protein length. Method reviewed in PMID 22772140
is_a: PRIDE:0000312 ! Label free
created_by: acsordas

[Term]
id: PRIDE:0000440
name: NSAF
comment: Spectral Abundance Factor normalized for the sum of all protein abundances in the sample. Method reviewed in PMID 22772140
is_a: PRIDE:0000312 ! Label free
created_by: acsordas

[Term]
id: PRIDE:0000441
name: APEX - Absolute Protein Expression
comment: Spectrum counting method using machine learning classification to derive peptide detection probabilities to predict detectable peptides for any protein. Method reviewed in PMID 22772140
is_a: PRIDE:0000312 ! Label free
created_by: acsordas

[Term]
id: PRIDE:0000442
name: Tissue not applicable to dataset
def: "Tissue not applicable to dataset." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: rw

[Term]
id: PRIDE:0000443
name: Original NCBI Peptidome submission files
def: "The NCBI FTP location of the original Sample - Experiment level Peptidome submission data." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: acsordas

[Term]
id: PRIDE:0000444
name: PRIDE experiment accession
def: "Accession number of a given PRIDE experiment (called assay in the PRIDE-3 system)." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: jav

[Term]
id: PRIDE:0000445
name: PRIDE Cluster score
def: "It is an integer that gives an indication about the quality of a peptide spectrum match in PRIDE-Q. It uses the PRIDE-Cluster algorithm (described in PMID: 23361086) and different criteria to assign it (number of spectra in a cluster, ratio of the predominant peptide identification in the cluster, etc)." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
created_by: jav

[Term]
id: PRIDE:0000446
name: PRIDE peptide score
def: "Score used in PRIDE-Q to give an indication of the quality of a peptide spectrum match. It is described in PMID:16964243." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
created_by: jav

[Term]
id: PRIDE:0000447
name: SWATH MS
def: "ABsciex Data Independent Acquisition method that consists of unfractionated samples acquisition by using duty cycles adapted to HPLC chromatography, acquiring sequential wide fragment ions spectra, typically covering the precursor mass space from 400 m/z to 1200 m/z on each duty cycle. Acquired data is interrogated by using libraries of peptide coordinates (normalised elution time, fragment ion masses and intensities). It is described in PMID:22261725." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition
created_by: jav

[Term]
id: PRIDE:0000448
name: Additional associated raw file URI
comment: Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: jav

[Term]
id: PRIDE:0000449
name: Gel image file URI
comment: URI of one gel image file associated to one PX submission.
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: tt


[Term]
id: PRIDE:0000450
name: Data-independent acquisition
def: "Predefined m/z ranges are interrogated either by fragmenting all ions entering the mass spectrometer at every single point in chromatographic time; or by dividing the m/z range into smaller m/z ranges for isolation and fragmentation. See review in PMID:24281846." [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: acsordas

[Term]
id: PRIDE:0000451
name: MSE
def: "Waters data independent acquisition method based on UPLC chromatography and MS acquisition of cycles of two spectra, in low and high energy respectively, in a QQ-TOF instrument. It is described in PMID: 16755610." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition
created_by: acsordas


[Term]
id: PRIDE:0000452
name: HDMSE
def: "Waters data independent acquisition method, which consists of using an additional on-line separation dimension (Ion Mobility drift) and an MSE acquisition. It is described in PMID: 22811061." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition
created_by: acsordas


[Term]
id: PRIDE:0000453
name: PAcIFIC
def: "Precursor Acquisition Independent From Ion Count. A Data Independent Acquisition method performed in ion traps that consists of the acquisition of 2.5 m/z width sequential windows over several injections of the same material, until a precursor m/z range of about 400 to 1200 m/z is covered. It is described in PMID: 21341720." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition
created_by: acsordas


[Term]
id: PRIDE:0000454
name: All-ion fragmentation
def: "MS Data Independent Acquisition performed in Thermo Orbitrap instruments. It consists of the acquisition of cycles of two spectra, a precursor mass MS1 spectrum, and a fragment ions MS2 spectrum where a wide mass filter (typically over 800 m/z) is applied to the precursors. It is described in PMID: 20610777." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition
created_by: acsordas

[Term]
id: PRIDE:0000455
name: Protein-protein cross-linking experiment
comment: Protein-protein cross-linking experiment to provide information about protein folding and protein-protein interaction.
is_a: PRIDE:0000430 ! Chemical cross-linking coupled with mass spectrometry proteomics
created_by: acsordas

[Term]
id: PRIDE:0000456
name: Protein-RNA cross-linking experiment
comment: Protein-RNA cross-linking experiment to provide information about Protein-RNA interaction.
is_a: PRIDE:0000430 ! Chemical cross-linking coupled with mass spectrometry proteomics
created_by: acsordas

[Term]
id: PRIDE:0000457
name: Experiment Type
comment: Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method.

