pride_cv.obo

format-version: 1.4
date: 13:08:2026 07:30
data-version: releases/2026-08-13
saved-by: Nithu Sara John
default-namespace: PRIDE
namespace-id-rule: * PRIDE:$sequence(7,0,9999999)$
import: http://purl.obolibrary.org/obo/chmo.owl
import: http://www.ebi.ac.uk/efo/efo.owl
remark: This work is licensed under the Creative Commons Attribution 4.0 International (CC BY 4.0) license.
remark: To view a copy of this license, visit https://creativecommons.org/licenses/by/4.0/
remark: URL: http://purl.obolibrary.org/obo/pride/pride_cv.obo
idspace: dce http://purl.org/dc/elements/1.1/
idspace: dcterms http://purl.org/dc/terms/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
idspace: ols http://www.ebi.ac.uk/ols/vocabulary/
property_value: dce:description "Proteomics Identification Database Ontology, terms describing proteomics data and experimental metadata" xsd:string
property_value: dce:title "Proteomics Identification Database Ontology" xsd:string
property_value: dce:license https://creativecommons.org/licenses/by/4.0/
property_value: dcterms:license https://creativecommons.org/licenses/by/4.0/
property_value: dce:creator "Deepti Jaiswal Kundu" xsd:string
property_value: dce:creator "Nithu Sara John" xsd:string
property_value: dce:creator "Yasset Perez-Riverol" xsd:string
property_value: dce:homepage https://github.com/PRIDE-Archive/pride-ontology
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000000
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000001
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000002
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000003
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000004
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000005
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000006
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000017
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000278
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000391
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000457
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000470
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000484
property_value: http://purl.obolibrary.org/obo/IAO_0000700 http://purl.obolibrary.org/obo/PRIDE_0000547
ontology: pride

[Typedef]
id: part_of
name: part_of
xref: BFO:0000050
is_transitive: true

[Term]
id: EFO:0002755
name: diet
def: "The regular course of eating and drinking adopted by a person or animal." [EFO:EFO]

[Term]
id: EFO:0004554
name: genomic measurement
def: "A quantification of some aspect of the genome, e.g. copy number variation at some locus." [EFO:EFO]

[Term]
id: EFO:0004324
name: body weights and measures
def: "Measurements of the height, weight, length, area, etc., of the human and animal body or its parts." [EFO:EFO]

[Term]
id: NCIT:C20189
name: Property or Attribute
def: "A distinguishing quality or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: NCIT:C25447
name: Characteristic
def: "The distinguishing qualities or prominent aspect of a person, object, action, process, or substance." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}
is_a: NCIT:C20189 ! Property or Attribute

[Term]
id: NCIT:C25162
name: Code
def: "A symbol or combination of symbols which is assigned to the members of a collection." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: NCIT:C12219
name: Anatomic Structure, System, or Substance
def: "A human biological structure, fluid or other substance; excludes single molecular entities." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: NCIT:C25347
name: Height
def: "The vertical measurement or distance from the base to the top of an object; the vertical dimension of extension." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: NCIT:C80248
name: Meal
def: "Any of the occasions for eating food that occur by custom or habit at more or less fixed times." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: NCIT:C19160
name: Occupation or Discipline
def: "A grouping of occupations and fields of study." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: NCIT:C16205
name: Healthcare Activity
def: "The actions of prevention, treatment, and management of illness and the preservation of mental and physical well-being through the services offered by the medical and allied health professions." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: NCIT:C45279
name: Log
def: "A written record of events." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"}

[Term]
id: PRIDE:0000000
name: Reference additional parameter
def: "Root node for terms relating to Reference additional parameters" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000001
name: Protocol step description additional parameter
def: "Root node for terms relating to the description of a protocol as ordered steps" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000002
name: ModificationItem additional parameter
def: "Root node for terms relating to the description of a ModificationItem" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000003
name: Peptide item additional parameter
def: "Root node for terms relating to the description of a PeptideItem" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000004
name: Identification additional parameter
def: "Root node for terms relating to the description of an Identification" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000005
name: Gel additional parameter
def: "Root node for terms relating to the description of a Gel parameter" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000006
name: Experiment additional parameter
def: "Root node for terms relating to the description of an Experiment" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000007
name: SearchEngineVersion
def: "Version number or identifier for search engine"[PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000008
name: Protein search engine output parameter
def: "Protein search engine output parameters are critical for analyzing and validating the results of peptide and protein identification" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000009
name: Ion mass tolerance
def: "Ion mass tolerence refers to the permissible deviation between the measured mass of an ion and its theoretical mass" [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000010
name: Precursor ion mass tolerance
def: "Precursor ion mass tolerance defines the acceptable range of deviation between the experimental mass-to-charge ratio (𝑚/𝑧)of a precursor ion and its theoretical (m/z) value during database searches" [PRIDE:PRIDE]
is_a: PRIDE:0000009 ! Ion mass tolerance

[Term]
id: PRIDE:0000011
name: MS2 ion mass tolerance
def: "MS2 ion mass tolerance refers to the acceptable deviation range between the experimentally measured fragment ion masses and their theoretical values during the identification of peptides and proteins in tandem mass spectrometry (MS/MS)" [PRIDE:PRIDE]
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
is_a: PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000013
name: X correlation
def: "A statistical measure used in proteomics to evaluate the quality of peptide-spectrum matches (PSMs) in tandem mass spectrometry (MS/MS) data" [PRIDE:PRIDE]
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)
def: "XCorrelation (+1) refers to the cross-correlation score adjustment applied during peptide-spectrum matching (PSM) in search engines like SEQUEST" [PRIDE:PRIDE]
is_a: PRIDE:0000013 ! X correlation

[Term]
id: PRIDE:0000015
name: X correlation (+2)
def: "XCorrelation (+2) refers to the cross-correlation (XCorr) scores for peptide-spectrum matches (PSMs) associated with doubly charged precursor ions (𝑧=2) in proteomics" [PRIDE:PRIDE]
is_a: PRIDE:0000013 ! X correlation

[Term]
id: PRIDE:0000016
name: X correlation (+3)
def: "XCorrelation (+3) refers to the cross-correlation (XCorr) scores associated with triply charged precursor ions (z=3) in proteomics data analysis" [PRIDE:PRIDE]
is_a: PRIDE:0000013 ! X correlation

[Term]
id: PRIDE:0000017
name: Sample description additional parameter
def: "Root term for parameters in the context of ExperimentCollection" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000018
name: Disease free
def: "The sample derives from an organism positively shown to be free of disease, e.g. as the consequence of a broad-spectrum screen." [PRIDE:PRIDE]
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
def: "Reduction generally refers to the chemical process used to break disulfide bonds between cysteine residues in proteins" [PRIDE:PRIDE]
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]
xref: MS:1003350
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000028
name: Cv Label
def: "Valid values for cvLabel entries referencing external database or ontology" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000029
name: PubMed
def: "PubMed is a free resource developed by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label

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

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

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

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

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

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

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

[Term]
id: PRIDE:0000037
name: Staining
def: "A technique used in biology, histology, and microscopy to enhance contrast in samples, making structures or components visible under a microscope" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter

[Term]
id: PRIDE:0000038
name: ISBN
def: "Valid value for the cvLabel entry referencing ISBN" [PRIDE:PRIDE]
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
def: "This CV term should be used in association with a value that is a free-text description of the experiment" [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000041
name: Search database protein sequence
def: "Database used to search the protein sequence" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000042
name: DOI
def: "The DOI system provides a persistent link to the journal's location on the internet, even if the URL changes" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000043
name: FIX
def: "Valid value for the cvLabel entry referencing FIX" [PRIDE:PRIDE]
is_a: PRIDE:0000028 ! Cv Label

[Term]
id: PRIDE:0000044
name: Search algorithm
def: "A method used to retrieve specific data from a collection of data, based on a given criterion" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000045
name: Sequest
def: "Sequest is one of the earliest and most widely used search engines for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE]
xref: MS:1001208
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000046
name: Mascot
def: "Mascot is a widely used search engine for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE]
xref: MS:1001207
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000571 ! Quantification Software
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000047
name: X!Tandem
def: "X!Tandem is an open-source search engine for protein identification in mass spectrometry-based proteomics" [PRIDE:PRIDE]
xref: MS:1001476
is_a: PRIDE:0000044 ! Search algorithm
is_a: PRIDE:0000573 ! Identification software

[Term]
id: PRIDE:0000048
name: Output parameter
def: "Output parameters in mass spectrometry search engines refer to the results and metrics provided after analyzing the experimental MS/MS spectra and comparing them to theoretical spectra from a protein database" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000049
name: Peptide search engine output parameter
def: "The output parameters of a peptide search engine refer to the key metrics, scores, and information that describe the results of matching experimental mass spectra (MS/MS) to theoretical spectra from a protein sequence database" [PRIDE:PRIDE]
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
is_a: 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
is_a: PRIDE:0000045 ! Sequest

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

[Term]
id: PRIDE:0000053
name: Sequest score
def: "Raw correlation score (Sequest)" [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000049 ! Peptide search engine output parameter
is_a: PRIDE:0000045 ! Sequest

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

[Term]
id: PRIDE:0000056
name: Bioworks
def: "A companion tool often used for processing and analyzing mass spectrometry data" [PRIDE:PRIDE]
xref: MS:1000533
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
is_a: PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000058
name: z score
def: "Bioworks z score" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
is_a: PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000059
name: File
def: "File is a digital container used to store information on a computer or other electronic device" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000060
name: Scan
def: "The scan refers to a unique identifier for a specific mass spectrum acquired during the experiment. Each scan corresponds to a particular fragmentation event in the mass spectrometer" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000061
name: Coverage
def: "Coverage refers to the proportion of a protein sequence that is represented by identified peptides in a given experiment" [PRIDE:PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000062
name: rsp
def: "It is used as a measure to assess the confidence of peptide identifications based on the output of peptide search engines such as Mascot, SEQUEST, X! Tandem, and others" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
is_a: PRIDE:0000056 ! Bioworks

[Term]
id: PRIDE:0000063
name: Protein description line
def: "A protein description line typically refers to a concise textual entry or annotation that provides information about a specific protein, such as its function, molecular characteristics, or role in biological processes" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000064
name: Secondary accession
def: "A secondary accession refers to an additional identifier assigned to a protein entry in databases like UniProt" [PRIDE:PRIDE]
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
def: "Referencing an experiment in scientific contexts, it's important to cite the original publication that reports the methods, results, or analysis involved in the experiment. Typically, this will involve citing the DOI (Digital Object Identifier), journal title, and other relevant details" [PRIDE:PRIDE]
is_a: PRIDE:0000000 ! Reference additional parameter

[Term]
id: PRIDE:0000068
name: Reference describing sample preparation
def: "Referencing sample preparation for mass spectrometry or proteomics, the specific protocols and methods can vary depending on the type of analysis being conducted (e.g., quantitative proteomics, post-translational modification analysis, etc.)" [PRIDE:PRIDE]
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]
xref: MS:1001171
is_a: PRIDE:0000049 ! Peptide search engine output parameter
is_a: 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
def: "Search engine settings refer to the specific parameters and configurations that are used to optimize how a peptide or protein search engine identifies and matches experimental data (e.g., MS/MS spectra) to theoretical peptide sequences in a database" [PRIDE:PRIDE]
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
def: "Fixed modifications refer to chemical modifications that are consistently present in all peptides of a given experiment, typically due to a sample preparation step or reagent used" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000073
name: Variable modification setting
def: "Variable modifications refer to post-translational modifications (PTMs) or other chemical changes that can occur at specific amino acid residues but do not necessarily occur in every peptide or protein" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000074
name: Maximum Missed Cleavages Setting
def: "The maximum missed cleavages setting refers to the number of missed enzyme cleavages allowed during peptide digestion" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000075
name: Mass value type setting
def: "It refers to how the mass of peptides, ions, or proteins is represented during a search or analysis" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000076
name: Mass value type setting monoisotopic
def: "The monoisotopic mass setting refers to the mass of a molecule based on the lightest isotope of each element, typically the most abundant isotope, like carbon-12 (12C) for carbon, hydrogen-1 (1H) for hydrogen, and oxygen-16 (16O) for oxygen" [PRIDE:PRIDE]
is_a: PRIDE:0000075 ! Mass value type setting

[Term]
id: PRIDE:0000077
name: Mass value type setting average
def: "The average mass setting refers to the weighted average mass of all isotopes of each element present in a molecule" [PRIDE:PRIDE]
is_a: PRIDE:0000075 ! Mass value type setting

[Term]
id: PRIDE:0000078
name: Peptide mass tolerance setting
def: "The peptide mass tolerance setting is a critical parameter used to define how much variation is acceptable between the observed mass of a peptide in the mass spectrum and the theoretical mass calculated from a database search" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000079
name: Accurate mass mode setting
def: "The Accurate Mass Mode setting refers to a mode of operation where the mass spectrometer is configured to measure the mass of ions with a higher degree of precision than in standard scanning modes" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000080
name: Accurate mass mode setting true
def: "Accurate mass mode setting typically refers to configuring the instrument to measure ion masses with high precision" [PRIDE:PRIDE]
is_a: PRIDE:0000079 ! Accurate mass mode setting

[Term]
id: PRIDE:0000081
name: Accurate mass mode setting false
def: "Accurate mass mode setting is set to false in mass spectrometry, it means that the instrument will not prioritize high-resolution mass measurements" [PRIDE:PRIDE]
is_a: PRIDE:0000079 ! Accurate mass mode setting

[Term]
id: PRIDE:0000082
name: Mass error type setting
def: "The mass error type setting refers to how mass errors are reported and interpreted during data acquisition and analysis" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000083
name: mass error type setting ppm
def: "The mass error type is set to ppm (parts per million), it specifies that the acceptable mass error is calculated relative to the theoretical mass of the ion, and it is expressed as parts per million (ppm)" [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000084
name: mass error type setting mmu
def: "Mass errors refer to discrepancies in the measured mass of ions compared to their theoretical or expected mass values" [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000085
name: mass error type setting percent
def: "Mass error type setting percent refers to the percentage of mass error in the measured mass-to-charge ratio (m/z) compared to the expected or theoretical value" [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000086
name: mass error type setting Daltons
def: "Mass error type daltons, how the discrepancy between the measured and expected mass is expressed in absolute units of mass (daltons), rather than as a percentage" [PRIDE:PRIDE]
is_a: PRIDE:0000082 ! Mass error type setting

[Term]
id: PRIDE:0000087
name: Protonated setting
def: "Protonated setting refers to the protonation of a molecule or ion during the ionization process, particularly in positive ion mode" [PRIDE:PRIDE]
is_a: PRIDE:0000071 ! Search engine setting

[Term]
id: PRIDE:0000088
name: Protonated setting MH+
def: "Protonated setting MH⁺ refers to the protonated molecular ion of a compound, where M represents the neutral molecule, and the H⁺ signifies the added proton" [PRIDE;PRIDE]
is_a: PRIDE:0000087 ! Protonated setting

[Term]
id: PRIDE:0000090
name: Protonated setting M-H-
def: "Protonated setting M-H⁻ refers to the deprotonated molecular ion (also known as the negative ion form), where M represents the neutral molecule, and H⁻ signifies the loss of a proton (H⁺), resulting in a negatively charged ion" [PRIDE:PRIDE]
is_a: PRIDE:0000087 ! Protonated setting

[Term]
id: PRIDE:0000091
name: Rank
def: "Rank represents the quality or confidence of the peptide-spectrum match (PSM), with the rank value showing the best match and progressively lower-ranked results indicating less confident identifications" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000092
name: All peptides matched
def: "The output of a peptide search engine where every peptide in a sample has been identified and matched against a database" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000093
name: All peptides matched true
def: "All peptides matched true is in a peptide search engine output (like Mascot, SEQUEST, X! Tandem, or Andromeda), it generally means that all detected peptide spectra were successfully matched to corresponding peptides in the protein database" [PRIDE:PRIDE]
is_a: PRIDE:0000092 ! All peptides matched

[Term]
id: PRIDE:0000094
name: All peptides matched false
def: "Some mass spectra from the experiment could not be linked to a known peptide sequence from the protein database" [PRIDE:PRIDE]
is_a: PRIDE:0000092 ! All peptides matched

[Term]
id: PRIDE:0000095
name: Masses matched
def: "Masses matched refers to the number (or percentage) of experimental mass-to-charge ratios (m/z) from a mass spectrum that were successfully matched to theoretical peptide masses in a protein database" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000096
name: Reported Chromosome
def: "Reported chromosome is the chromosomal location of the protein or peptide that has been identified" [PRIDE:PRIDE]
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
is_a: 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
is_a: PRIDE:0000102 ! ProteinProphet

[Term]
id: PRIDE:0000101
name: PeptideProphet
def: "The PeptideProphet algorithm" [PRIDE:PRIDE]
xref: MS:1002287
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]
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]
is_a: 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 [PRIDE]
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 [PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000114
name: obsolete iTRAQ reagent 114
def: "OBSOLETE. Use ITRAQ114 (PRIDE:0000532) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000532

[Term]
id: PRIDE:0000115
name: obsolete iTRAQ reagent 115
def: "OBSOLETE. Use ITRAQ115 (PRIDE:0000533) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000533

[Term]
id: PRIDE:0000116
name: obsolete iTRAQ reagent 116
def: "OBSOLETE. Use ITRAQ116 (PRIDE:0000534) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000534

[Term]
id: PRIDE:0000117
name: obsolete iTRAQ reagent 117
def: "OBSOLETE. Use ITRAQ117 (PRIDE:0000535) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000535

[Term]
id: PRIDE:0000118
name: obsolete iTRAQ intensity 114
def: "OBSOLETE. Use ITRAQ114 (PRIDE:0000532) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000532

[Term]
id: PRIDE:0000119
name: obsolete iTRAQ intensity 115
def: "OBSOLETE. Use ITRAQ115 (PRIDE:0000533) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000533

[Term]
id: PRIDE:0000120
name: obsolete iTRAQ intensity 116
def: "OBSOLETE. Use ITRAQ116 (PRIDE:0000534) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000534

[Term]
id: PRIDE:0000121
name: obsolete iTRAQ intensity 117
def: "OBSOLETE. Use ITRAQ117 (PRIDE:0000535) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000535

[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]
synonym: "2-DE" EXACT []
synonym: "two-dimensional gel electrophoresis" EXACT []
xref: CHMO:0001106
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]
is_a: 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: "Polyacrylamide gel electrophoresis using sodium dodecyl sulfate (SDS) to denature proteins into linear monomers, so that migration is a function of molecular size." [PRIDE:PRIDE]
xref: CHMO:0001027
is_a: 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]
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]
is_a: 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]
is_a: PRIDE:0000124 ! Sodium dodecyl sulfate polyacrylamide gel electrophoresis

[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
is_a: 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
def: "Precision metric for peptide-spectrum matches produced by the PepSplice search engine, measuring the proportion of correct identifications among reported results." [PRIDE:PRIDE]
is_a: PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000147
name: PepSplice false discovery rate
def: "PepSlice false discovery rate is a critical metric used to control the number of false positives (incorrect peptide-spectrum matches or PSMs) in the search results" [PRIDE:PRIDE]
is_a: 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]
is_a: 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]
is_a: PRIDE:0000145 ! PepSplice
is_a: PRIDE:0000145 ! PepSplice

[Term]
id: PRIDE:0000150
name: PepSplice Score Count
def: "The score count" [PRIDE:PRIDE]
is_a: 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]
is_a: 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]
is_a: 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: "Unsuccessful 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 Identifier" EXACT [NCIT]
is_a: 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
def: "It refers to the process of identifying and characterizing molecules, especially proteins, peptides, metabolites, and small molecules, using mass spectrometry (MS) data" [PRIDE:PRIDE]
is_a: PRIDE:0000157 ! Search type

[Term]
id: PRIDE:0000159
name: MS/MS search
def: "Identification of peptides or proteins by matching tandem mass spectrometry (MS/MS) fragmentation spectra against a sequence database or spectral library." [PRIDE:PRIDE]
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
def: "A nucleic acid sequence refers to the linear arrangement of nucleotides (the basic building blocks of DNA and RNA) in a specific order" [PRIDE:PRIDE]
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
def: "The start position of a nucleic acid sequence on a chromosome refers to the location or coordinate where the sequence begins within the linear structure of a chromosome" [PRIDE:PRIDE]
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
def: "The stop position of a nucleic acid sequence on a chromosome refers to the ending coordinate where the sequence finishes on the chromosome" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter

[Term]
id: PRIDE:0000171
name: funding reference
def: "A funding reference is a formal acknowledgment of financial support provided by an organization, institution, or agency for a research project, study, or publication" [PRIDE:PRIDE]
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 [PRIDE]
is_a: PRIDE:0000008 ! Protein search engine output parameter
is_a: 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 [PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000188
name: product ion m/z
def: "Mass" [PRIDE:PRIDE]
xref: MS:1001225
synonym: "Fragment ion mass" EXACT [PRIDE]
is_a: PRIDE:0000187 ! Fragment Ion Annotation

[Term]
id: PRIDE:0000189
name: product ion intensity
def: "Intensity" [PRIDE]
xref: MS:1001226
synonym: "Fragment ion intensity" EXACT [PRIDE]
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 [PRIDE]
is_a: PRIDE:0000187 ! Fragment Ion Annotation

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

[Term]
id: PRIDE:0000193
name: y ion
def: "Y ion type" [PRIDE:PRIDE]
xref: MS:1001220
synonym: "y fragment ion" EXACT [PRIDE]
is_a: PRIDE:0000192 ! product ion type

[Term]
id: PRIDE:0000194
name: b ion
def: "B ion type" [PRIDE:PRIDE]
xref: MS:1001224
synonym: "b fragment ion" EXACT [PRIDE]
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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
synonym: "In-source ion" EXACT [PRIDE]
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 [PRIDE]
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 [PRIDE]
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_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000206
name: Heavy stable isotope label residue
def: "Heavy stable isotope label residue" [PRIDE:PRIDE]
is_a: PRIDE:0000205 ! Heavy stable isotope label

[Term]
id: PRIDE:0000207
name: Light stable isotope label
def: "Light stable isotope label" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000208
name: Light stable isotope label residue
def: "The precise amino acid that has been modified" [PRIDE:PRIDE]
is_a: PRIDE:0000207 ! Light stable isotope label

[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: "Parent retention time error in minutes" [PRIDE:PRIDE]
is_a: PRIDE:0000202 ! Parent Ion Annotation

[Term]
id: PRIDE:0000227
name: x ion
def: "X ion type" [PRIDE:PRIDE]
xref: MS:1001228
synonym: "x fragment ion" EXACT [PRIDE]
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 [PRIDE]
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 [PRIDE]
is_a: PRIDE:0000227 ! x ion

[Term]
id: PRIDE:0000230
name: z ion
def: "Z ion type" [PRIDE:PRIDE]
xref: MS:1001230
synonym: "z fragment ion" EXACT [PRIDE]
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 [PRIDE]
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 [PRIDE]
is_a: PRIDE:0000230 ! z ion

[Term]
id: PRIDE:0000233
name: a ion
def: "A ion type" [PRIDE:PRIDE]
xref: MS:1001229
synonym: "a fragment ion" EXACT [PRIDE]
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 [PRIDE]
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 [PRIDE]
is_a: PRIDE:0000233 ! a ion

[Term]
id: PRIDE:0000236
name: c ion
def: "C ion type" [PRIDE:PRIDE]
xref: MS:1001231
synonym: "c fragment ion" EXACT [PRIDE]
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 [PRIDE]
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 [PRIDE]
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]
xref: MS:1001239
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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
is_a: PRIDE:0000263 ! precursor ion

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

[Term]
id: PRIDE:0000264
name: obsolete iTRAQ reagent 113
def: "OBSOLETE. Use ITRAQ113 (PRIDE:0000531) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000531

[Term]
id: PRIDE:0000265
name: obsolete iTRAQ reagent 118
def: "OBSOLETE. Use ITRAQ118 (PRIDE:0000536) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000536

[Term]
id: PRIDE:0000266
name: obsolete iTRAQ reagent 119
def: "OBSOLETE. Use ITRAQ119 (PRIDE:0000537) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000537

[Term]
id: PRIDE:0000267
name: obsolete iTRAQ reagent 121
def: "OBSOLETE. Use ITRAQ121 (PRIDE:0000538) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000538

[Term]
id: PRIDE:0000268
name: obsolete iTRAQ intensity 113
def: "OBSOLETE. Use ITRAQ113 (PRIDE:0000531) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000531

[Term]
id: PRIDE:0000269
name: obsolete iTRAQ intensity 118
def: "OBSOLETE. Use ITRAQ118 (PRIDE:0000536) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000536

[Term]
id: PRIDE:0000270
name: obsolete iTRAQ intensity 119
def: "OBSOLETE. Use ITRAQ119 (PRIDE:0000537) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000537

[Term]
id: PRIDE:0000271
name: obsolete iTRAQ intensity 121
def: "OBSOLETE. Use ITRAQ121 (PRIDE:0000538) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000538

[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
def: "The SloMo score threshold for a valid modification location is a statistical cutoff used in mass spectrometry (MS/MS) to determine the confidence that a specific position within a peptide or protein is modified" [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000274
name: MaxQuant percentage threshold for valid modification location
def: "In MaxQuant, the percentage threshold for a valid modification location is typically based on the site probability for post-translational modification (PTM) localization. This probability indicates the confidence that a particular amino acid (residue) within a peptide is modified" [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000275
name: SloMo score
def: "The SloMo score is a quantitative measure used in mass spectrometry (MS/MS) for the localization of modification sites within a peptide or protein sequence" [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000276
name: MaxQuant percentage
def: "It refers to typically relates to the localization probability of a post-translational modification (PTM) on a peptide" [PRIDE:PRIDE]
is_a: PRIDE:0000044 ! Search algorithm

[Term]
id: PRIDE:0000277
name: Valid location
def: "A valid location refers to a site on a peptide or protein sequence that has been confidently identified as being modified" [PRIDE:PRIDE]
is_a: PRIDE:0000002 ! ModificationItem additional parameter

[Term]
id: PRIDE:0000278
name: Processing method additional parameter
def: "A processing method refers to the specific steps or algorithms used to analyze raw MS data, identify peptides, and assign modifications. These processing methods often come with additional parameters that allow users to customize the analysis based on their experimental needs" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[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 [PRIDE]
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 [PRIDE]
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: "SEQUEST Sf score calculated by a neural network combining Xcorr, DeltaCn, Sp, RSp, peptide mass, charge state, and number of matched peptides. Protein Sf is the sum of its peptide Sf scores." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter
is_a: PRIDE:0000045 ! Sequest

[Term]
id: PRIDE:0000285
name: obsolete TMT reagent 126
def: "OBSOLETE. Use TMT126 (PRIDE:0000516) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000516

[Term]
id: PRIDE:0000286
name: obsolete TMT reagent 127
def: "OBSOLETE. Use TMT127 (PRIDE:0000517) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000517

[Term]
id: PRIDE:0000287
name: obsolete TMT reagent 128
def: "OBSOLETE. Use TMT128 (PRIDE:0000520) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000520

[Term]
id: PRIDE:0000288
name: obsolete TMT reagent 129
def: "OBSOLETE. Use TMT129 (PRIDE:0000523) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000523

[Term]
id: PRIDE:0000289
name: obsolete TMT reagent 130
def: "OBSOLETE. Use TMT130 (PRIDE:0000526) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000526

[Term]
id: PRIDE:0000290
name: obsolete TMT reagent 131
def: "OBSOLETE. Use TMT131 (PRIDE:0000529) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000529

[Term]
id: PRIDE:0000291
name: obsolete TMT intensity 126
def: "OBSOLETE. Use TMT126 (PRIDE:0000516) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000516

[Term]
id: PRIDE:0000292
name: obsolete TMT intensity 127
def: "OBSOLETE. Use TMT127 (PRIDE:0000517) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000517

[Term]
id: PRIDE:0000293
name: obsolete TMT intensity 128
def: "OBSOLETE. Use TMT128 (PRIDE:0000520) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000520

[Term]
id: PRIDE:0000294
name: obsolete TMT intensity 129
def: "OBSOLETE. Use TMT129 (PRIDE:0000523) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000523

[Term]
id: PRIDE:0000295
name: obsolete TMT intensity 130
def: "OBSOLETE. Use TMT130 (PRIDE:0000526) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000526

[Term]
id: PRIDE:0000296
name: obsolete TMT intensity 131
def: "OBSOLETE. Use TMT131 (PRIDE:0000529) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000529

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

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

[Term]
id: PRIDE:0000299
name: Submitted Protein Accession
def: "The original submitted protein accession for this identification. This might have been curated as part of the submission process" [PRIDE:PRIDE]
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

[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

[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

[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

[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

[Term]
id: PRIDE:0000305
name: Gel-based experiment
def: "Defines a gel-based proteomics experiment" [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics

[Term]
id: PRIDE:0000306
name: Imported from NCBI Peptidome
def: "It refers to the process of retrieving peptide data from the NCBI Peptidome database for use in various proteomics analyses" [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000307
name: Quantification method
def: "Defines various quantification methods" [PRIDE:PRIDE]
is_a: PRIDE:0000391 ! Quantification parameter

[Term]
id: PRIDE:0000308
name: Gel-based quantification method
def: "Describes gel-based quantification methods" [PRIDE:PRIDE]
is_a: PRIDE:0000307 ! Quantification method

[Term]
id: PRIDE:0000309
name: Gel-free quantification method
def: "Describes gel-free quantification methods" [PRIDE:PRIDE]
is_a: PRIDE:0000307 ! Quantification method

[Term]
id: PRIDE:0000310
name: Isotope labeling
def: "Describes quantification techniques using isotope labeling" [PRIDE:PRIDE]
is_a: PRIDE:0000309 ! Gel-free quantification method

[Term]
id: PRIDE:0000311
name: obsolete Selected Reaction Monitoring
def: "OBSOLETE. Describes quantification techniques based on selected / multiple reaction monitoring" [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000630

[Term]
id: PRIDE:0000312
name: Label free
def: "Describes label free quantification techniques" [PRIDE:PRIDE]
synonym: "LFQ" EXACT []
synonym: "label-free quantification" EXACT []
xref: MS:1001834
xref: MS:1001835
is_a: PRIDE:0000309 ! Gel-free quantification method

[Term]
id: PRIDE:0000313
name: obsolete iTRAQ
def: "OBSOLETE. Use ITRAQ (PRIDE:0000530) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000530

[Term]
id: PRIDE:0000314
name: TMT
def: "Tandem Mass Tag is an MSn based isobaric labeling quantification technique" [PRIDE:PRIDE]
synonym: "Tandem Mass Tag" EXACT [PRIDE]
xref: MS:1002615
is_a: PRIDE:0000317 ! MS2 based isotope labeling
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000315
name: SILAC
def: "Stable isotope labeling with amino acids in cell culture is a MS1 based istope labeling technique for quantification" [PRIDE:PRIDE]
synonym: "Stable isotope labeling with amino acids in cell culture" EXACT [PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000316
name: MS1 based isotope labeling
def: "Describes isotope labeling quantification techniques detectable at MS1 level" [PRIDE:PRIDE]
is_a: PRIDE:0000310 ! Isotope labeling

[Term]
id: PRIDE:0000317
name: MS2 based isotope labeling
def: "Describes isotope labeling quantification techniques detectable at MS2 level" [PRIDE:PRIDE]
is_a: PRIDE:0000310 ! Isotope labeling