[Term]
id: PRIDE:0000458
name: Metaproteomics
def: "Studying all protein samples of diverse host environments like the human body, soil or sea water." [PRIDE:PRIDE]
is_a: PRIDE:0000457 ! Experiment Type
synonym: "Community Proteomics" EXACT []
synonym: "Environmental Proteomics" RELATED []
created_by: acsordas

[Term]
id: PRIDE:0000459
name: Human Metaproteomics
def: "Investigating both human host proteins and associated microbial proteins at the same time from human samples." [PRIDE:PRIDE]
is_a: PRIDE:0000458 ! Metaproteomics
created_by: acsordas

[Term]
id: PRIDE:0000460
name: Proteogenomics
comment: "Studies that use proteomic information to improve genome annotation. Proteogenomics approaches are also increasingly used in personalised medicine studies."
is_a: PRIDE:0000457 ! Experiment Type
created_by: acsordas

[Term]
id: PRIDE:0000461
name: Multi-omics study
def: "Studies that use various omics methods like proteomics, genomics, transcriptomics, metabolomics to analyse the same biological samples." [PRIDE:PRIDE]
is_a: PRIDE:0000457 ! Experiment Type
created_by: acsordas

[Term]
id: PRIDE:0000462
name: SONAR
def: "Waters data independent acquisition method." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition 
created_by: acsordas

[Term]
id: PRIDE:0000463
name: PRM
def: "Using Selected Reaction Monitoring (SRM) with parallel detection of all transitions in a single analysis." [PRIDE:PRIDE]
is_a: PRIDE:0000311 ! Selected Reaction Monitoring

[Term]
id: PRIDE:0000464
name: Fasta file URI
comment: URI of one external Fasta file associated to the PRIDE experiment (maybe through a PX submission).
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: ypriverol

[Term]
id: PRIDE:0000465
name: Spectral Library file URI
comment: URI of one external Spectral Library file associated to the PRIDE experiment (maybe through a PX submission).
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: ypriverol

[Term]
id: PRIDE:0000466
name: Quantification result file URI
comment: URI of one external Quantification file associated to the PRIDE experiment (maybe through a PX submission).
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: ypriverol

[Term]
id: PRIDE:0000467
name: MS Image file URI
comment: URI of one external Mass spectrometry Image file associated to the PRIDE experiment (maybe through a PX submission).
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: ypriverol

[Term]
id: PRIDE:0000468
name: Aspera Protocol
comment: URI for an Aspera Download Protocol
xref: value-type:xsd\:string "The allowed value-type for this CV term."
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: ypriverol

[Term]
id: PRIDE:0000469
name: FTP Protocol
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: ypriverol
creation_date: 2018-08-29T14:26:28Z

[Term]
id: PRIDE:0000470
name: File Properties
def: "PRIDE File Properties for all type of files." [PRIDE:PRIDE]
created_by: ypriverol
creation_date: 2018-08-29T14:26:28Z

[Term]
id: PRIDE:0000471
name: MS File Properties
def: "Properties for MS , Peaks files" [PRIDE:PRIDE]
is_a: PRIDE:0000470 ! File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:31:06Z

[Term]
id: PRIDE:0000472
name: MS min charge
def: "Minimum charge for all precursor in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:33:01Z

[Term]
id: PRIDE:0000473
name: MS max charge
def: "Maximum charge for all precursor in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:35:57Z

[Term]
id: PRIDE:0000474
name: MS min RT
def: "Minimum retention time in the File." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:36:50Z

[Term]
id: PRIDE:0000475
name: MS max RT
def: "Maximum retention time in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:37:30Z

[Term]
id: PRIDE:0000476
name: MS min MZ
def: "Minimum precursor mass to charge in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:38:19Z

[Term]
id: PRIDE:0000477
name: MS max MZ
def: "Maximum precursor mass to charge in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:39:06Z

[Term]
id: PRIDE:0000478
name: Number of scans
def: "Total number of scans in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:40:05Z

[Term]
id: PRIDE:0000479
name: MS scan range
def: "Range of scan number in the ms file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:41:09Z

[Term]
id: PRIDE:0000480
name: Number of MS
def: "Number of MS in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:43:09Z

[Term]
id: PRIDE:0000481
name: Number of MS1 spectra
def: "Number of MS1 spectra." [PRIDE:PRIDE]
is_a: PRIDE:0000480 ! Number of MS
created_by: ypriverol
creation_date: 2018-08-29T14:45:21Z

[Term]
id: PRIDE:0000482
name: Number of MS2 spectra
def: "Number of MS2 spectra in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000480 ! Number of MS
created_by: ypriverol
creation_date: 2018-08-29T14:46:01Z

[Term]
id: PRIDE:0000483
name: Number of MS3 spectra
def: "Total number of MS3 spectra in the file." [PRIDE:PRIDE]
is_a: PRIDE:0000480 ! Number of MS
created_by: ypriverol
creation_date: 2018-08-29T14:48:35Z

[Term]
id: NCIT:C69199
name: Content Creation date
def: "The date on which data creation began [NCI]" [PRIDE:PRIDE]
is_a: PRIDE:0000470 ! File Properties
created_by: ypriverol
creation_date: 2018-08-29T14:52:49Z

[Term]
id: PRIDE:0000484
name: Result analysis parameters
def: "The result analysis parameters is a term to group all the parameters for proteomics data analysis." [PRIDE:PRIDE]
created_by: yperez
creation_date: 2018-09-05T09:08:58Z

[Term]
id: PRIDE:0000485
name: Global result parameters
def: "Result analysis parameters share by multiple search engine and Quantiative tools." [PRIDE:PRIDE]
is_a: PRIDE:0000484 ! Result analysis parameters
created_by: yperez
creation_date: 2018-09-05T09:11:41Z

[Term]
id: PRIDE:0000486
name: Tool specific analysis parameters
is_a: PRIDE:0000484 ! Result analysis parameters
created_by: yperez
creation_date: 2018-09-05T09:14:02Z