[Term]
id: PRIDE:0000318
name: 18O
def: "The 18O quantification method relies on the differentiation of two samples using different stable isotopes of oxygen" [PRIDE:PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000597 ! metabolic label

[Term]
id: PRIDE:0000319
name: ICAT
def: "Isotope-Coded Affinity Tags is an isotope labeling quantification technique and uses tags that consist of three elements" [PRIDE:PRIDE]
synonym: "Isotope-Coded Affinity Tags" EXACT [PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000320
name: AQUA
def: "AQUA is an isotope labeling based quantification technique that uses known peptides" [PRIDE:PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling

[Term]
id: PRIDE:0000321
name: ICPL
def: "Isotope-coded protein labels is an isotope labeling based quantification method where peptides are labelled with reagents of different masses" [PRIDE:PRIDE]
synonym: "Isotope-coded protein label" EXACT [PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000322
name: emPAI
def: "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" [PRIDE:PRIDE]
synonym: "Exponentially Modified Protein Abundance Index" EXACT [PRIDE]
is_a: PRIDE:0000312 ! Label free

[Term]
id: PRIDE:0000323
name: TIC
def: "The Total Ion Current (TIC) can be measured or calculated in order to target specific ions" [PRIDE:PRIDE]
synonym: "Total Ion Current" EXACT [PRIDE]
is_a: PRIDE:0000312 ! Label free

[Term]
id: PRIDE:0000324
name: Quantification reagent
def: "A reagent used for quantification" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000391 ! Quantification parameter

[Term]
id: PRIDE:0000325
name: SILAC heavy
def: "The heavy label used in SILAC experiments" [PRIDE:PRIDE]
is_a: PRIDE:0000315 ! SILAC

[Term]
id: PRIDE:0000326
name: SILAC light
def: "The light reagent used in SILAC experiments" [PRIDE:PRIDE]
is_a: PRIDE:0000315 ! SILAC

[Term]
id: PRIDE:0000327
name: SILAC medium
def: "The medium weight reagent used in SILAC experiments" [PRIDE:PRIDE]
is_a: PRIDE:0000315 ! SILAC

[Term]
id: PRIDE:0000328
name: obsolete SILAC reagent
def: "OBSOLETE. Use SILAC (PRIDE:0000315) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000315

[Term]
id: PRIDE:0000329
name: obsolete iTRAQ reagent
def: "OBSOLETE. Use ITRAQ (PRIDE:0000530) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000530

[Term]
id: PRIDE:0000330
name: Arbitrary quantification unit
def: "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" [PRIDE:PRIDE]
is_a: PRIDE:0000392 ! Quantification unit

[Term]
id: PRIDE:0000331
name: Counts
def: "Quantification values reported as arbitrary counts (most often ion counts)" [PRIDE:PRIDE]
is_a: PRIDE:0000330 ! Arbitrary quantification unit

[Term]
id: PRIDE:0000337
name: obsolete TMT reagent
def: "OBSOLETE. Use TMT (PRIDE:0000314) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000314

[Term]
id: PRIDE:0000344
name: obsolete ICAT reagent
def: "OBSOLETE. Use ICAT (PRIDE:0000319) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000319

[Term]
id: PRIDE:0000345
name: obsolete ICAT light reagent
def: "OBSOLETE. Use ICAT light (PRIDE:0000542) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000542

[Term]
id: PRIDE:0000346
name: obsolete ICAT heavy reagent
def: "OBSOLETE. Use ICAT heavy (PRIDE:0000541) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000541

[Term]
id: PRIDE:0000347
name: obsolete ICPL reagent
def: "OBSOLETE. Use ICPL (PRIDE:0000321) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000321

[Term]
id: PRIDE:0000348
name: ICPL0
def: "ICPL channel 0, the light isotopic label providing a reference point for quantitative proteomic analyses" [PRIDE:PRIDE]
synonym: "ICPL 0 reagent" EXACT [PRIDE]
is_a: PRIDE:0000321 ! ICPL
relationship: part_of PRIDE:0000883 ! ICPL4PLEX

[Term]
id: PRIDE:0000349
name: ICPL4
def: "ICPL channel 4, mass shift of approximately 4.0251 Da per labeled amino acid compared to ICPL0" [PRIDE:PRIDE]
synonym: "ICPL 4 reagent" EXACT [PRIDE]
is_a: PRIDE:0000321 ! ICPL
relationship: part_of PRIDE:0000883 ! ICPL4PLEX

[Term]
id: PRIDE:0000350
name: ICPL6
def: "ICPL channel 6, mass shift of approximately 6.0204 Da per labeled amino group" [PRIDE:PRIDE]
synonym: "ICPL 6 reagent" EXACT [PRIDE]
is_a: PRIDE:0000321 ! ICPL
relationship: part_of PRIDE:0000883 ! ICPL4PLEX

[Term]
id: PRIDE:0000351
name: ICPL10
def: "ICPL channel 10, mass shift of approximately 10 Da per labeled amino group" [PRIDE:PRIDE]
synonym: "ICPL 10 reagent" EXACT [PRIDE]
is_a: PRIDE:0000321 ! ICPL
relationship: part_of PRIDE:0000883 ! ICPL4PLEX

[Term]
id: PRIDE:0000882
name: ICAT2PLEX
def: "ICAT 2-plex labeling kit has 2 channels (heavy, light)" [PRIDE:PRIDE]
is_a: PRIDE:0000319 ! ICAT

[Term]
id: PRIDE:0000883
name: ICPL4PLEX
def: "ICPL 4-plex labeling kit has 4 channels (ICPL0, ICPL4, ICPL6, ICPL10)" [PRIDE:PRIDE]
is_a: PRIDE:0000321 ! ICPL

[Term]
id: PRIDE:0000352
name: Quantification value
def: "Parameters to report quantification values"[PRIDE:PRIDE]
is_a: PRIDE:0000391 ! Quantification parameter

[Term]
id: PRIDE:0000353
name: Multiplexed quantification value
def: "Parameters describing quantification values for multiplexed samples" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000352 ! Quantification value

[Term]
id: PRIDE:0000354
name: Intensity subsample 1
def: "Intensity subsampling 1 typically refers to selecting first subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000355
name: Intensity subsample 2
def: "Intensity subsampling 2 typically refers to selecting second subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000356
name: Intensity subsample 3
def: "Intensity subsampling 3 typically refers to selecting third subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000357
name: Intensity subsample 4
def: "Intensity subsampling 4 typically refers to selecting fourth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000358
name: Intensity subsample 5
def: "Intensity subsampling 5 typically refers to selecting fifth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000359
name: Intensity subsample 6
def: "Intensity subsampling 6 typically refers to selecting sixth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000360
name: Intensity subsample 7
def: "Intensity subsampling 7 typically refers to selecting seventh subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000361
name: Intensity subsample 8
def: "Intensity subsampling 8 typically refers to selecting eighth subset of intensity values from a spectrum to analyze specific peaks or regions of interest" [PRIDE:PRIDE]
is_a: PRIDE:0000353 ! Multiplexed quantification value

[Term]
id: PRIDE:0000362
name: Other quantification value
def: "Values from other quantification techniques" [PRIDE:PRIDE]
is_a: PRIDE:0000352 ! Quantification value

[Term]
id: PRIDE:0000363
name: emPAI value
def: "The emPAI for the protein" [PRIDE:PRIDE]
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000362 ! Other quantification value

[Term]
id: PRIDE:0000364
name: TIC value
def: "The Total Ion Count for the given entity" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000362 ! Other quantification value

[Term]
id: PRIDE:0000365
name: Multiplexed sample description
def: "Describes multiples subsamples" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000366
name: Contains multiple subsamples
def: "Identifies samples that are made up of multiplexed subsamples" [PRIDE:PRIDE]
is_a: PRIDE:0000365 ! Multiplexed sample description

[Term]
id: PRIDE:0000391
name: Quantification parameter
def: "Quantification related parameter" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000392
name: Quantification unit
def: "Unit used to report quantification results" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter
is_a: PRIDE:0000004 ! Identification additional parameter
is_a: PRIDE:0000391 ! Quantification parameter

[Term]
id: PRIDE:0000393
name: Relative quantification unit
def: "Unit to report relative quantification results" [PRIDE:PRIDE]
is_a: PRIDE:0000392 ! Quantification unit

[Term]
id: PRIDE:0000394
name: Absolute quantification unit
def: "Unit used to describe absolute quantification results" [PRIDE:PRIDE]
is_a: PRIDE:0000392 ! Quantification unit

[Term]
id: PRIDE:0000395
name: Ratio
def: "Quantification results represent ratios" [PRIDE:PRIDE]
is_a: PRIDE:0000393 ! Relative quantification unit

[Term]
id: PRIDE:0000396
name: Copies per cell
def: "Quantification results are reported as copies per cell" [PRIDE:PRIDE]
is_a: PRIDE:0000394 ! Absolute quantification unit

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

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

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

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

[Term]
id: PRIDE:0000402
name: Original data
def: "A dataset is not a reanalysis of previously published data" [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

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

[Term]
id: PRIDE:0000404
name: associated raw file uri
def: "URI of a raw data file associated to the PRIDE experiment (maybe through a 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

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

[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

[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

[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

[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

[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

[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

[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

[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

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

[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

[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

[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

[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

[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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
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 [PRIDE]
is_a: PRIDE:0000193 ! y ion

[Term]
id: PRIDE:0000425
name: MS1 intensity based label-free quantification method
def: "A a widely used approach in mass spectrometry-based proteomics for quantifying protein abundances across different samples" [PRIDE:PRIDE]
is_a: PRIDE:0000309 ! Gel-free quantification method

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

[Term]
id: PRIDE:0000427
name: Top-down proteomics
def: "A mass spectrometry-based approach that analyzes intact proteins rather than digesting them into peptides (as in bottom-up proteomics)" [PRIDE:PRIDE]
xref: MS:1003351
is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy
is_a: PRIDE:0000457 ! Experiment Type

[Term]
id: PRIDE:0000428
name: Bottom-up proteomics
def: "Proteins go through proteolytic digestion yielding peptides before entering the mass spectrometer" [PRIDE:PRIDE]
synonym: "shotgun proteomics" EXACT []
xref: MS:1003355
is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy
is_a: PRIDE:0000457 ! Experiment Type

[Term]
id: PRIDE:0000429
name: MS/MS shotgun proteomics
def: "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" [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics

[Term]
id: PRIDE:0000430
name: Chemical cross-linking coupled with mass spectrometry proteomics
def: "Chemical cross-linking of proteins coupled with mass spectrometry analysis to provide information about protein folding and protein-protein interaction" [PRIDE:PRIDE]
synonym: "XL-MS" EXACT []
synonym: "CLMS" EXACT []
is_a: PRIDE:0000428 ! Bottom-up proteomics

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

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

[Term]
id: PRIDE:0000433
name: Reagents used in Labeled Methods
def: "Labeled reagents used for quantification" [PRIDE:PRIDE]
is_a: PRIDE:0000324 ! Quantification reagent

[Term]
id: PRIDE:0000434
name: Unlabeled sample
def: "An unlabeled sample used for quantification" [PRIDE:PRIDE]
is_a: PRIDE:0000324 ! Quantification reagent

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

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

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

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

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

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

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

[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

[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

[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

[Term]
id: PRIDE:0000445
name: PRIDE Cluster score
def: "Integer quality score for a peptide-spectrum match in PRIDE-Q, derived from the PRIDE-Cluster algorithm using cluster size and predominant identification ratio (PMID:23361086)." [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[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

[Term]
id: PRIDE:0000447
name: SWATH MS
def: "ABSciex data-independent acquisition method using sequential wide precursor isolation windows (typically 400-1200 m/z) per duty cycle, with peptide identification via spectral libraries. Described in PMID:22261725." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition

[Term]
id: PRIDE:0000448
name: Additional associated raw file URI
def: "Additional URI of one raw data file associated to the PRIDE experiment (maybe through a PX submission). The URI is provided via an additional resource to PRIDE" [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

[Term]
id: PRIDE:0000449
name: Gel image file URI
def: "URI of one gel image 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

[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]
synonym: "DIA" EXACT []
xref: MS:1003215
is_a: PRIDE:0000428 ! Bottom-up proteomics
is_a: PRIDE:0000659 ! Proteomics data acquisition method

[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

[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

[Term]
id: PRIDE:0000453
name: PAcIFIC
def: "Precursor Acquisition Independent From Ion Count. A DIA method using 2.5 m/z sequential windows across multiple injections to cover the 400-1200 m/z precursor range in ion traps (PMID:21341720)." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition

[Term]
id: PRIDE:0000454
name: All-ion fragmentation
def: "DIA method on Thermo Orbitrap instruments acquiring alternating MS1 and MS2 scans with a wide precursor isolation window (typically over 800 m/z). Described in PMID:20610777." [PRIDE:PRIDE]
is_a: PRIDE:0000450 ! Data-independent acquisition

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

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

[Term]
id: PRIDE:0000457
name: Experiment Type
def: "Domain-specific mass spectrometry experiment type focusing on the scientific knowledge gained, not the mass spectrometry method" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[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 [PRIDE]
synonym: "Environmental Proteomics" RELATED [PRIDE:PRIDE]

[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

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

[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

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

[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:0000630 ! Selected reaction monitoring

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

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

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

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

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

[Term]
id: PRIDE:0000469
name: FTP Protocol
def: "URI for an FTP Download Protocol" [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000470
name: File Properties
def: "PRIDE File Properties for all type of files" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: PRIDE:0000471
name: MS File Properties
def: "Properties for MS and Peaks files" [PRIDE:PRIDE]
is_a: PRIDE:0000470 ! File Properties

[Term]
id: PRIDE:0000472
name: MS min charge
def: "Minimum charge for all precursors in the file" [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties

[Term]
id: PRIDE:0000473
name: MS max charge
def: "Maximum charge for all precursors in the file" [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties

[Term]
id: PRIDE:0000474
name: MS min RT
def: "Minimum retention time in the file" [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties

[Term]
id: PRIDE:0000475
name: MS max RT
def: "Maximum retention time in the file" [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties

[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

[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

[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

[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

[Term]
id: PRIDE:0000480
name: Number of MS
def: "Number of MS in the file" [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties

[Term]
id: PRIDE:0000481
name: Number of MS1 spectra
def: "Number of MS1 spectra" [PRIDE:PRIDE]
is_a: PRIDE:0000480 ! Number of MS

[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

[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

[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

[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]
is_a: BFO:0000001 ! entity

[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

[Term]
id: PRIDE:0000486
name: Tool specific analysis parameters
def: "Result analysis parameters specific to a search engine or quantitative tool" [PRIDE:PRIDE]
is_a: PRIDE:0000484 ! Result analysis parameters

[Term]
id: PRIDE:0000487
name: Min charge
def: "Minimum charge of precursor to be search" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[Term]
id: PRIDE:0000488
name: Max charge
def: "Maximum charge of precursor to be search" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[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

[Term]
id: PRIDE:0000490
name: Max RT
def: "Maximum precursor RT to be search" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[Term]
id: PRIDE:0000491
name: Number of missed cleavages
def: "Number of missed cleavages" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[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

[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

[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

[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

[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

[Term]
id: PRIDE:0000497
name: Use Multi Modification
def: "Use Multi Modification"[PRIDE:PRIDE] 
is_a: PRIDE:0000485 ! Global result parameters

[Term]
id: PRIDE:0000498
name: Use Additional Variable Modifications
def: "Use Additional Variable Modifications" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[Term]
id: PRIDE:0000499
name: Do Mass Filtering
def: "Do Mass Filtering" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[Term]
id: PRIDE:0000500
name: Intensity Threshold
def: "Intensity Threshold" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[Term]
id: PRIDE:0000501
name: Max Labeled AA
def: "Max Labeled AA" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[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