[Term]
id: PRIDE:0000487
name: Min charge
def: "Minimum charge of precursor to be search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:26:36Z

[Term]
id: PRIDE:0000488
name: Max charge
def: "Maximum charge of precursor to be search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:28:29Z

[Term]
id: PRIDE:0000489
name: Min RT
def: "Min Retention time for precursor to be search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:30:51Z

[Term]
id: PRIDE:0000490
name: Max RT
def: "Maximum precursor RT to be search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:31:35Z

[Term]
id: PRIDE:0000491
name: Number of missed cleavages
def: "Number of missed cleavages." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:37:09Z

[Term]
id: PRIDE:0000492
name: Max peptide AA length
def: "Max peptide amino acid length for search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:43:03Z

[Term]
id: PRIDE:0000493
name: Min peptide AA length
def: "Minimum peptide amino acid length for search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:43:54Z

[Term]
id: PRIDE:0000494
name: Min precursor MZ
def: "Min precursor MZ (mass) for precursor to search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:47:03Z

[Term]
id: PRIDE:0000495
name: Max precursor MZ
def: "Max precursor MZ (mass) for precursor to search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T09:48:08Z

[Term]
id: PRIDE:0000496
name: Min peak length
def: "Min number of peaks in the spectrum to be search." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000497
name: Use Multi Modification
def: "Use Multi Modification"[PRIDE:PRIDE] 
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000498
name: Use Additional Variable Modifications
def: "Use Additional Variable Modifications" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000499
name: Do Mass Filtering
def: "Do Mass Filtering" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000500
name: Intensity Threshold
def: "Intensity Threshold" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000501
name: Max Labeled AA
def: "Max Labeled AA" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000502
name: Max Number of Modifications (PTMs)
def: "Max Number of Modifications (PTMs)" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000503
name: First Search Precursor Tolerance
def: "First Search Precursor Tolerance" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000504
name: Main Search Precursor Tolerance
def: "Main Search Precursor Tolerance" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000505
name: Individual Accession
def: "Accession or Code of the individual in the sample." [PRIDE:PRIDE]
is_a: PRIDE:0000017 !  Sample description additional parameter
created_by: yperez
creation_date: 2018-09-05T10:38:29Z

[Term]
id: PRIDE:0000506
name: Number identified proteins
def: "Total number of reported proteins. This property can be used to report the number of proteins identified in an Assay or experiment." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2019-06-06T13:51:41Z

[Term]
id: PRIDE:0000507
name: Number of identified peptides
def: "Total number of identified peptides in an experiment or assay." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2019-06-06T13:53:23Z

[Term]
id: PRIDE:0000508
name: Number of modified peptides
def: "The total number of peptides identified with post-translational modifications." [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2019-06-06T13:54:46Z

[Term]
id: PRIDE:0000509
name: Number of PSMs
def: "Total number of reported identified Peptide Spectrum matches (PSMs)" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters
created_by: yperez
creation_date: 2019-06-06T13:56:00Z

[Term]
id: PRIDE:0000510
name: File size
def: "The size of the file in MB." [PRIDE:PRIDE]
is_a: PRIDE:0000470 ! File Properties
created_by: mwalzer
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000511
name: Pass submitter threshold
def: "Pass submitter threshold" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000512
name: RNA mass spectrometry
def: "RNA mass spectrometry" [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000513
name: Dimethyl Labeling
def: "Dimethyl Labeling (DML)" [PRIDE:PRIDE]
is_a: PRIDE:0000310 ! Isotope labeling
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000514
name: Label
def: "Quantification channel label" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000515
name: TMT
def: "TMT" [PRIDE:PRIDE]
is_a: PRIDE:0000514 ! Quantification channel label
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000516
name: TMT126
def: "TMT126" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000517
name: TMT127
def: "TMT127" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000518
name: TMT127C
def: "TMT127C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000519
name: TMT127N
def: "TMT127N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000520
name: TMT128
def: "TMT128" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000521
name: TMT128C
def: "TMT128C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000522
name: TMT128N
def: "TMT128N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000523
name: TMT129
def: "TMT129" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000524
name: TMT129C
def: "TMT129C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000525
name: TMT129N
def: "TMT129N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000526
name: TMT130
def: "TMT130" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000527
name: TMT130C
def: "TMT130C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000528
name: TMT130N
def: "TMT130N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000529
name: TMT131
def: "TMT131" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000530
name: ITRAQ
def: "ITRAQ channel label" [PRIDE:PRIDE]
is_a: PRIDE:0000514 ! Quantification channel label
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000531
name: ITRAQ113
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:02:43Z

[Term]
id: PRIDE:0000532
name: ITRAQ114
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:03:15Z

[Term]
id: PRIDE:0000533
name: ITRAQ115
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:03:31Z

[Term]
id: PRIDE:0000534
name: ITRAQ116
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:03:49Z

[Term]
id: PRIDE:0000535
name: ITRAQ117
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:04:10Z

[Term]
id: PRIDE:0000536
name: ITRAQ118
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:04:30Z

[Term]
id: PRIDE:0000537
name: ITRAQ119
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:04:49Z

[Term]
id: PRIDE:0000538
name: ITRAQ121
is_a: PRIDE:0000530 ! ITRAQ
created_by: yperez
creation_date: 2020-03-16T18:05:06Z