[Term]
id: PRIDE:0000503
name: First Search Precursor Tolerance
def: "First Search Precursor Tolerance" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[Term]
id: PRIDE:0000504
name: Main Search Precursor Tolerance
def: "Main Search Precursor Tolerance" [PRIDE:PRIDE]
is_a: PRIDE:0000485 ! Global result parameters

[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

[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

[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

[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

[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

[Term]
id: PRIDE:0000510
name: File size
def: "The size of the file in MB" [PRIDE:PRIDE]
is_a: PRIDE:0000470 ! File Properties

[Term]
id: PRIDE:0000511
name: Pass submitter threshold
def: "Pass submitter threshold" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000512
name: RNA mass spectrometry
def: "RNA mass spectrometry" [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics

[Term]
id: PRIDE:0000513
name: Dimethyl Labeling
def: "Dimethyl Labeling (DML)" [PRIDE:PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000514
name: Label
def: "Quantification channel label" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter


[Term]
id: PRIDE:0000516
name: TMT126
def: "TMT126" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000666 ! TMT6PLEX
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000517
name: TMT127
def: "TMT127" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000666 ! TMT6PLEX

[Term]
id: PRIDE:0000518
name: TMT127C
def: "TMT127C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000519
name: TMT127N
def: "TMT127N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000520
name: TMT128
def: "TMT128" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000666 ! TMT6PLEX

[Term]
id: PRIDE:0000521
name: TMT128C
def: "TMT128C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000522
name: TMT128N
def: "TMT128N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000523
name: TMT129
def: "TMT129" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000666 ! TMT6PLEX

[Term]
id: PRIDE:0000524
name: TMT129C
def: "TMT129C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000525
name: TMT129N
def: "TMT129N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000526
name: TMT130
def: "TMT130" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000666 ! TMT6PLEX

[Term]
id: PRIDE:0000527
name: TMT130C
def: "TMT130C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000528
name: TMT130N
def: "TMT130N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000529
name: TMT131
def: "TMT131" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000666 ! TMT6PLEX
relationship: part_of PRIDE:0000667 ! TMT10PLEX
relationship: part_of PRIDE:0000858 ! TMT11PLEX

[Term]
id: PRIDE:0000530
name: ITRAQ
def: "Isobaric Tags for Relative and Absolute Quantitation, an MSn based isobaric labeling quantification technique using reporter ions" [PRIDE:PRIDE]
synonym: "iTRAQ" EXACT [PRIDE]
synonym: "Isobaric Tags for Relative and Absolute Quantitation" EXACT [PRIDE]
xref: MS:1002622
is_a: PRIDE:0000317 ! MS2 based isotope labeling
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000531
name: ITRAQ113
def: "ITRAQ113 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000532
name: ITRAQ114
def: "ITRAQ114 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000856 ! ITRAQ4PLEX
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000533
name: ITRAQ115
def: "ITRAQ115 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000856 ! ITRAQ4PLEX
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000534
name: ITRAQ116
def: "ITRAQ116 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000856 ! ITRAQ4PLEX
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000535
name: ITRAQ117
def: "ITRAQ117 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000856 ! ITRAQ4PLEX
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000536
name: ITRAQ118
def: "ITRAQ118 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000537
name: ITRAQ119
def: "ITRAQ119 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000538
name: ITRAQ121
def: "ITRAQ121 channel" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ
relationship: part_of PRIDE:0000857 ! ITRAQ8PLEX

[Term]
id: PRIDE:0000541
name: ICAT heavy
def: "ICAT heavy" [PRIDE:PRIDE]
is_a: PRIDE:0000319 ! ICAT
relationship: part_of PRIDE:0000882 ! ICAT2PLEX

[Term]
id: PRIDE:0000542
name: ICAT light
def: "ICAT light" [PRIDE:PRIDE]
is_a: PRIDE:0000319 ! ICAT
relationship: part_of PRIDE:0000882 ! ICAT2PLEX

[Term]
id: PRIDE:0000543
name: Quality Control
def: "MS experiments conducted to control the quality of measurements" [PRIDE:PRIDE]
is_a: PRIDE:0000457 ! Experiment Type

[Term]
id: PRIDE:0000544
name: quality control sample
def: "Control sample run to monitor assay, batch, or instrument performance and stability over time, without primarily serving as the quantitative calibration anchor." [PRIDE:PRIDE]
is_a: PRIDE:0001014 ! control sample

[Term]
id: PRIDE:0000545
name: QC1 sample
def: "QC1 sample as described in 10.1371/journal.pone.0189209" [PRIDE:PRIDE]
comment: Historically used for low-complexity MS instrument QC (QCloud nomenclature). [PRIDE:PRIDE]
is_obsolete: true
replaced_by: 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]
comment: Historically used for high-complexity MS instrument QC (QCloud nomenclature). [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000544 ! quality control sample

[Term]
id: PRIDE:0000547
name: Instrument properties
def: "Instrument properties" [PRIDE:PRIDE]
is_a: BFO:0000001 ! entity

[Term]
id: MS:1000451
name: mass analyzer
def: "Mass analyzer" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties

[Term]
id: PRIDE:0000548
name: MS1 mass analyzer
def: "MS1 mass analyzer" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties
is_a: MS:1000451 ! mass analyzer

[Term]
id: PRIDE:0000549
name: MS2 mass analyzer
def: "MS2 mass analyzer" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties
is_a: MS:1000451 ! mass analyzer

[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 separation 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:0000571
name: Quantification software
def: "A software that perform protein quantification using mass spectrometry data" [PRIDE:PRIDE]
is_a: MS:1001456 ! analysis software

[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

[Term]
id: PRIDE:0000573
name: Identification software
def: "A software that perform peptide/protein identification using mass spectrometry data" [PRIDE:PRIDE]
is_a: MS:1001456 ! analysis software

[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

[Term]
id: PRIDE:0000575
name: precursor mass tolerance
def: "Threshold at precursor level to compare experimental mass with theoretical mass" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000576
name: fragment mass tolerance
def: "Threshold at fragment level to compare experimental mass with theoretical mass" [PRIDE:PRIDE]
is_a: PRIDE:0000003 ! Peptide item additional parameter

[Term]
id: PRIDE:0000577
name: file uri
def: "URI of one external file associated to the PRIDE experiment on SDRF files definitions" [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

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

[Term]
id: PRIDE:0000579
name: Depleted fraction
def: "The depleted fraction after a depletion process" [PRIDE:PRIDE]
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]
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000580
name: TMT131N
def: "TMT131N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000581
name: TMT131C
def: "TMT131C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000858 ! TMT11PLEX
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000582
name: TMT132N
def: "TMT132N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000583
name: TMT132C
def: "TMT132C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[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

[Term]
id: PRIDE:0000585
name: Enrichment
def: "Enrichment of specific post-translational modifications" [PRIDE:PRIDE]
is_a: PRIDE:0000001 ! Protocol step description additional parameter
is_a: EFO:0009090 ! enrichment process

[Term]
id: PRIDE:0000586
name: Enrichment method
def: "The specific method or technique used for enrichment of 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 [PRIDE]
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
is_a: PRIDE:0000591 ! CID

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

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

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

[Term]
id: PRIDE:0000597
name: metabolic label
def: "Metabolic label" [PRIDE:PRIDE]
is_a: PRIDE:0000514 ! Label

[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

[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

[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

[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

[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

[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

[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

[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

[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

[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

[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

[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

[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

[Term]
id: PRIDE:0000611
name: SILAC light R:12C(6)14N(4)
def: "The light amino acid arginine used in SILAC experiments, using the following isotopes:12C(6)14N(4)" [PRIDE:PRIDE]
is_a: PRIDE:0000326 ! SILAC light

[Term]
id: PRIDE:0000612
name: SILAC light L:12C(6)
def: "The light amino acid leucine used in SILAC experiments, using the following isotopes:12C(6)" [PRIDE:PRIDE]
is_a: PRIDE:0000326 ! SILAC light

[Term]
id: PRIDE:0000613
name: SILAC light K:12C(6)14N(2)
def: "The light amino acid lysine used in SILAC experiments, using the following isotopes:12C(6)14N(2)" [PRIDE:PRIDE]
is_a: PRIDE:0000326 ! SILAC light

[Term]
id: PRIDE:0000614
name: SILAC light P:12C(5)
def: "The light amino acid proline used in SILAC experiments, using the following isotopes:12C(5)" [PRIDE:PRIDE]
is_a: PRIDE:0000326 ! SILAC light

[Term]
id: PRIDE:0000615
name: SILAC heavy R:13C(6)15N(4)
def: "The heavy amino acid arginine used in SILAC experiments, using the following isotopes:13C(6)15N(4)" [PRIDE:PRIDE]
is_a: PRIDE:0000325 ! SILAC heavy

[Term]
id: PRIDE:0000616
name: SILAC heavy L:13C(6)
def: "The heavy amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)" [PRIDE:PRIDE]
is_a: PRIDE:0000325 ! SILAC heavy

[Term]
id: PRIDE:0000617
name: SILAC heavy K:13C(6)15N(2)
def: "The heavy amino acid lysine used in SILAC experiments, using the following isotopes:13C(6)15N(2)" [PRIDE:PRIDE]
is_a: PRIDE:0000325 ! SILAC heavy

[Term]
id: PRIDE:0000618
name: SILAC medium R:13C(6)14N(4)
def: "The medium amino acid arginine used in SILAC experiments, using the following isotopes: 13C(6)14N(4)" [PRIDE:PRIDE]
is_a: PRIDE:0000327 ! SILAC medium

[Term]
id: PRIDE:0000619
name: SILAC medium K:13C(6)14N(2)
def: "The medium amino acid lysine used in SILAC experiments, using the following isotopes: 13C(6)14N(2)" [PRIDE:PRIDE]
is_a: PRIDE:0000327 ! SILAC medium

[Term]
id: PRIDE:0000879
name: SILAC heavy P:13C(5)
def: "The heavy amino acid proline used in SILAC experiments, using the following isotopes: 13C(5)" [PRIDE:PRIDE]
is_a: PRIDE:0000325 ! SILAC heavy

[Term]
id: PRIDE:0000880
name: SILAC medium L:13C(6)
def: "The medium amino acid leucine used in SILAC experiments, using the following isotopes: 13C(6)" [PRIDE:PRIDE]
is_a: PRIDE:0000327 ! SILAC medium

[Term]
id: PRIDE:0000881
name: SILAC medium P:12C(5)2H(6)
def: "The medium amino acid proline used in SILAC experiments, using the following isotopes: 12C(5)2H(6)" [PRIDE:PRIDE]
is_a: PRIDE:0000327 ! SILAC medium

[Term]
id: PRIDE:0000620
name: 15N
def: "The 15N metabolic labeling quantification method uses the incorporation of nitrogen-15 stable isotope into proteins for relative quantification" [PRIDE:PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000597 ! metabolic label

[Term]
id: PRIDE:0000621
name: 13C
def: "The 13C metabolic labeling quantification method uses the incorporation of carbon-13 stable isotope into proteins for relative quantification" [PRIDE:PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000597 ! metabolic label

[Term]
id: PRIDE:0000884
name: 15N heavy
def: "The heavy channel in a 15N metabolic labeling experiment, containing proteins with incorporated nitrogen-15" [PRIDE:PRIDE]
is_a: PRIDE:0000620 ! 15N
relationship: part_of PRIDE:0000890 ! 15N2PLEX

[Term]
id: PRIDE:0000885
name: 15N light
def: "The light channel in a 15N metabolic labeling experiment, containing proteins with natural nitrogen-14" [PRIDE:PRIDE]
is_a: PRIDE:0000620 ! 15N
relationship: part_of PRIDE:0000890 ! 15N2PLEX

[Term]
id: PRIDE:0000886
name: 13C heavy
def: "The heavy channel in a 13C metabolic labeling experiment, containing proteins with incorporated carbon-13" [PRIDE:PRIDE]
is_a: PRIDE:0000621 ! 13C
relationship: part_of PRIDE:0000891 ! 13C2PLEX

[Term]
id: PRIDE:0000887
name: 13C light
def: "The light channel in a 13C metabolic labeling experiment, containing proteins with natural carbon-12" [PRIDE:PRIDE]
is_a: PRIDE:0000621 ! 13C
relationship: part_of PRIDE:0000891 ! 13C2PLEX

[Term]
id: PRIDE:0000888
name: 18O heavy
def: "The heavy channel in an 18O labeling experiment, containing peptides with incorporated oxygen-18" [PRIDE:PRIDE]
is_a: PRIDE:0000318 ! 18O
relationship: part_of PRIDE:0000892 ! 18O2PLEX

[Term]
id: PRIDE:0000889
name: 18O light
def: "The light channel in an 18O labeling experiment, containing peptides with natural oxygen-16" [PRIDE:PRIDE]
is_a: PRIDE:0000318 ! 18O
relationship: part_of PRIDE:0000892 ! 18O2PLEX

[Term]
id: PRIDE:0000890
name: 15N2PLEX
def: "15N 2-plex metabolic labeling has 2 channels (heavy, light)" [PRIDE:PRIDE]
is_a: PRIDE:0000620 ! 15N

[Term]
id: PRIDE:0000891
name: 13C2PLEX
def: "13C 2-plex metabolic labeling has 2 channels (heavy, light)" [PRIDE:PRIDE]
is_a: PRIDE:0000621 ! 13C

[Term]
id: PRIDE:0000892
name: 18O2PLEX
def: "18O 2-plex labeling has 2 channels (heavy, light)" [PRIDE:PRIDE]
is_a: PRIDE:0000318 ! 18O

[Term]
id: PRIDE:0000623
name: source name
def: "Reference to the Sample. This term is used for cross-reference samples in SDRF for proteomics" [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000624
name: SpectraCluster MaxRatio
def: "Spectra Cluster Maximum Ratio for the cluster" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000625
name: NIST ProbCorr
def: "NIST Probability Correlation" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000626
name: NIST Dotbest
def: "NIST best dot product" [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000627
name: Data-dependent acquisition
def: "Data-dependent acquisition" [PRIDE:PRIDE]
synonym: "DDA" EXACT []
xref: MS:1003221
is_a: PRIDE:0000428 ! Bottom-up proteomics
is_a: PRIDE:0000659 ! Proteomics data acquisition method

[Term]
id: PRIDE:0000629
name: Parallel reaction monitoring
def: "Parallel Reaction Monitoring (PRM)" [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics
is_a: PRIDE:0000659 ! Proteomics data acquisition method

[Term]
id: PRIDE:0000630
name: Selected reaction monitoring
def: "Selected reaction monitoring (SRM)" [PRIDE:PRIDE]
synonym: "SRM" EXACT []
synonym: "MRM" EXACT []
xref: MS:1000206
is_a: PRIDE:0000428 ! Bottom-up proteomics
is_a: PRIDE:0000659 ! Proteomics data acquisition method

[Term]
id: PRIDE:0000631
name: Mass spectrometry imaging
def: "Mass spectrometry imaging" [PRIDE:PRIDE]
is_a: PRIDE:0000426 ! Mass spectrometry proteomics experimental strategy

[Term]
id: PRIDE:0000632
name: TMT133N
def: "TMT133N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000633
name: TMT133C
def: "TMT133C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000634
name: obsolete TMT134
def: "OBSOLETE. Use TMT134N (PRIDE:0000643) instead." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0000643

[Term]
id: PRIDE:0000635
name: Affinity proteomics
def: "The field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes" [PRIDE:PRIDE]
is_a: PRIDE:0000457 ! Experiment Type

[Term]
id: PRIDE:0000636
name: SomaScan affinity proteomics
def: "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" [PRIDE:PRIDE]
is_a: PRIDE:0000635 ! Affinity proteomics

[Term]
id: PRIDE:0000637
name: Olink affinity proteomics
def: "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" [PRIDE:PRIDE]
is_a: PRIDE:0000635 ! Affinity proteomics