[Term]
id: PRIDE:0000539
name: SILAC
def: "SILAC channel label" [PRIDE:PRIDE]
is_a: PRIDE:0000514 ! Quantification channel label
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000540
name: ICAT
def: "ICAT channel label" [PRIDE:PRIDE]
is_a: PRIDE:0000514 ! Quantification channel label
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000541
name: ICAT heavy
def: "ICAT heavy" [PRIDE:PRIDE]
is_a: PRIDE:0000540 ! ICAT channel label
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000542
name: ICAT light
def: "ICAT light" [PRIDE:PRIDE]
is_a: PRIDE:0000540 ! ICAT channel label
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000543
name: Quality Control
def: "MS experiments conducted to control the quality of measurements. Includes the acquisition of samples for SST and longitudinal monitoring." [PRIDE:PRIDE]
comment: Example description of such experiments in 10.1002/pmic.201000578
is_a: PRIDE:0000457 ! Experiment Type

[Term]
id: PRIDE:0000544
name: Quality Control Sample
def: "Sample with known content and quantities designed to control the consistent quality of measurement for a particular method and settings." [PRIDE:PRIDE]
comment: Example description of such samples in 10.1002/pmic.201000578
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000545
name: QC1 sample
def: "QC1 sample as described in 10.1371/journal.pone.0189209." [PRIDE:PRIDE]
is_a: PRIDE:0000544 ! Quality Control Sample

[Term]
id: PRIDE:0000546
name: QC2 sample
def: "QC2 sample as described in 10.1371/journal.pone.0189209." [PRIDE:PRIDE]
is_a: PRIDE:0000544 ! Quality Control Sample


[Term]
id: PRIDE:0000547
name: Instrument properties
def: "Instrument properties" [PRIDE:PRIDE]
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: MS:1000451
name: mass analyzer
def: "mass analyzer" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000548
name: MS1 mass analyzer
def: "MS1 mass analyzer" [PRIDE:PRIDE]
is_a: MS:1000451 ! mass analyzer
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000549
name: MS2 mass analyzer
def: "MS2 mass analyzer" [PRIDE:PRIDE]
is_a: MS:1000451 ! mass analyzer
created_by: yperez
creation_date: 2020-03-16T18:01:06Z

[Term]
id: PRIDE:0000550
name: Fractionation method
def: "Umbrella term for different types of fractionation methods." [PRIDE:PRIDE]
is_a: PRIDE:0000021 ! Fractionation

[Term]
id: PRIDE:0000551
name: Separation method
def: "Umbrella term for different types of fractionation methods." [PRIDE:PRIDE]
is_a: PRIDE:0000022 ! Separation

[Term]
id: PRIDE:0000552
name: Off-gel electrophoresis
def: "Fractionate peptides into discrete liquid fractions based on isoelectric electrophoresis (10.1002/elps.200390030)." [PRIDE:PRIDE]
is_a: PRIDE:0000550 ! Fractionation method

[Term]
id: PRIDE:0000553
name: Isoelectric focusing
def: "An electrophoresis method for the separation of amphoteric analytes according to their isoelectric points by the application of an electric field along a pH gradient." [PRIDE:PRIDE]
is_a: PRIDE:0000550 ! Fractionation method

[Term]
id: PRIDE:0000554
name: Hydrophilic interaction chromatography (HILIC)
def: "Liquid chromatography where the stationary phase is hydrophilic, the mobile phase is organic and separation is achieved based on polarity." [PRIDE:PRIDE]
is_a: PRIDE:0000562 ! Normal-phase liquid chromatography (NP)


[Term]
id: PRIDE:0000555
name: ERLIC
def: "Electrostatic repulsion hydrophilic interaction chromatography (ERLIC). Hydrophilic interaction chromatography where the chromatography column is an ion-exchange column and the mobile phase is predominantly organic." [PRIDE:PRIDE]
is_a: PRIDE:0000562 ! Normal-phase liquid chromatography (NP)

[Term]
id: PRIDE:0000556
name: Ion-exchange chromatography 
def: "A chromatography method where the separation is caused by differences in ion-exchange affinity." [PRIDE:PRIDE]
is_a: PRIDE:0000565 ! High-performance liquid chromatography

[Term]
id: PRIDE:0000557
name: Size-exclusion chromatography (SEC)
def: "A chromatography method where the separation is caused by differences in molecular size." [PRIDE:PRIDE]
is_a: PRIDE:0000565 ! High-performance liquid chromatography

[Term]
id: PRIDE:0000558
name: Strong anion-exchange chromatography (SAX)
def: "A chromatography method with the stationary phase being a strong anion exchanger." [PRIDE:PRIDE]
is_a: PRIDE:0000556 ! Ion-exchange chromatography

[Term]
id: PRIDE:0000559
name: Weak anion-exchange chromatography (WAX)
def: "A chromatography method with the stationary phase being a weak anion exchanger." [PRIDE:PRIDE]
is_a: PRIDE:0000556 ! Ion-exchange chromatography

[Term]
id: PRIDE:0000560
name: Weak cation-exchange chromatography (WCX)
def: "A chromatography method with the stationary phase being a weak cation exchanger." [PRIDE:PRIDE]
is_a: PRIDE:0000556 ! Ion-exchange chromatography

[Term]
id: PRIDE:0000561
name: Strong cation-exchange chromatography (SCX)
def: "A chromatography method with the stationary phase being a strong cation exchanger." [PRIDE:PRIDE]
is_a: PRIDE:0000556 ! Ion-exchange chromatography