[Term]
id: PRIDE:0000638
name: Instrument model
def: "Instrument model" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties

[Term]
id: PRIDE:0000639
name: SomaLogic platform
def: "SomaLogic platform" [PRIDE:PRIDE]
synonym: "SomaLogic instrument model" EXACT []
is_a: PRIDE:0000912 ! assay platform

[Term]
id: PRIDE:0000640
name: SomaScan assay v4.0
def: "SomaScan assay v4.0" [PRIDE:PRIDE]
is_a: PRIDE:0000639 ! SomaLogic platform

[Term]
id: PRIDE:0000641
name: SomaScan assay v4.1
def: "SomaScan assay v4.1" [PRIDE:PRIDE]
is_a: PRIDE:0000639 ! SomaLogic platform

[Term]
id: PRIDE:0000642
name: TMT134C
def: "TMT134C" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000643
name: TMT134N
def: "TMT134N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
synonym: "TMT134" EXACT [PRIDE]
relationship: part_of PRIDE:0000668 ! TMT16PLEX
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000644
name: MS2 dissociation method
def: "Fragmentation method used for dissociation or fragmentation for MS2" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties
is_a: MS:1000044 ! dissociation method

[Term]
id: PRIDE:0000645
name: MS3 dissociation method
def: "Fragmentation method used for dissociation or fragmentation for MS3" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties
is_a: MS:1000044 ! dissociation method

[Term]
id: PRIDE:0000646
name: MS3 mass analyzer
def: "MS3 mass analyzer" [PRIDE:PRIDE]
is_a: PRIDE:0000547 ! Instrument properties
is_a: MS:1000451 ! mass analyzer

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

[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

[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

[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

[Term]
id: PRIDE:0000653
name: NPX
def: "Normalized Protein eXpression" [PRIDE:PRIDE]
is_a: PRIDE:0000652 ! Relative quantification

[Term]
id: PRIDE:0000654
name: Olink platform
def: "Olink platform" [PRIDE:PRIDE]
synonym: "Olink instrument model" EXACT []
is_a: PRIDE:0000912 ! assay platform

[Term]
id: PRIDE:0000655
name: Olink Target 96
def: "Olink Target 96 is a proteomics platform offering targeted analysis of 92 specific protein biomarkers per panel using proximity extension assay (PEA) technology" [PRIDE:PRIDE]
is_a: PRIDE:0000672 ! Olink Target

[Term]
id: PRIDE:0000656
name: Olink Explore 1536
def: "Olink Explore 1536" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Olink Explore

[Term]
id: PRIDE:0000657
name: Olink Explore 3072/384
def: "Olink Explore 3072 includes eight 384-plex panels for efficient, large-scale, disease- and process-focused studies" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Olink Explore

[Term]
id: PRIDE:0000658
name: Olink Explore 384
def: "Olink Explore 384" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Olink Explore

[Term]
id: PRIDE:0000659
name: Proteomics data acquisition method
def: "Proteomics data acquisition method" [PRIDE:PRIDE]
is_a: PRIDE:0000428 ! Bottom-up proteomics

[Term]
id: PRIDE:0000660
name: Ion Mobility Separation
def: "Ion Mobility Separation" [PRIDE:PRIDE]
is_a: PRIDE:0000551 ! Separation method

[Term]
id: PRIDE:0000661
name: Differential mobility Separation
def: "Differential mobility Separation" [PRIDE:PRIDE]
is_a: PRIDE:0000551 ! Separation method

[Term]
id: PRIDE:0000662
name: SelexION Separation Method
def: "SelexION differential mobility separation device" [PRIDE:PRIDE]
is_a: PRIDE:0000660 ! Ion Mobility Separation
is_a: PRIDE:0000661 ! Differential mobility Separation

[Term]
id: PRIDE:0000663
name: technology type
def: "The technology type or platform used to perform the study" [EFO:EFO_0005521]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000664
name: proteomic profiling by mass spectrometry
def: "An assay where proteins in a sample are detected, quantified or otherwise analysed using mass spectrometry" [EFO:EFO_0002766]
is_a: PRIDE:0000663 ! technology type

[Term]
id: PRIDE:0000665
name: Glycoproteomics
def: "Study of proteins that identifies, catalogs, and characterizes those proteins that contain carbohydrates as posttranslational modifications" [PRIDE:PRIDE]
is_a: PRIDE:0000457 ! Experiment Type

[Term]
id: PRIDE:0000666
name: TMT6PLEX
def: "TMT 6-plex labeling kit has 6 channels" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000667
name: TMT10PLEX
def: "TMT 10-plex labeling kit has 10 channels" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000668
name: TMT16PLEX
def: "TMT 16-plex labeling kit has 16 channels" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000669
name: TMT18PLEX
def: "TMT 18-plex labeling kit has 18 channels" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000670
name: TMT135N
def: "TMT135N" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
synonym: "TMT135" EXACT [PRIDE:PRIDE]
relationship: part_of PRIDE:0000669 ! TMT18PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000671
name: Olink Explore
def: "Olink Explore is a high-throughput proteomics platform that quantifies protein biomarkers across multiple samples using proximity extension assay (PEA) technology" [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink platform

[Term]
id: PRIDE:0000672
name: Olink Target
def: "Olink Target is a proteomics platform designed for focused, customizable analysis of specific protein biomarker panels using proximity extension assay (PEA) technology" [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink platform

[Term]
id: PRIDE:0000673
name: Olink Explore HT
def: "The Olink Explore HT is a high-throughput proteomics platform for large-scale biomarker discovery, enabling simultaneous measurement of thousands of proteins from minimal sample volumes" [PRIDE:PRIDE]
is_a: PRIDE:0000671 ! Olink Explore

[Term]
id: PRIDE:0000674
name: human gut
def: "A collection of terms appropriate when collecting samples and sequencing samples obtained from a person to examine their gut-associated microbiome." [PRIDE:PRIDE]
is_a: PRIDE:0000904 ! metaproteomics sample
is_a: UBERON:0005409 ! gastrointestinal system

[Term]
id: PRIDE:0000675
name: sample name
def: "A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. MIXS:0001107" [PRIDE:PRIDE]
xref: NCIT:C25507
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000676
name: project name
def: "Name of the project within which the sequencing was organized. MIXS:0000092" [PRIDE:PRIDE]
xref: NCIT:C25507
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000677
name: gastrointestinal tract disorder
def: "History of gastrointestinal tract disorders; can include multiple disorders. MIXS:0000280" [PRIDE:PRIDE]
is_a: MONDO:0000001 ! Disease
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000678
name: liver disorder
def: "History of liver disorders; can include multiple disorders. MIXS:0000282" [PRIDE:PRIDE]
is_a: MONDO:0000001 ! Disease
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000679
name: special diet
def: "Specification of special diet; can include multiple special diets. MIXS:0000905" [PRIDE:PRIDE]
is_a: EFO:0002755 ! Diet
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000680
name: host subject id
def: "A unique identifier by which each subject can be referred to, de-identified. MIXS:0000861" [PRIDE:PRIDE]
xref: NCIT:C25507
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000681
name: host age
def: "Age of host at the time of sampling; relevant scale depends on species and study, e.g. Could be seconds for amoebae or centuries for trees. MIXS:0000255" [PRIDE:PRIDE]
synonym: "host age slot" EXACT []
xref: NCIT:C25507
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000682
name: host disease status
def: "List of diseases with which the host has been diagnosed; can include multiple diagnoses. MIXS:0000031" [PRIDE:PRIDE]
synonym: "host disease slot" EXACT []
xref: NCIT:C25507
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000683
name: IHMC medication code
def: "Can include multiple medication codes. MIXS:0000884" [PRIDE:PRIDE]
is_a: NCIT:C25162 ! Code
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000684
name: chemical administration
def: "List of chemical compounds administered to the host or site where sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can include multiple compounds. MIXS:0000751" [PRIDE:PRIDE]
is_a: PECO:0007086 ! chemical fertilizer exposure
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000685
name: host body site
def: "Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc.).  MIXS:0000867" [PRIDE:PRIDE]
is_a: NCIT:C12219 ! Anatomic Structure, System, or Substance
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000686
name: host body product
def: "Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from.  MIXS:0000888" [PRIDE:PRIDE]
is_a: NCIT:C12219 ! Anatomic Structure, System, or Substance
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000687
name: host total mass
def: "Total mass of the host at collection, the unit depends on host. MIXS:0000263" [PRIDE:PRIDE]
is_a: OBA:2045413 ! anatomical entity mass
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000688
name: host height
def: "The height of subject. MIXS:0000264" [PRIDE:PRIDE]
synonym: "body height" EXACT []
is_a: NCIT:C25347 ! Height
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000689
name: host diet
def: "Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. MIXS:0000869" [PRIDE:PRIDE]
is_a: EFO:0002755 ! Diet
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000690
name: host last meal
def: "Content of last meal and time since feeding; can include multiple values. MIXS:0000870" [PRIDE:PRIDE]
is_a: NCIT:C80248 ! Meal
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000691
name: host family relationship
def: "Relationships to other hosts in the same study; can include multiple relationships. MIXS:0000872" [PRIDE:PRIDE]
synonym: "family relationship" EXACT []
is_a: BFO:0000016 ! disposition
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000692
name: host genotype
def: "Observed genotype MIXS:0000365" [PRIDE:PRIDE]
is_a: EFO:0004554 ! genomic measurement
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000693
name: host phenotype
def: "Phenotype of human or other host. Use terms from the phenotypic quality ontology (pato) or the Human Phenotype Ontology (HP). MIXS:0000274" [PRIDE:PRIDE]
is_a: BFO:0000019 ! quality
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000694
name: host body temperature
def: "Core body temperature of the host when sample was collected. MIXS:0000874" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000695
name: host body-mass index
def: "Body mass index, calculated as weight/(height)squared. MIXS:0000317" [PRIDE:PRIDE]
is_a: EFO:0004324 ! body weights and measurements
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000696
name: ethnicity
def: "A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. MIXS:0000895" [PRIDE:PRIDE]
is_a: BFO:0000019 ! quality
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000697
name: host occupation
def: "Most frequent job performed by subject. MIXS:0000896" [PRIDE:PRIDE]
is_a: NCIT:C19160 ! Occupation or Discipline
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000698
name: medical history performed
def: "Whether full medical history was collected. MIXS:0000897" [PRIDE:PRIDE]
is_a: NCIT:C16205 ! Healthcare activity
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000699
name: host pulse
def: "Resting pulse, measured as beats per minutes. MIXS:0000333" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000700
name: perturbation
def: "Type and regimen of perturbation applied to the sample (e.g. chemical administration, physical disturbance), including frequency, duration, and timing. MIXS:0000754" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000701
name: salinity
def: "Total concentration of all dissolved salts in a liquid or solid sample, typically derived from conductivity measurements (practical salinity). MIXS:0000183" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000702
name: oxygenation status of sample
def: "Oxygenation status of the sample. MIXS:0000753" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000703
name: temperature
def: "Temperature of the sample at the time of sampling. MIXS:0000113" [PRIDE:PRIDE]
xref: NCIT:C25206
is_a: NCIT:C25447 ! Characteristic
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000704
name: organism count
def: "Total cell count of any organism per gram, volume, or area of sample, including organism name, count, and enumeration method (e.g. qPCR, ATP, MPN). MIXS:0000103" [PRIDE:PRIDE]
is_a: MMO:0000222 ! isolated cell method
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000705
name: sample storage temperature
def: "Temperature at which sample was stored, e.g. -80 degree Celsius. MIXS:0000110" [PRIDE:PRIDE]
is_a: NCIT:C45279 ! Log
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000706
name: sample volume or weight for DNA extraction
def: "Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001). MIXS:0000111" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000707
name: sample storage duration
def: "Duration for which the sample was stored. Indicate the duration for which the sample was stored written in ISO 8601 format. MIXS:0000116" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000708
name: observed host symbionts
def: "The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. The sampled symbiont can have its own symbionts. For example, parasites may have hyperparasites (=parasites of the parasite). MIXS:0001298" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000709
name: sample storage location
def: "Location at which sample was stored, usually name of a specific freezer/room. MIXS:0000755" [PRIDE:PRIDE]
is_a: GENEPIO:0100586 ! data field
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000710
name: miscellaneous parameter
def: "Any other measurement performed or parameter collected, that is not listed here. MIXS:0000752" [PRIDE:PRIDE]
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000711
name: depth
def: "The vertical distance below local surface. For sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples MIXS:0000018" [PRIDE:PRIDE]
is_a: NCIT:C25447 ! Characteristic
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000712
name: elevation
def: "Height of the sampling site above mean sea level. MIXS:0000093" [PRIDE:PRIDE]
is_a: PATO:0000140 ! Position
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000713
name: current land use
def: "Present state of sample site MIXS:0001080" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000714
name: current vegetation
def: "Vegetation classification from one or more standard classification systems, or agricultural crop MIXS:0000312" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000715
name: current vegetation method
def: "Reference or method used in vegetation classification MIXS:0000314" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000716
name: history of previous land use
def: "Previous land use and dates MIXS:0000315" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000717
name: history of previous land use method
def: "Reference or method used in determining previous land use and dates MIXS:0000316" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000718
name: history of crop rotation
def: "Whether or not crop is rotated, and if yes, rotation schedule MIXS:0000318" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000719
name: history of agrochemical additions
def: "Addition of fertilizers, pesticides, etc. - amount and time of applications MIXS:0000639" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000720
name: history of tillage
def: "Note method(s) used for tilling MIXS:0001081" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000721
name: history of fire
def: "Historical and/or physical evidence of fire MIXS:0001086" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000722
name: history of flooding
def: "Historical and/or physical evidence of flooding MIXS:0000319" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000723
name: history of extreme event
def: "Unusual physical events that may have affected microbial populations MIXS:0000320" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000724
name: obsolete soil horizon
def: "OBSOLETE. Use soil horizon (PRIDE:0001002) instead. Was incorrectly linked to Water environment." [PRIDE:PRIDE]
is_obsolete: true
replaced_by: PRIDE:0001002

[Term]
id: PRIDE:0000725
name: horizon method
def: "Reference or method used in determining the horizon MIXS:0000321" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000726
name: sieving
def: "Collection design of pooled samples and/or sieve size and amount of sample sieved MIXS:0000322" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000727
name: water content
def: "Water content measurement MIXS:0000185" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000728
name: water content method
def: "Reference or method used in determining the water content of soil MIXS:0000323" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000729
name: pooling of DNA extracts
def: "Indicate whether multiple DNA extractions were mixed. If the answer yes, the number of extracts that were pooled should be given MIXS:0000325" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000730
name: storage conditions
def: "Explain how and for how long the soil sample was stored before DNA extraction (fresh/frozen/other) MIXS:0000327" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000731
name: link to climate information
def: "Link to climate resource MIXS:0000328" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000732
name: mean annual temperature
def: "Mean annual temperature MIXS:0000642" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000733
name: mean seasonal temperature
def: "Mean seasonal temperature MIXS:0000643" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000734
name: mean annual precipitation
def: "The average of all annual precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000644" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000735
name: mean seasonal precipitation
def: "The average of all seasonal precipitation values known, or an estimated equivalent value derived by such methods as regional indexes or Isohyetal maps MIXS:0000645" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000736
name: link to classification information
def: "Link to digitized soil maps or other soil classification information MIXS:0000329" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000737
name: soil taxonomic of FAO classification
def: "Soil classification from the FAO World soil distribution from International Soil Reference and Information Centre (ISRIC). The list of available soil classifications can be found at https://www.isric.org/explore/world-soil-distribution MIXS:0001083" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000738
name: soil taxonomic of local classification
def: "Soil classification based on local soil classification system MIXS:0000330" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000739
name: soil taxonomic of local classification method
def: "Reference or method used in determining the local soil classification MIXS:0000331" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000740
name: slope gradient
def: "Commonly called 'slope'. The angle between ground surface and a horizontal line (in percent). This is the direction that overland water would flow. This measure is usually taken with a hand level meter or clinometer MIXS:0000646" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000741
name: slope aspect
def: "The direction a slope faces. While looking down a slope use a compass to record the direction you are facing (direction or degrees); e.g., nw or 315 degrees. This measure provides an indication of sun and wind exposure that will influence soil temperature and evapotranspiration MIXS:0000647" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000742
name: profile position
def: "Cross-sectional position in the hillslope where sample was collected.sample area position in relation to surrounding areas MIXS:0001084" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000743
name: drainage classification
def: "Drainage classification from a standard system such as the USDA system MIXS:0001085" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000744
name: soil texture
def: "The relative proportion of different grain sizes of mineral particles in a soil, as described using a standard system; express as % sand (50 um to 2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty clay loam) optional MIXS:0000335" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000745
name: soil texture method
def: "Reference or method used in determining soil texture MIXS:0000336" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000746
name: pH
def: "Ph measurement of the sample, or liquid portion of sample, or aqueous phase of the fluid MIXS:0001001" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000747
name: pH method
def: "Reference or method used in determining pH MIXS:0001106" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000748
name: organic matter
def: "Concentration of organic matter MIXS:0000204" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000749
name: total organic carbon
def: "Total organic carbon content MIXS:0000533" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000750
name: total organic carbon method
def: "Reference or method used in determining total organic carbon MIXS:0000337" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000751
name: total nitrogen content
def: "Total nitrogen content of the sample MIXS:0000530" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000752
name: total nitrogen content method
def: "Reference or method used in determining the total nitrogen MIXS:0000338" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000753
name: microbial biomass
def: "The part of the organic matter in the soil that constitutes living microorganisms smaller than 5-10 micrometer. If you keep this, you would need to have correction factors used for conversion to the final units MIXS:0000650" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000754
name: microbial biomass method
def: "Reference or method used in determining microbial biomass MIXS:0000339" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000755
name: links to additional analysis
def: "Link to additional analysis results performed on the sample MIXS:0000340" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000756
name: extreme unusual properties of heavy metals
def: "Heavy metals present in the sequenced sample and their concentrations. For multiple heavy metals and concentrations, add multiple copies of this field MIXS:0000652" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000757
name: extreme unusual properties of heavy metals method
def: "Reference or method used in determining heavy metals MIXS:0000343" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000758
name: extreme unusual properties of AI saturation
def: "Aluminum saturation (esp. For tropical soils) MIXS:0000607" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000759
name: extreme unusual properties of AI saturation method
def: "Reference or method used in determining Al saturation MIXS:0000324" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000760
name: alkalinity
def: "Alkalinity, the ability of a solution to neutralize acids to the equivalence point of carbonate or bicarbonate MIXS:0000421" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000761
name: alkalinity method
def: "Method used for alkalinity measurement MIXS:0000298" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000762
name: alkyl diethers
def: "Concentration of alkyl diethers MIXS:0000490" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000763
name: aminopeptidase activity
def: "Measurement of aminopeptidase activity MIXS:0000172" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000764
name: ammonium
def: "Concentration of ammonium in the sample MIXS:0000427" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000765
name: atmospheric data
def: "Measurement of atmospheric data; can include multiple data MIXS:0001097" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000766
name: bacterial carbon production
def: "Measurement of bacterial carbon production MIXS:0000173" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000767
name: bacterial production
def: "Bacterial production in the water column measured by isotope uptake MIXS:0000683" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000768
name: bacterial respiration
def: "Measurement of bacterial respiration in the water column MIXS:0000684" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000769
name: biomass
def: "Amount of biomass; should include the name for the part of biomass measured, e.g. Microbial, total. Can include multiple measurements MIXS:0000174" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000770
name: bishomohopanol
def: "Concentration of bishomohopanol MIXS:0000175" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000771
name: bromide
def: "Concentration of bromide MIXS:0000176" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000772
name: calcium
def: "Concentration of calcium in the sample MIXS:0000432" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000773
name: carbon nitrogen ratio
def: "Ratio of amount or concentrations of carbon to nitrogen MIXS:0000310" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000774
name: chloride
def: "Concentration of chloride in the sample MIXS:0000429" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000775
name: chlorophyll
def: "Concentration of chlorophyll MIXS:0000177" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000776
name: conductivity
def: "Electrical conductivity of water MIXS:0000692" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000777
name: density
def: "Density of the sample, which is its mass per unit volume (aka volumetric mass density) MIXS:0000435" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000778
name: diether lipids
def: "Concentration of diether lipids; can include multiple types of diether lipids MIXS:0000178" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000779
name: dissolved carbon dioxide
def: "Concentration of dissolved carbon dioxide in the sample or liquid portion of the sample MIXS:0000436" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000780
name: dissolved hydrogen
def: "Concentration of dissolved hydrogen MIXS:0000179" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000781
name: dissolved inorganic carbon
def: "Dissolved inorganic carbon concentration in the sample, typically measured after filtering the sample using a 0.45 micrometer filter MIXS:0000434" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000784
name: dissolved inorganic nitrogen
def: "Concentration of dissolved inorganic nitrogen MIXS:0000698" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000785
name: dissolved inorganic phosphorus
def: "Concentration of dissolved inorganic phosphorus in the sample MIXS:0000106" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000786
name: dissolved organic carbon
def: "Concentration of dissolved organic carbon in the sample, liquid portion of the sample, or aqueous phase of the fluid MIXS:0000433" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000787
name: dissolved organic nitrogen
def: "Dissolved organic nitrogen concentration measured as; total dissolved nitrogen - NH4 - NO3 - NO2 MIXS:0000162" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000788
name: dissolved oxygen
def: "Concentration of dissolved oxygen MIXS:0000119" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000789
name: downward PAR
def: "Visible waveband radiance and irradiance measurements in the water column MIXS:0000703" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000790
name: fluorescence
def: "Raw or converted fluorescence of water MIXS:0000704" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000791
name: glucosidase activity
def: "Measurement of glucosidase activity MIXS:0000137" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000792
name: light intensity
def: "Measurement of light intensity MIXS:0000706" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000793
name: magnesium
def: "Concentration of magnesium in the sample MIXS:0000431" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000794
name: mean friction velocity
def: "Measurement of mean friction velocity MIXS:0000498" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000795
name: mean peak friction velocity
def: "Measurement of mean peak friction velocity MIXS:0000502" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000796
name: nitrate
def: "Concentration of nitrate in the sample MIXS:0000425" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000797
name: nitrite
def: "Concentration of nitrite in the sample MIXS:0000426" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000798
name: nitrogen
def: "Concentration of nitrogen (total) MIXS:0000504" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000799
name: organic carbon
def: "Concentration of organic carbon MIXS:0000508" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000800
name: organic nitrogen
def: "Concentration of organic nitrogen MIXS:0000205" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000801
name: particulate organic carbon
def: "Concentration of particulate organic carbon MIXS:0000515" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000802
name: particulate organic nitrogen
def: "Concentration of particulate organic nitrogen MIXS:0000719" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000803
name: petroleum hydrocarbon
def: "Concentration of petroleum hydrocarbon MIXS:0000516" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000804
name: phaeopigments
def: "Concentration of phaeopigments; can include multiple phaeopigments MIXS:0000180" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000805
name: phosphate
def: "Concentration of phosphate MIXS:0000505" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000806
name: phospholipid fatty acid
def: "Concentration of phospholipid fatty acids; can include multiple values MIXS:0000181" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000807
name: photon flux
def: "Measurement of photon flux MIXS:0000725" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000808
name: potassium
def: "Concentration of potassium in the sample MIXS:0000430" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000809
name: pressure
def: "Pressure to which the sample is subject to, in atmospheres MIXS:0000412" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000810
name: primary production
def: "Measurement of primary production, generally measured as isotope uptake MIXS:0000728" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000811
name: redox potential
def: "Redox potential, measured relative to a hydrogen cell, indicating oxidation or reduction potential MIXS:0000182" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000812
name: silicate
def: "Concentration of silicate MIXS:0000184" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000813
name: size-fraction lower threshold
def: "Refers to the mesh/pore size used to pre-filter/pre-sort the sample. Materials smaller than the size threshold are excluded from the sample MIXS:0000735" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000814
name: size-fraction upper threshold
def: "Mesh or pore size of the device used to retain the sample. Materials larger than the size threshold are excluded from the sample MIXS:0000736" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000815
name: sodium
def: "Sodium concentration in the sample MIXS:0000428" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000816
name: soluble reactive phosphorus
def: "Concentration of soluble reactive phosphorus MIXS:0000738" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000817
name: sulfate
def: "Concentration of sulfate in the sample MIXS:0000423" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000818
name: sulfide
def: "Concentration of sulfide in the sample MIXS:0000424" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000819
name: suspended particulate matter
def: "Concentration of suspended particulate matter MIXS:0000741" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000820
name: tidal stage
def: "Stage of tide MIXS:0000750" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000821
name: total depth of water column
def: "Measurement of total depth of water column MIXS:0000634" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000822
name: total dissolved nitrogen
def: "Total dissolved nitrogen concentration, reported as nitrogen, measured by: total dissolved nitrogen = NH4 + NO3NO2 + dissolved organic nitrogen MIXS:0000744" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000823
name: total inorganic nitrogen
def: "Total inorganic nitrogen content MIXS:0000745" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000824
name: total nitrogen concentration
def: "Total nitrogen concentration of water samples, calculated by: total nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured without filtering, reported as nitrogen MIXS:0000102" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000825
name: total particulate carbon
def: "Total particulate carbon content MIXS:0000747" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000826
name: total phosphorus
def: "Total phosphorus concentration in the sample, calculated by: total phosphorus = total dissolved phosphorus + particulate phosphorus MIXS:0000117" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000827
name: turbidity
def: "Measure of the amount of cloudiness or haziness in water caused by individual particles MIXS:0000191" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0000828
name: soil
def: "A collection of terms appropriate when collecting samples and sequencing samples obtained from the uppermost layer of Earth's crust, contributed by the Terragenome Consortium" [PRIDE:PRIDE]
is_a: PRIDE:0000904 ! metaproteomics sample
is_a: ENVO:00010483 ! environmental material

[Term]
id: PRIDE:0000829
name: water
def: "A collection of terms appropriate when collecting samples and sequencing water samples obtained from any aquatic environment" [PRIDE:PRIDE]
is_a: PRIDE:0000904 ! metaproteomics sample
is_a: ENVO:00002006 ! liquid water

[Term]
id: PRIDE:0000830
name: Olink Reveal
def: "Olink Reveal is an NGS-based proteomics platform that measures approximately 1,000 proteins with high sensitivity from just 4 µL of sample, using standard lab equipment, with a focus on immune and inflammation markers" [PRIDE:PRIDE]
is_a: PRIDE:0000654 ! Olink platform

[Term]
id: PRIDE:0000831
name: file format
def: "A defined organization or layout representing and structuring data in a file. The file format specifies how information is encoded, stored, and interpreted within the file." [PRIDE:PRIDE]
synonym: "file_format" EXACT [PRIDE]
xref: NCIT:C171252
is_a: PRIDE:0000470 ! File Properties

[Term]
id: PRIDE:0000832
name: sdrf template
def: "The template name and version used to annotate an SDRF file, specified as 'template_name,version=vX.Y.Z' format. Multiple templates can be combined (e.g., human + ms-proteomics)" [PRIDE:PRIDE]
synonym: "template" EXACT [PRIDE]
is_a: PRIDE:0000470 ! File Properties

[Term]
id: PRIDE:0000834
name: sdrf validation hash
def: "A cryptographic hash (e.g., SHA-256) generated after successful validation of an SDRF file against a specific template, used to verify file integrity and validation status" [PRIDE:PRIDE]
synonym: "validation_hash" EXACT [PRIDE]
is_a: PRIDE:0000470 ! File Properties

[Term]
id: PRIDE:0000835
name: cellosaurus accession
def: "An accession to a cellosaurus cell line that could be used to annotate SDRF samples" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000836
name: cellosaurus name
def: "A name to a cellosaurus cell line that could be used to annotate SDRF samples" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000837
name: material type
def: "Material type describes the type of biological material" [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: EFO:0009090
name: enrichment process
def: "A process by which a cell or organism is exposed to specific substances or conditions to selectively enrich for specific molecules or modifications." [EFO:EFO]

[Term]
id: EFO:0010806
name: enrichment of phosphorylated protein
def: "A sample enrichment process where phosphorylated proteins or peptides are selectively enriched prior to analysis." [EFO:EFO]
is_a: EFO:0009090 ! enrichment process

[Term]
id: PRIDE:0000838
name: enrichment of cross-linked peptides
def: "Selective enrichment of cross-linked peptides prior to mass spectrometry analysis, typically using size exclusion or strong cation exchange chromatography." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: EFO:0009090 ! enrichment process

[Term]
id: PRIDE:0000839
name: sdrf version
def: "The version of the SDRF-Proteomics specification used to annotate the file, following semantic versioning format (e.g., v1.1.0)" [PRIDE:PRIDE]
synonym: "sdrf_version" EXACT [PRIDE]
is_a: PRIDE:0000470 ! File Properties

[Term]
id: PRIDE:0000840
name: sdrf annotation tool
def: "The software tool, script, or manual curation method used to generate or annotate SDRF metadata and column values" [PRIDE:PRIDE]
synonym: "annotation_tool" EXACT [PRIDE]
is_a: PRIDE:0000470 ! File Properties

[Term]
id: PRIDE:0000841
name: MS min IM
def: "Minimum ion mobility value in the file" [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties

[Term]
id: PRIDE:0000842
name: MS max IM
def: "Maximum ion mobility value in the file" [PRIDE:PRIDE]
is_a: PRIDE:0000471 ! MS File Properties

[Term]
id: PRIDE:0000843
name: DIMETHYL2PLEX
def: "Dimethyl 2-plex labeling kit has 2 channels" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling

[Term]
id: PRIDE:0000844
name: DIMETHYL3PLEX
def: "Dimethyl 3-plex labeling kit has 3 channels" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling

[Term]
id: PRIDE:0000845
name: DIMETHYL5PLEX
def: "Dimethyl 5-plex labeling kit has 5 channels" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling

[Term]
id: PRIDE:0000846
name: mTRAQ
def: "mTRAQ is a non-isobaric mass difference labeling technique for multiplexed quantification" [PRIDE:PRIDE]
is_a: PRIDE:0000316 ! MS1 based isotope labeling
is_a: PRIDE:0000514 ! Label

[Term]
id: PRIDE:0000847
name: MTRAQ3PLEX
def: "mTRAQ 3-plex labeling kit has 3 channels (0, 4, 8)" [PRIDE:PRIDE]
is_a: PRIDE:0000846 ! mTRAQ

[Term]
id: PRIDE:0000848
name: DIMETHYL0
def: "Dimethyl channel 0, base mass 28.0313 Da, delta 0" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling
relationship: part_of PRIDE:0000843 ! DIMETHYL2PLEX
relationship: part_of PRIDE:0000844 ! DIMETHYL3PLEX
relationship: part_of PRIDE:0000845 ! DIMETHYL5PLEX

[Term]
id: PRIDE:0000849
name: DIMETHYL2
def: "Dimethyl channel 2, delta +2.0126 Da from channel 0" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling
relationship: part_of PRIDE:0000843 ! DIMETHYL2PLEX
relationship: part_of PRIDE:0000844 ! DIMETHYL3PLEX
relationship: part_of PRIDE:0000845 ! DIMETHYL5PLEX

[Term]
id: PRIDE:0000850
name: DIMETHYL4
def: "Dimethyl channel 4, delta +4.0251 Da from channel 0" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling
relationship: part_of PRIDE:0000844 ! DIMETHYL3PLEX
relationship: part_of PRIDE:0000845 ! DIMETHYL5PLEX