[Term]
id: PRIDE:0000562
name: Normal-phase liquid chromatography (NP)
def: "Liquid chromatography where the stationary phase is more polar than the mobile phase. This is the default for liquid chromatography." [PRIDE:PRIDE]
is_a: PRIDE:0000565 ! High-performance liquid chromatography

[Term]
id: PRIDE:0000563
name: Reversed-phase chromatography (RP)
def: "Liquid chromatography where the mobile phase is significantly more polar than the stationary phase." [PRIDE:PRIDE]
is_a: PRIDE:0000565 ! High-performance liquid chromatography

[Term]
id: PRIDE:0000564
name: High-pH reversed-phase chromatography (hpHRP)
def: "Liquid chromatography where the mobile phase is of high pH and significantly more polar than the stationary phase." [PRIDE:PRIDE]
is_a: PRIDE:0000563 ! Reversed-phase chromatography (RP)

[Term]
id: PRIDE:0000565
name: High-performance liquid chromatography
def: "Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small particles and the inlet pressure is relatively high." [PRIDE:PRIDE]
xref: http://purl.obolibrary.org/obo/CHMO_0001009
is_a: PRIDE:0000550 ! Fractionation method
is_a: PRIDE:0000551 ! Separation method

[Term]
id: PRIDE:0000566
name: High-resolution isoelectric focusing (HiRIEF)
def: "An electrophoresis method with significantly higher resolution than common isoelectric focusing methods." [PRIDE:PRIDE]
is_a: PRIDE:0000553 ! Isoelectric focusing

[Term]
id: PRIDE:0000567
name: Gel electrophoresis
def: "Gel electrophoresis" [PRIDE:PRIDE]
is_a: PRIDE:0000550 ! Fractionation method [PRIDE:PRIDE]
is_a: PRIDE:0000551 ! Separation method

[Term]
id: PRIDE:0000568
name: SDS PAGE
def: "SDS-PAGE is an electrophoresis method that allows protein separation by mass. The medium/matrix is a polyacrylamide-based discontinuous gel" [PRIDE:PRIDE]
is_a: PRIDE:0000567 ! Gel electrophoresis

[Term]
id: PRIDE:0000569
name: 2D PAGE
def: "2D-PAGE is a form of gel electrophoresis in which separation and identification of proteins in a sample are done by displacement in 2 dimensions oriented at right angles to one another(orthogonal)" [PRIDE:PRIDE]
is_a: PRIDE:0000567 ! Gel electrophoresis

[Term]
id: PRIDE:0000570
name: Decoy protein
def: "Indicates that this protein identification comes from the used decoy database." [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
created_by: yperez
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000571
name: Quantification software
def: "A software that perform protein quantification using mass spectrometry data." [PRIDE:PRIDE]
created_by: yperez
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000572
name: OpenMS
def: "OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software." [PRIDE:PRIDE]
is_a: PRIDE:0000571 ! Quantification software
is_a: PRIDE:0000573 ! Identification software
created_by: yperez
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000573
name: Identification software
def: "A software that perform peptide/protein identification using mass spectrometry data." [PRIDE:PRIDE]
created_by: yperez
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000574
name: MaxQuant
def: "MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data." [PRIDE:PRIDE]
is_a: PRIDE:0000571 ! Quantification software
is_a: PRIDE:0000573 ! Identification software
created_by: yperez
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000575
name: precursor mass tolerance
def: "Threshold at precursor level to compare experimental mass with theoretical mass" [PRIDE:PRIDE]
created_by: yperez
is_a: PRIDE:0000003 ! Peptide item additional parameter
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000576
name: fragment mass tolerance
def: "Threshold at fragment level to compare experimental mass with theoretical mass" [PRIDE:PRIDE]
created_by: yperez
is_a: PRIDE:0000003 ! Peptide item additional parameter
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000577
name: file uri
def: "URI of one external file associated to the PRIDE experiment (maybe through a PX submission)" [PRIDE:PRIDE]
created_by: yperez
is_a: PRIDE:0000006 ! Experiment additional parameter
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000578
name: Bound fraction
def: "The bound fraction after a depletion process" [PRIDE:PRIDE]
created_by: lisavetasol
is_a: PRIDE:0000020 ! Depletion

[Term]
id: PRIDE:0000579
name: Depleted fraction
def: "The depleted fraction after a depletion process" [PRIDE:PRIDE]
created_by: lisavetasol
is_a: PRIDE:0000020 ! Depletion

[Term]
id: MS:1002038
name: label free sample
def: "A sample that has not been labelled or modified" [PRIDE:PRIDE]
created_by: yperez
is_a: PRIDE:0000514 ! Quantification channel label
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000580
name: TMT131N
def: "TMT131N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000581
name: TMT131C
def: "TMT131C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000582
name: TMT132N
def: "TMT132N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000583
name: TMT132C
def: "TMT132C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000584
name: Experimental design file URI
def: "Experimental design file URI" [PRIDE:PRIDE]
is_a: PRIDE:0000403 ! Associated file URI
is_a: PRIDE:0000577 ! file uri
created_by: yperez
creation_date: 2019-08-07T15:21:19Z

[Term]
id: PRIDE:0000585
name: Enrichment
def: "Enrichment of specific post-translational modifications" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000586
name: Enrichment method
def: "Enrichment method Enrichment of specific post-translational modifications" [PRIDE:PRIDE]
is_a: PRIDE:0000585 ! Enrichment