[Term]
id: PRIDE:0000851
name: DIMETHYL6
def: "Dimethyl channel 6, delta +6.0377 Da from channel 0" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling
relationship: part_of PRIDE:0000845 ! DIMETHYL5PLEX

[Term]
id: PRIDE:0000852
name: DIMETHYL8
def: "Dimethyl channel 8, delta +8.0444 Da from channel 0" [PRIDE:PRIDE]
is_a: PRIDE:0000513 ! Dimethyl Labeling
relationship: part_of PRIDE:0000845 ! DIMETHYL5PLEX

[Term]
id: PRIDE:0000853
name: MTRAQ0
def: "mTRAQ reagent channel 0, base mass 140.0950 Da, delta 0" [PRIDE:PRIDE]
is_a: PRIDE:0000846 ! mTRAQ
relationship: part_of PRIDE:0000847 ! MTRAQ3PLEX

[Term]
id: PRIDE:0000854
name: MTRAQ4
def: "mTRAQ reagent channel 4, delta +4.0071 Da from channel 0" [PRIDE:PRIDE]
is_a: PRIDE:0000846 ! mTRAQ
relationship: part_of PRIDE:0000847 ! MTRAQ3PLEX

[Term]
id: PRIDE:0000855
name: MTRAQ8
def: "mTRAQ reagent channel 8, delta +8.0142 Da from channel 0" [PRIDE:PRIDE]
is_a: PRIDE:0000846 ! mTRAQ
relationship: part_of PRIDE:0000847 ! MTRAQ3PLEX

[Term]
id: PRIDE:0000856
name: ITRAQ4PLEX
def: "iTRAQ 4-plex labeling kit has 4 channels (114, 115, 116, 117)" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ

[Term]
id: PRIDE:0000857
name: ITRAQ8PLEX
def: "iTRAQ 8-plex labeling kit has 8 channels (113, 114, 115, 116, 117, 118, 119, 121)" [PRIDE:PRIDE]
is_a: PRIDE:0000530 ! ITRAQ

[Term]
id: PRIDE:0000858
name: TMT11PLEX
def: "TMT 11-plex labeling kit has 11 channels (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131, 131C)" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000859
name: TMT32PLEX
def: "TMTpro 32-plex labeling kit has 32 channels: 16 non-deuterated (126-134N) and 16 deuterated (127D-135ND)" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000860
name: TMT35PLEX
def: "TMTpro 35-plex labeling kit has 35 channels: 18 non-deuterated (126-135N) and 16 deuterated (127D-135ND) plus 135CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000878
name: TMT34PLEX
def: "TMTpro 34-plex labeling kit has 34 channels: 32-plex (16 non-deuterated + 16 deuterated) plus 134C and 135CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT

[Term]
id: PRIDE:0000861
name: TMT127D
def: "TMTpro deuterated channel 127D" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000862
name: TMT128ND
def: "TMTpro deuterated channel 128ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000863
name: TMT128CD
def: "TMTpro deuterated channel 128CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000864
name: TMT129ND
def: "TMTpro deuterated channel 129ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000865
name: TMT129CD
def: "TMTpro deuterated channel 129CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000866
name: TMT130ND
def: "TMTpro deuterated channel 130ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000867
name: TMT130CD
def: "TMTpro deuterated channel 130CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000868
name: TMT131ND
def: "TMTpro deuterated channel 131ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000869
name: TMT131CD
def: "TMTpro deuterated channel 131CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000870
name: TMT132ND
def: "TMTpro deuterated channel 132ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000871
name: TMT132CD
def: "TMTpro deuterated channel 132CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000872
name: TMT133ND
def: "TMTpro deuterated channel 133ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000873
name: TMT133CD
def: "TMTpro deuterated channel 133CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000874
name: TMT134ND
def: "TMTpro deuterated channel 134ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000875
name: TMT134CD
def: "TMTpro deuterated channel 134CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000876
name: TMT135ND
def: "TMTpro deuterated channel 135ND" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000859 ! TMT32PLEX
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000877
name: TMT135CD
def: "TMTpro deuterated channel 135CD" [PRIDE:PRIDE]
is_a: PRIDE:0000314 ! TMT
relationship: part_of PRIDE:0000878 ! TMT34PLEX
relationship: part_of PRIDE:0000860 ! TMT35PLEX

[Term]
id: PRIDE:0000893
name: MHC typing
def: "MHC allelic composition of a biological sample following IPD-MHC nomenclature." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
xref: NCIT:C71329

[Term]
id: PRIDE:0000894
name: MHC typing method
def: "Method used to determine MHC alleles of a biological sample. Common methods include NGS-based typing, sequence-based typing." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
xref: NCIT:C71329

[Term]
id: PRIDE:0000895
name: sample type
def: "Classification of the sample role in a proteomics experiment. Distinguishes study samples under investigation from controls, references, and other channel roles in multiplexed or plate-based experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
xref: NCIT:C210102

[Term]
id: PRIDE:0001013
name: study sample
def: "Biological or experimental sample representing a unit under investigation in the study, as opposed to control, reference, calibration, or quality-monitoring materials." [PRIDE:PRIDE]
synonym: "experimental sample" EXACT []
synonym: "analyte sample" RELATED []
is_a: PRIDE:0000895 ! sample type

[Term]
id: PRIDE:0000897
name: single cell
def: "A sample consisting of a single isolated cell for single-cell proteomics analysis." [PRIDE:PRIDE]
is_a: PRIDE:0000895 ! sample type

[Term]
id: PRIDE:0000898
name: multiplex sample
def: "A sample role in multiplexed experiments (TMT, iTRAQ) or plate-based assays (Olink, SomaScan). Groups channel-specific roles like reference, bridge, carrier, pooled, and empty." [PRIDE:PRIDE]
is_a: PRIDE:0000895 ! sample type

[Term]
id: PRIDE:0000899
name: reference
def: "A reference sample used for normalization across multiplexed sets (TMT/iTRAQ batches) or plates. Provides a common baseline for quantitative comparison." [PRIDE:PRIDE]
is_a: PRIDE:0000898 ! multiplex sample

[Term]
id: PRIDE:0000900
name: bridge
def: "A bridge sample shared across multiplexed sets or plates to enable cross-batch normalization and data integration." [PRIDE:PRIDE]
is_a: PRIDE:0000898 ! multiplex sample

[Term]
id: PRIDE:0000901
name: carrier
def: "A carrier proteome sample used in carrier-assisted single-cell proteomics methods (e.g. SCoPE-MS) to boost peptide identification." [PRIDE:PRIDE]
is_a: PRIDE:0000898 ! multiplex sample

[Term]
id: PRIDE:0000902
name: pooled
def: "A pooled sample created by combining material from multiple sources, used as a reference or normalization standard in multiplexed experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000898 ! multiplex sample

[Term]
id: PRIDE:0000903
name: empty
def: "An intentionally empty channel or well used for signal-to-noise assessment or as a blank in multiplexed experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000898 ! multiplex sample

[Term]
id: PRIDE:0000904
name: metaproteomics sample
def: "A sample collected for metaproteomics analysis. Groups metaproteomics-specific metadata collections such as human gut, soil, and water." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000905
name: negative control
def: "A negative control sample containing no analyte of interest, used to assess background signal and non-specific binding." [PRIDE:PRIDE]
is_a: PRIDE:0001014 ! control sample

[Term]
id: PRIDE:0000906
name: positive control
def: "A positive control sample with known analyte content, used to verify assay sensitivity and specificity." [PRIDE:PRIDE]
is_a: PRIDE:0001014 ! control sample

[Term]
id: PRIDE:0000907
name: bulk control
def: "A bulk sample used as a control in single-cell proteomics experiments to benchmark single-cell measurements against bulk-level measurements." [PRIDE:PRIDE]
is_a: PRIDE:0001014 ! control sample

[Term]
id: PRIDE:0000908
name: standard
def: "A calibration sample with well-characterized known composition used as a reference material for quantification or method benchmarking (e.g. digested proteome standards in mass spectrometry workflows)." [PRIDE:PRIDE]
is_a: PRIDE:0001015 ! calibration sample

[Term]
id: PRIDE:0000909
name: calibrator
def: "Calibration sample used during assay or instrument processing to set or correct measurement values (e.g. Olink Calibrator, SomaScan Calibrator Control)." [PRIDE:PRIDE]
is_a: PRIDE:0001015 ! calibration sample

[Term]
id: PRIDE:0000910
name: plate control
def: "A plate-level control sample used in plate-based assays (Olink, SomaScan) to monitor intra-plate and inter-plate variability." [PRIDE:PRIDE]
is_a: PRIDE:0001014 ! control sample

[Term]
id: PRIDE:0000911
name: buffer control
def: "A buffer-only control sample used to assess background signal from reagents and sample processing." [PRIDE:PRIDE]
is_a: PRIDE:0001014 ! control sample

[Term]
id: PRIDE:0000912
name: assay platform
def: "The specific assay platform or instrument system used to perform a proteomics experiment, such as Olink Explore, SomaScan, or other affinity-based or mass-spectrometry-based platforms." [PRIDE:PRIDE]
is_a: PRIDE:0000663 ! technology type

[Term]
id: PRIDE:0000913
name: assay panel
def: "A defined set of protein targets measured simultaneously in a proteomics assay, such as an Olink panel or SomaScan menu." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000914
name: Olink panel
def: "A panel of protein biomarkers measured using Olink proximity extension assay (PEA) technology." [PRIDE:PRIDE]
is_a: PRIDE:0000913 ! assay panel

[Term]
id: PRIDE:0000915
name: Olink Inflammation
def: "Olink Target 96 Inflammation panel measuring 92 inflammation-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000916
name: Olink Cardiovascular II
def: "Olink Target 96 Cardiovascular II panel measuring 92 cardiovascular-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000917
name: Olink Cardiovascular III
def: "Olink Target 96 Cardiovascular III panel measuring 92 cardiovascular-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000918
name: Olink Cardiometabolic
def: "Olink Target 96 Cardiometabolic panel measuring 92 cardiometabolic-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000919
name: Olink Immuno-Oncology
def: "Olink Target 96 Immuno-Oncology panel measuring 92 immuno-oncology-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000920
name: Olink Immune Response
def: "Olink Target 96 Immune Response panel measuring 92 immune response-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000921
name: Olink Neurology
def: "Olink Target 96 Neurology panel measuring 92 neurology-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000922
name: Olink Neuro Exploratory
def: "Olink Target 96 Neuro Exploratory panel measuring 92 neurology-related protein biomarkers for exploratory research." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000923
name: Olink Oncology II
def: "Olink Target 96 Oncology II panel measuring 92 oncology-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000924
name: Olink Oncology III
def: "Olink Target 96 Oncology III panel measuring 92 oncology-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000925
name: Olink Organ Damage
def: "Olink Target 96 Organ Damage panel measuring 92 organ damage-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000926
name: Olink Development
def: "Olink Target 96 Development panel measuring 92 developmental biology-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000927
name: Olink Metabolism
def: "Olink Target 96 Metabolism panel measuring 92 metabolism-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000928
name: Olink Cell Regulation
def: "Olink Target 96 Cell Regulation panel measuring 92 cell regulation-related protein biomarkers." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000929
name: Olink Mouse Exploratory
def: "Olink Target 96 Mouse Exploratory panel measuring 92 mouse protein biomarkers for exploratory research." [PRIDE:PRIDE]
is_a: PRIDE:0000914 ! Olink panel

[Term]
id: PRIDE:0000930
name: SomaScan panel
def: "A panel (menu) of protein targets measured using SomaLogic SomaScan aptamer-based proteomics technology." [PRIDE:PRIDE]
is_a: PRIDE:0000913 ! assay panel

[Term]
id: PRIDE:0000931
name: SomaScan 1.3K
def: "SomaScan 1.3K assay menu measuring approximately 1,300 protein targets using SOMAmer reagents." [PRIDE:PRIDE]
is_a: PRIDE:0000930 ! SomaScan panel

[Term]
id: PRIDE:0000932
name: SomaScan Select 3.7K
def: "SomaScan Select 3.7K assay menu measuring approximately 3,700 protein targets using SOMAmer reagents." [PRIDE:PRIDE]
is_a: PRIDE:0000930 ! SomaScan panel

[Term]
id: PRIDE:0000933
name: SomaScan 5K
def: "SomaScan 5K assay menu (v4.0) measuring approximately 5,000 protein targets using SOMAmer reagents." [PRIDE:PRIDE]
is_a: PRIDE:0000930 ! SomaScan panel

[Term]
id: PRIDE:0000934
name: SomaScan 7K
def: "SomaScan 7K assay menu (v4.1) measuring 7,288 protein targets using SOMAmer reagents." [PRIDE:PRIDE]
is_a: PRIDE:0000930 ! SomaScan panel

[Term]
id: PRIDE:0000935
name: SomaScan 11K
def: "SomaScan 11K assay menu (v5.0) measuring 10,776 protein targets using SOMAmer reagents." [PRIDE:PRIDE]
is_a: PRIDE:0000930 ! SomaScan panel

[Term]
id: PRIDE:0000936
name: flow cytometry parameter
def: "A parameter measured during flow cytometry or fluorescence-activated cell sorting (FACS) that describes a physical or optical property of individual cells." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000937
name: forward scatter
def: "Forward scatter (FSC) measurement from flow cytometry, representing the amount of laser light scattered at small angles as a cell passes through the beam. Used as a proxy for cell size in FACS-based single-cell isolation." [PRIDE:PRIDE]
is_a: PRIDE:0000936 ! flow cytometry parameter

[Term]
id: PRIDE:0000938
name: side scatter
def: "Side scatter (SSC) measurement from flow cytometry, representing the amount of laser light scattered at approximately 90 degrees as a cell passes through the beam. Used as a proxy for cell granularity and internal complexity in FACS-based single-cell isolation." [PRIDE:PRIDE]
is_a: PRIDE:0000936 ! flow cytometry parameter

[Term]
id: PRIDE:0000939
name: spatial coordinates
def: "X,Y coordinates describing the physical location of a cell or region of interest within a tissue section, used in spatially resolved single-cell proteomics experiments such as laser capture microdissection (LCM)." [PRIDE:PRIDE]
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0000940
name: enrichment marker
def: "Markers used for cell sorting or enrichment in single-cell proteomics experiments, including surface markers, fluorescent proteins, and viability dyes with optional intensity values (e.g., CD45+, GFP+, CD34:APC-Cy7-A=276.0, PI-)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000941
name: environmental sample
def: "An environmental sample analyzed in metaproteomics experiments, such as soil, water, sediment, air, or biofilm collected from a natural or engineered environment." [PRIDE:PRIDE]
is_a: PRIDE:0000895 ! sample type

[Term]
id: PRIDE:0000942
name: crosslinking sample property
def: "A property describing experimental conditions of a chemical crosslinking reaction applied to a sample in crosslinking mass spectrometry (XL-MS) experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000943
name: reaction time
def: "Duration of a chemical reaction applied to a sample during sample preparation (e.g., crosslinking, labeling, digestion)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000944
name: reaction temperature
def: "Temperature at which a chemical reaction is carried out on a sample during sample preparation (e.g., crosslinking, labeling, digestion)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000945
name: reagent concentration
def: "Concentration of a chemical reagent used in sample preparation (e.g., crosslinker, labeling reagent, protease)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000946
name: reagent to protein ratio
def: "Molar ratio of a chemical reagent to protein in a sample preparation reaction (e.g., crosslinker-to-protein ratio, labeling reagent-to-protein ratio)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000947
name: quenching reagent
def: "Reagent used to stop or quench a chemical reaction during sample preparation (e.g., Tris, glycine, ammonium bicarbonate for crosslinking; hydroxylamine for TMT labeling)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000948
name: crosslink distance
def: "Spacer arm length of a chemical crosslinker in angstroms, defining the maximum distance between crosslinked residues." [PRIDE:PRIDE]
synonym: "spacer arm length" EXACT []
is_a: PRIDE:0000942 ! crosslinking sample property