[Term]
id: PRIDE:0000587
name: IMAC
def: "The combination of immobilized metal affinity chromatography (IMAC) and mass spectrometry is a widely used technique for enrichment and sequencing of phosphopeptides" [PRIDE:PRIDE]
is_a: PRIDE:0000586 ! Enrichment method

[Term]
id: PRIDE:0000588
name: TIO2
def: "Titanium dioxide (TiO2) has very high affinity for phosphopeptides and in recent years it has become one of the most popular methods for phosphopeptide enrichment from complex biological samples" [PRIDE:PRIDE]
is_a: PRIDE:0000586 ! Enrichment method

[Term]
id: MS:1000044
name: dissociation method
def: "Fragmentation method used for dissociation or fragmentation" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000589
name: EThcD
def: "A dissociation process combining electron-transfer and higher-energy collision dissociation (EThcD). It combines ETD (reaction time) followed by HCD (activation energy)." [PRIDE:PRIDE]
is_a: MS:1000044 ! dissociation method
is_a: PRIDE:0000644 ! MS2 dissociation method
is_a: PRIDE:0000645 ! MS3 dissociation method

[Term]
id: PRIDE:0000590
name: HCD
def: "beam-type collision-induced dissociation" [PRIDE:PRIDE]
is_a: MS:1000044 ! dissociation method
is_a: PRIDE:0000644 ! MS2 dissociation method
is_a: PRIDE:0000645 ! MS3 dissociation method

[Term]
id: PRIDE:0000591
name: CID
def: "collision-induced dissociation" [PRIDE:PRIDE]
is_a: MS:1000044 ! dissociation method
is_a: PRIDE:0000644 ! MS2 dissociation method
is_a: PRIDE:0000645 ! MS3 dissociation method

[Term]
id: PRIDE:0000592
name: ETciD
def: "ETD with supplemental activation" [PRIDE:PRIDE]
synonym: "ETcaD" EXACT []
is_a: MS:1000044 ! dissociation method
is_a: PRIDE:0000644 ! MS2 dissociation method
is_a: PRIDE:0000645 ! MS3 dissociation method

[Term]
id: MS:1000045
name: collision energy
def: "Energy for an ion experiencing collision with a stationary gas particle resulting in dissociation of the ion." [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000593
name: CID collision energy
def: "CID collision energy" [PRIDE:PRIDE]
is_a: MS:1000045 ! collision energy
relationship: part_of PRIDE:0000591 ! CID

[Term]
id: PRIDE:0000594
name: HCD collision energy
def: "HCD collision energy" [PRIDE:PRIDE]
is_a: MS:1000045 ! collision energy
relationship: part_of PRIDE:0000590 ! HCD

[Term]
id: PRIDE:0000595
name: EThcD collision energy
def: "EThcD collision energy" [PRIDE:PRIDE]
is_a: MS:1000045 ! collision energy
relationship: part_of PRIDE:0000589 ! EThcD

[Term]
id: PRIDE:0000596
name: ETciD collision energy
def: "ETciD collision energy" [PRIDE:PRIDE]
is_a: MS:1000045 ! collision energy
relationship: part_of PRIDE:0000592 ! ETciD

[Term]
id: PRIDE:0000597
name: metabolic label
def: "metabolic label" [PRIDE:PRIDE]
created_by: yperez
is_a: PRIDE:0000514 ! Quantification channel label
creation_date: 2020-05-12T11:58:52Z

[Term]
id: PRIDE:0000598
name: Alkylation reagent
def: "The alkylation reagent that is used to covalently modify cysteine SH-groups after reduction, preventing them from forming unwanted novel disulfide bonds" [PRIDE:PRIDE]
is_a: PRIDE:0000026 ! Alkylation
created_by: lisavetasol

[Term]
id: PRIDE:0000599
name: Iodoacetamide (IAA)
def: "The alkylation reagent 2-iodoacetamide with the chemical formula - C2H4INO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000600
name: Chloroacetamide (ClAA)
def: "The alkylation reagent 2-chloroacetamide with the chemical formula - C2H4ClNO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 4) - 57.021 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000601
name: Iodoacetic acid (IAC)
def: "The derivative of acetic acid with the chemical formula - C2H3IO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000602
name: Chloroacetic acid (ClAC)
def: "The derivative of acetic acid with the chemical formula - C2H3ClO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 6)- 58.005 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000603
name: Acrylamide (AA)
def: "The alkylation reagent acrylamide (or acrylic amide) with the chemical formula - C3H5NO. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 24) - 71.037 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000604
name: 4-Vinylpyridine (4-VP)
def: "The derivative of pyridine with a vinyl group in the 4-position with the chemical formula - C7H7N. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 31) - 105.058 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000605
name: Methyl methanethiosulfonate (MMTS)
def: "The alkylation reagent that can reversibly sulfenylate thiol-containing molecules, chemical formula - C2H6O2S2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 39) - 45.988 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000606
name: N-ethylmaleimide (NEM)
def: "The derivative of maleic acid, chemical formula - C6H7NO2. The corresponding mass shift at the cysteine residue (UNIMODE Accession # 108) - 125.048 Da" [PRIDE:PRIDE]
is_a: PRIDE:0000598 ! Alkylation reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000607
name: Reduction reagent
def: "The chemical reagent that is used to break disulfide bonds in proteins" [PRIDE:PRIDE]
is_a: PRIDE:0000025 ! Reduction
created_by: lisavetasol