[Term]
id: PRIDE:0000949
name: crosslinking reaction time
def: "Duration of the crosslinking reaction applied to a sample in crosslinking mass spectrometry (XL-MS) experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000942 ! crosslinking sample property
is_a: PRIDE:0000943 ! reaction time

[Term]
id: PRIDE:0000950
name: crosslinking temperature
def: "Temperature during the crosslinking reaction in crosslinking mass spectrometry (XL-MS) experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000942 ! crosslinking sample property
is_a: PRIDE:0000944 ! reaction temperature

[Term]
id: PRIDE:0000951
name: crosslinker concentration
def: "Concentration of crosslinking reagent used in crosslinking mass spectrometry (XL-MS) experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000942 ! crosslinking sample property
is_a: PRIDE:0000945 ! reagent concentration

[Term]
id: PRIDE:0000952
name: crosslinker to protein ratio
def: "Molar ratio of crosslinker to protein in crosslinking mass spectrometry (XL-MS) experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000942 ! crosslinking sample property
is_a: PRIDE:0000946 ! reagent to protein ratio

[Term]
id: PRIDE:0000953
name: crosslinking quenching reagent
def: "Reagent used to quench the crosslinking reaction (e.g., Tris, glycine, ammonium bicarbonate)." [PRIDE:PRIDE]
is_a: PRIDE:0000942 ! crosslinking sample property
is_a: PRIDE:0000947 ! quenching reagent

[Term]
id: PRIDE:0000954
name: antibody enrichment
def: "Antibody used for enrichment in proteomics experiments, such as immunoprecipitation (IP), immunoaffinity purification, or immunopeptidomics (e.g., anti-HLA antibody for MHC peptide isolation)." [PRIDE:PRIDE]
synonym: "antibody used" EXACT []
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000955
name: cell line authentication
def: "Method used to authenticate the identity of a cell line, such as STR (Short Tandem Repeat) profiling, SNP analysis, karyotyping, or isoenzyme analysis." [PRIDE:PRIDE]
synonym: "cell line authentication method" EXACT []
synonym: "authentication method" EXACT []
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000956
name: metagenome accession
def: "Accession number of the associated metagenomic database or assembly used for peptide identification in metaproteomics experiments (e.g., NCBI BioProject, MGnify, or custom metagenome-assembled genome accession)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000957
name: DIA-NN score
def: "A score or metric produced by the DIA-NN software for data-independent acquisition proteomics data processing." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000958
name: DIA-NN:CScore
def: "DIA-NN confidence score combining multiple scoring features. Higher values indicate better confidence." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000959
name: DIA-NN:Evidence
def: "DIA-NN co-elution evidence score measuring the agreement between observed and expected chromatographic elution profiles. Higher values indicate better evidence." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000960
name: DIA-NN:Decoy.CScore
def: "DIA-NN confidence score for the paired decoy match. Used for target-decoy FDR estimation. Higher values indicate better decoy confidence." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000961
name: DIA-NN:Decoy.Evidence
def: "DIA-NN evidence score for the paired decoy match. Used for target-decoy FDR estimation. Higher values indicate better decoy evidence." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000962
name: DIA-NN:Mass.Evidence
def: "DIA-NN mass accuracy scoring contribution reflecting the agreement between observed and theoretical precursor masses. Higher values indicate better mass accuracy." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000963
name: DIA-NN:Averagine
def: "DIA-NN isotope pattern fit score against the Averagine model. Measures how well the observed isotope envelope matches the theoretical pattern. Higher values indicate better fit." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000964
name: DIA-NN:Ms1.Profile.Corr
def: "DIA-NN correlation between MS1 and MS2 chromatographic elution profiles. Measures how well the precursor and fragment ion traces co-elute. Higher values indicate better correlation." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000965
name: DIA-NN:Quantity.Quality
def: "DIA-NN quantification quality score calculated as 1/(1+SD) where SD is the standard deviation of fragment ion ratios. Higher values indicate more consistent quantification." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000966
name: DIA-NN:Translated.Quality
def: "DIA-NN plexDIA translation quality score measuring the quality of multiplexed DIA quantification. Higher values indicate better translation quality." [PRIDE:PRIDE]
is_a: PRIDE:0000957 ! DIA-NN score

[Term]
id: PRIDE:0000967
name: DIA-NN q-value
def: "A q-value calculated by DIA-NN for false discovery rate estimation." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000968
name: DIA-NN:Q.Value
def: "DIA-NN run-level precursor q-value for false discovery rate estimation at the precursor level within a single run. Lower values indicate higher confidence." [PRIDE:PRIDE]
is_a: PRIDE:0000967 ! DIA-NN q-value

[Term]
id: PRIDE:0000969
name: DIA-NN:Global.Q.Value
def: "DIA-NN global q-value for false discovery rate estimation at the experiment level across all runs. Lower values indicate higher confidence." [PRIDE:PRIDE]
is_a: PRIDE:0000967 ! DIA-NN q-value

[Term]
id: PRIDE:0000970
name: DIA-NN:Translated.Q.Value
def: "DIA-NN plexDIA translated q-value for false discovery rate estimation in multiplexed DIA experiments. Lower values indicate higher confidence." [PRIDE:PRIDE]
is_a: PRIDE:0000967 ! DIA-NN q-value

[Term]
id: PRIDE:0000971
name: MSFragger score
def: "A score or metric produced by the MSFragger search engine for peptide identification." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000972
name: MSFragger:Expectation
def: "MSFragger expectation value representing the expected number of peptides with a score equal to or better than the observed score by chance. Lower values indicate better matches." [PRIDE:PRIDE]
is_a: PRIDE:0000971 ! MSFragger score

[Term]
id: PRIDE:0000973
name: MSFragger:Hyperscore
def: "MSFragger hyperscore combining the number and intensity of matched fragment ions. Higher values indicate better peptide-spectrum matches." [PRIDE:PRIDE]
is_a: PRIDE:0000971 ! MSFragger score

[Term]
id: PRIDE:0000974
name: Sage score
def: "A score or metric produced by the Sage search engine for peptide identification." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000975
name: Sage:hyperscore
def: "Sage search engine hyperscore measuring the quality of a peptide-spectrum match. Higher values indicate better matches." [PRIDE:PRIDE]
is_a: PRIDE:0000974 ! Sage score

[Term]
id: PRIDE:0000976
name: MaxLFQ intensity
def: "Label-free quantification intensity calculated using the MaxLFQ algorithm in MaxQuant. Represents protein abundance estimated by delayed normalization and maximal peptide ratio extraction." [PRIDE:PRIDE]
is_a: PRIDE:0000391 ! Quantification parameter

[Term]
id: PRIDE:0000977
name: consensus support
def: "The number of search engines that support a given peptide identification in a consensus or multi-engine search strategy. Higher values indicate broader agreement." [PRIDE:PRIDE]
is_a: PRIDE:0000049 ! Peptide search engine output parameter

[Term]
id: PRIDE:0000978
name: parent ion fraction
def: "The fraction of target peak intensity relative to the total intensity within the precursor isolation window. Higher values indicate less co-fragmentation interference." [PRIDE:PRIDE]
is_a: PRIDE:0000391 ! Quantification parameter

[Term]
id: PRIDE:0000979
name: precursor quantification score
def: "A score reflecting the confidence of precursor-level quantification, typically derived from QuantUMS or similar algorithms. Higher values indicate more reliable quantification." [PRIDE:PRIDE]
is_a: PRIDE:0000391 ! Quantification parameter

[Term]
id: PRIDE:0000980
name: single cell isolation instrument parameter
def: "A parameter describing the instrument or device configuration used for single cell isolation in single-cell proteomics experiments." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0000981
name: FACS nozzle size
def: "Nozzle diameter used for fluorescence-activated cell sorting (FACS) based single cell isolation, typically measured in micrometers (e.g., 70 um, 100 um, 130 um)." [PRIDE:PRIDE]
is_a: PRIDE:0000980 ! single cell isolation instrument parameter

[Term]
id: PRIDE:0000982
name: FACS sorting mode
def: "Sorting mode used during fluorescence-activated cell sorting (FACS) for single cell isolation (e.g., single cell, purity, yield, 4-way purity)." [PRIDE:PRIDE]
is_a: PRIDE:0000980 ! single cell isolation instrument parameter

[Term]
id: PRIDE:0000983
name: microfluidics chip type
def: "Type and manufacturer of the microfluidics chip used for single cell isolation and processing (e.g., Fluidigm C1, Cellenion cellenCHIP, nanowell chip)." [PRIDE:PRIDE]
is_a: PRIDE:0000980 ! single cell isolation instrument parameter

[Term]
id: PRIDE:0000984
name: LCM microscope model
def: "Model of the laser capture microdissection (LCM) microscope used for single cell isolation from tissue sections (e.g., Leica LMD7, Zeiss PALM MicroBeam)." [PRIDE:PRIDE]
is_a: PRIDE:0000980 ! single cell isolation instrument parameter

[Term]
id: PRIDE:0000985
name: nanoPOTS chip version
def: "Version of the nanoPOTS (nanodroplet Processing in One pot for Trace Samples) chip used for single cell sample preparation (e.g., nanoPOTS v1, nanoPOTS v2, 9-well chip)." [PRIDE:PRIDE]
is_a: PRIDE:0000980 ! single cell isolation instrument parameter

[Term]
id: PRIDE:0000986
name: microbiome source
def: "Source of the microbiome being studied in a metaproteomics experiment (e.g., gut microbiome, rhizosphere microbiome, oral microbiome, skin microbiome)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000987
name: mock community
def: "Identifier or name of the mock community standard used as a quality control reference in metaproteomics experiments (e.g., ZymoBIOMICS Microbial Community Standard, ATCC MSA-1000)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000988
name: mock community composition
def: "Description of the mock community composition including species and ratios used as a quality control reference in metaproteomics experiments (e.g., 8 bacteria + 2 yeasts at defined ratios)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000989
name: expected organism list
def: "Semicolon-separated list of organisms expected in a mock community or defined microbial mixture used in metaproteomics experiments (e.g., E. coli;B. subtilis;S. cerevisiae)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000990
name: biomass estimation
def: "Estimated microbial biomass in the sample used in metaproteomics experiments (e.g., 1e9 cells/g, high biomass, low biomass)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000991
name: host contamination level
def: "Level of host protein contamination in a metaproteomics sample, if known (e.g., low <5%, moderate 5-20%, high >20%)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000992
name: contaminant database
def: "Contaminant database(s) used in database search for metaproteomics experiments (e.g., cRAP, MaxQuant contaminants)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000993
name: environmental sample type
def: "Type of environmental sample analyzed in metaproteomics, such as soil, water, or sediment. Classifies the sample by its environmental origin." [PRIDE:PRIDE]
synonym: "env_sample_type" EXACT []
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000994
name: environmental medium
def: "Environmental material from which the sample was obtained. Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. MIXS:0000014" [PRIDE:PRIDE]
synonym: "env_medium" EXACT [GSCMIXS:0000014]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000995
name: geographic location
def: "The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list or the GAZ ontology. MIXS:0000010" [PRIDE:PRIDE]
synonym: "geo_loc_name" EXACT [GSCMIXS:0000010]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000996
name: collection date
def: "The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated (ISO 8601 compliant). MIXS:0000011" [PRIDE:PRIDE]
synonym: "collection_date" EXACT [GSCMIXS:0000011]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000997
name: sample collection method
def: "The method employed for collecting the sample. MIXS:0001225" [PRIDE:PRIDE]
synonym: "samp_collect_method" EXACT [GSCMIXS:0001225]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut
is_a: PRIDE:0000828 ! Soil
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0000998
name: host organism
def: "NCBI taxon id or name of the host organism from which a host-associated microbiome sample was collected (e.g. Homo sapiens, 9606). MIXS:0000250" [PRIDE:PRIDE]
synonym: "host_taxid" EXACT [GSCMIXS:0000250]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0000999
name: host sex
def: "Gender or physical sex of the host. MIXS:0000811" [PRIDE:PRIDE]
synonym: "host_sex" EXACT [GSCMIXS:0000811]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0001000
name: antibiotic treatment
def: "Information about treatment involving antibiotic administration; should include the name of antibiotic, amount administered, and treatment regimen. MIXS:0000553" [PRIDE:PRIDE]
synonym: "host_antibiot_regm" EXACT [GSCMIXS:0000553]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000674 ! Human gut

[Term]
id: PRIDE:0001001
name: soil type
def: "Description of the soil type or classification. This field accepts terms under soil (ENVO:00001998). MIXS:0000332" [PRIDE:PRIDE]
synonym: "soil_type" EXACT [GSCMIXS:0000332]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0001002
name: soil horizon
def: "Specific layer in the land area which measures parallel to the soil surface and possesses physical characteristics which differ from the layers above and beneath. MIXS:0001082" [PRIDE:PRIDE]
synonym: "soil_horizon" EXACT [GSCMIXS:0001082]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0001003
name: vegetation
def: "Dominant vegetation type at the sampling site in metaproteomics studies." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0001004
name: water body type
def: "Type of water body from which the sample was collected (e.g. ocean, lake, river, estuary, pond)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0001005
name: sampling depth zone
def: "Ecological depth zone of the aquatic sampling site (e.g. epipelagic, mesopelagic, bathypelagic, benthic, surface)." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0001006
name: water current velocity
def: "Water current velocity at the sampling site. Measured speed and direction of water flow. MIXS:0000051" [PRIDE:PRIDE]
synonym: "current" EXACT [GSCMIXS:0000051]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0001007
name: total dissolved solids
def: "Total dissolved solids (TDS) concentration in a water sample. Includes all inorganic and organic substances in solution." [PRIDE:PRIDE]
is_a: PRIDE:0000017 ! Sample description additional parameter
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0001008
name: n-alkanes
def: "Concentration of n-alkanes (MIXS:0000503)" [PRIDE:PRIDE]
is_a: PRIDE:0000829 ! Water

[Term]
id: PRIDE:0001009
name: soil type method
def: "Reference or method used in determining soil series name or other lower-level classification (MIXS:0000334)" [PRIDE:PRIDE]
is_a: PRIDE:0000828 ! Soil

[Term]
id: PRIDE:0001010
name: associated data file
def: "Name of an additional data file required to interpret the primary data file (e.g. an AB Sciex .wiff.scan companion to a .wiff file). Used in SDRF as comment[associated data file]." [PRIDE:PRIDE]
xref: value-type:xsd\:string "The allowed value-type for this CV term"
is_a: PRIDE:0000006 ! Experiment additional parameter

[Term]
id: PRIDE:0001011
name: broad-scale environmental context
def: "Report the major environmental system the sample or specimen came from (MIXS:0000012)." [PRIDE:PRIDE]
is_a: PRIDE:0000458 ! Metaproteomics
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0001012
name: local environmental context
def: "Report the entity or entities which are in the sample or specimen s local vicinity and which you believe have significant causal influences on your sample or specimen (MIXS:0000013)." [PRIDE:PRIDE]
is_a: PRIDE:0000458 ! Metaproteomics
is_a: PRIDE:0000017 ! Sample description additional parameter

[Term]
id: PRIDE:0001014
name: control sample
def: "Sample included in an experiment or assay plate to validate performance, establish measurement scale, or monitor stability, as opposed to study samples under investigation." [PRIDE:PRIDE]
is_a: PRIDE:0000895 ! sample type

[Term]
id: PRIDE:0001015
name: calibration sample
def: "Control sample with known or assigned reference values used to establish, adjust, or verify the quantitative measurement scale of an assay or instrument." [PRIDE:PRIDE]
is_a: PRIDE:0001014 ! control sample