[Term]
id: PRIDE:0000608
name: Dithiothreitol (DTT)
def: "The commonly used small redox reagent dithiothreitol (also known as Cleland's reagent) with chemical formula C4H10O2S2" [PRIDE:PRIDE]
is_a: PRIDE:0000607 ! Reduction reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000609
name: Tris(2-carboxyethyl)phosphine (TCEP)
def: "The reduction agent with chemincal formuls C9H15O6P" [PRIDE:PRIDE]
is_a: PRIDE:0000607 ! Reduction reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000610
name: Beta-mercaptoethanol (BME)
def: "The reduction agent 2-mercaptoethanol (2-sulfanylethan-1-ol) with chemincal formuls C2H6OS" [PRIDE:PRIDE]
is_a: PRIDE:0000607 ! Reduction reagent
created_by: lisavetasol

[Term]
id: PRIDE:0000611
name: SILAC light R:12C(6)14N(4)
comment: The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4)
is_a: PRIDE:0000326 ! SILAC light
created_by: yperez
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000612
name: SILAC light L:12C(6)
comment: The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6)
is_a: PRIDE:0000326 ! SILAC light
created_by: yperez
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000613
name: SILAC light K:12C(6)14N(2)
comment: The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2)
is_a: PRIDE:0000326 ! SILAC light
created_by: yperez
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000614
name: SILAC light P:12C(5)
comment: The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5)
is_a: PRIDE:0000326 ! SILAC light
created_by: yperez
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000615
name: SILAC heavy R:13C(6)15N(4)
comment: The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4)
is_a: PRIDE:0000325 !  SILAC heavy
created_by: yperez
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000616
name: SILAC heavy L:13C(6)
comment: The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)
is_a: PRIDE:0000325 !  SILAC heavy
created_by: yperez
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000617
name: SILAC heavy K:13C(6)15N(2)
comment: The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2)
is_a: PRIDE:0000325 !  SILAC heavy
created_by: yperez
creation_date: 2011-07-22T09:45:40Z

[Term]
id: PRIDE:0000618
name: SILAC medium R:13C(6)14N(4)
comment: The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4).
is_a: PRIDE:0000327 ! SILAC medium
created_by: yperez
creation_date: 2011-07-22T09:47:09Z

[Term]
id: PRIDE:0000619
name: SILAC medium K:13C(6)14N(2)
comment: The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2).
is_a: PRIDE:0000327 ! SILAC medium
created_by: yperez
creation_date: 2011-07-22T09:47:09Z

[Term]
id: PRIDE:0000620
name: 15N
comment: Metabolic label 15N
is_a: PRIDE:0000597 ! metabolic label
created_by: yperez
creation_date: 2011-07-22T09:47:09Z

[Term]
id: PRIDE:0000621
name: 13C
comment: Metabolic label 13C
is_a: PRIDE:0000597 ! metabolic label
created_by: yperez
creation_date: 2011-07-22T09:47:09Z

[Term]
id: PRIDE:0000622
name: 18O
comment: Metabolic label 18O
is_a: PRIDE:0000597 ! metabolic label
created_by: yperez
creation_date: 2011-07-22T09:47:09Z

[Term]
id: PRIDE:0000623
name: original source name
comment: Reference to the Sample. This term is use for cross-reference samples in SDRF for proteomics
is_a: PRIDE:0000006 ! Experiment additional parameter
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000624
name: SpectraCluster MaxRatio
comment: Spectra Cluster Maximum Ratio for the cluster
is_a: PRIDE:0000049 ! Peptide search engine output parameter
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000625
name: NIST ProbCorr
comment: NIST Probability Correlation
is_a: PRIDE:0000049 ! Peptide search engine output parameter
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000626
name: NIST Dotbest
comment: NIST best dot product
is_a: PRIDE:0000049 ! Peptide search engine output parameter
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000627
name: Data-dependent acquisition
comment: Data-dependent acquisition
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000629
name: Parallel reaction monitoring
comment: Parallel Reaction Monitoring (PRM)
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000630
name: Selected reaction monitoring
comment: Selected reaction monitoring (SRM)
is_a: PRIDE:0000428 ! Bottom-up proteomics
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000631
name: Mass spectrometry imaging
comment: Mass spectrometry imaging
is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy
created_by: yperez
creation_date: 2020-23-22T09:47:09Z

[Term]
id: PRIDE:0000632
name: TMT133N
def: "TMT133N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2022-08-07T15:21:19Z

[Term]
id: PRIDE:0000633
name: TMT133C
def: "TMT133C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2022-08-07T15:21:19Z

[Term]
id: PRIDE:0000634
name: TMT134N
def: "TMT134N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: yperez
creation_date: 2022-08-07T15:21:19Z

[Term]
id: PRIDE:0000635
name: Affinity proteomics
comment: The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes.
is_a: PRIDE:0000457 ! Experiment Type
created_by: yperez
creation_date: 2023-08-05T15:21:19Z

[Term]
id: PRIDE:0000636
name: SomaScan affinity proteomics
comment: Refer to technologies like SomaScan that employ aptamers as the binding agents for protein detection. SomaScan utilizes Slow Off-rate Modified Aptamers (SOMAmers) for protein targeting and measurement.
is_a: PRIDE:0000635 ! Affinity proteomics
created_by: yperez
creation_date: 2023-08-05T15:21:19Z

[Term]
id: PRIDE:0000637
name: Olink affinity proteomics
comment: Refer to technologies like Olink that utilize antibodies as the primary binding agents for protein detection. Olink's Proximity Extension Assay (PEA) technology relies on using antibody pairs to generate protein-specific signals.
is_a: PRIDE:0000635 ! Affinity proteomics
created_by: yperez
creation_date: 2023-08-05T15:21:19Z

[Term]
id: PRIDE:0000638
name: Instrument model
def: "Instrument model" [PRIDE:PRIDE]
created_by: yperez
creation_date: 2023-08-05T15:21:19Z

[Term]
id: PRIDE:0000639
name: Somalogic instrument model
def: "Somalogic instrument model" [PRIDE:PRIDE]
is_a: PRIDE:0000638 ! Instrument model
created_by: yperez
creation_date: 2023-08-05T15:21:19Z

[Term]
id: PRIDE:0000640
name: SomaScan assay v4.0
def: "SomaScan assay v4.0" [PRIDE:PRIDE]
is_a: PRIDE:0000639 ! Somalogic instrument model
created_by: yperez
creation_date: 2023-08-05T15:21:19Z

[Term]
id: PRIDE:0000641
name: SomaScan assay v4.1
def: "SomaScan assay v4.1" [PRIDE:PRIDE]
is_a: PRIDE:0000639 ! Somalogic instrument model
created_by: yperez
creation_date: 2023-08-05T15:21:19Z

[Term]
id: PRIDE:0000642
name: TMT134C
def: "TMT134C" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: Roman-Si 
creation_date: 2023-10-05T11:44:19Z

[Term]
id: PRIDE:0000643
name: TMT135N
def: "TMT135N" [PRIDE:PRIDE]
is_a: PRIDE:0000515 ! TMT
created_by: Roman-Si 
creation_date: 2023-10-05T11:44:19Z

[Term]
id: PRIDE:0000644
name: MS2 dissociation method
def: "Fragmentation method used for dissociation or fragmentation for MS2" [PRIDE:PRIDE]
is_a: MS:1000044 ! dissociation method
created_by: yperez
creation_date: 2023-10-12T11:44:19Z

[Term]
id: PRIDE:0000645
name: MS3 dissociation method
def: "Fragmentation method used for dissociation or fragmentation for MS3" [PRIDE:PRIDE]
is_a: MS:1000044 ! dissociation method
created_by: yperez
creation_date: 2023-10-12T11:44:19Z

[Term]
id: PRIDE:0000646
name: MS3 mass analyzer
def: "MS3 mass analyzer" [PRIDE:PRIDE]
is_a: MS:1000451 ! mass analyzer
created_by: yperez
creation_date: 2023-10-12T18:01:06Z

[Term]
id: PRIDE:0000649
name: Immunopeptidomics
comment: Immunopeptidomics is a large-scale method capable of identifying and quantifying the presented HLA immunopeptidome.
is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy
is_a: PRIDE:0000457 ! Experiment Type
created_by: yperez

[Term]
id: PRIDE:0000650
name: diaPASEF
def: "Data-independent acquisition parallel accumulation-serial fragmentation, PMID: 33257825" [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition
created_by: yperez

[Term]
id: PRIDE:0000651
name: Absolute quantification
def: "Absolute quantification precisely measures the concentration of a specific analyte in a sample" [PRIDE:PRIDE]
is_a: PRIDE:0000307 ! Quantification method
created_by: deepti
creation_date: 2024-01-22T14:42:08Z

[Term]
id: PRIDE:0000652
name: Relative quantification
def: "Relative quantification compares the concentrations of analytes (e.g., a proteins) across different samples" [PRIDE:PRIDE]
is_a: PRIDE:0000307 ! Quantification method
created_by: deepti
creation_date: 2024-01-23T16:25:25Z

[Term]
id: PRIDE:0000653
name: NPX
def: "Normalized Protein eXpression" [PRIDE:PRIDE]
is_a: PRIDE:0000652 ! Relative quantification
created_by: deepti
creation_date: 2024-01-23T16:25:25Z

[Term]
id: PRIDE:0000654
name: Olink instrument model
def: "Olink instrument model" [PRIDE:PRIDE]
is_a: PRIDE:0000638 ! Instrument model
created_by: deepti
creation_date: 2024-01-30T15:45:45Z

[Term]
id: PRIDE:0000655
name: Olink Target 96
def: "Olink Target 96" [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink instrument model
created_by: deepti
creation_date: 2024-01-30T15:55:50Z

[Term]
id: PRIDE:0000656
name: Olink Explore 1536
def: "Olink Explore 1536" [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink instrument model
created_by: deepti
creation_date: 2024-01-30T15:55:50Z

[Term]
id: PRIDE:0000657
name: Olink Explore 3072
def: "Olink Explore 3072" [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink instrument model
created_by: deepti
creation_date: 2024-01-30T15:55:50Z

[Term]
id: PRIDE:0000658
name: Olink Explore 384
def: "Olink Explore 384" [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink instrument model
created_by: deepti
creation_date: 2024-01-30T15:55:50Z

[Typedef]
id: http://purl.obolibrary.org/obo/PRIDE_part_of
name: part_of
is_transitive: true

[Typedef]
id: has_units
name: has_units