term type ontology_term_accession usage values description allow_not_available allow_not_applicable allow_pooled source name anchor column PRIDE:0000623 base, ms-proteomics, affinity-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition free text Unique identifier for the biological sample false false false assay name anchor column NCIT:C178857 base, ms-proteomics, affinity-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition free text Unique identifier for the assay or sample within a study (e.g. MS run name for mass spectrometry, sample ID from platform data file for affinity proteomics) false false false technology type anchor column PRIDE:0000663 base, ms-proteomics, affinity-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition fixed: proteomic profiling by mass spectrometry, protein expression profiling by antibody array, protein expression profiling by aptamer array Type of technology used false false false organism characteristics COB:0000022 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, dia-acquisition NCBITaxon Species of the sample false true false organism part characteristics EFO:0000635 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, dia-acquisition UBERON, BTO Main normalized anatomical term for the sample; use the clearest ontology-backed anatomy term available for integration across datasets true true false tissue supergroup characteristics sample-metadata, ms-proteomics, human, vertebrates, invertebrates, plants, clinical-metadata, oncology-metadata, cell-lines, single-cell, immunopeptidomics, crosslinking, dia-acquisition UBERON, BTO Optional broader anatomical bucket or system-level grouping for the sample, used alongside organism part for higher-level organization (e.g., digestive system, nervous system). true true false disease characteristics EFO:0000408 sample-metadata, ms-proteomics, human, vertebrates, invertebrates, plants, clinical-metadata, oncology-metadata, cell-lines, single-cell, immunopeptidomics, crosslinking, dia-acquisition MONDO, EFO, DOID, PATO Disease state of the sample (use 'normal' from PATO for healthy samples) true true false cell type characteristics EFO:0000324 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, dia-acquisition CL, BTO, CLO Cell type of the sample true true false material type characteristics PRIDE:0000837 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, dia-acquisition, clinical-metadata fixed: tissue, cell, cell line, organism part, whole organism, synthetic Type of biological material being analyzed (derived from MAGE-TAB specification) true true false biological replicate characteristics MS:1001809 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, dia-acquisition integer or pooled Identifier for the biological replicate false false true ancestry category characteristics HANCESTRO:0004 human, cell-lines HANCESTRO Ancestry or ethnic background of the donor true true false age characteristics EFO:0000246 human pattern: {Number}{Unit} (Y/M/W/D), anonymized, or pooled Age of the donor at sample collection true false true sex characteristics PATO:0000047 human, vertebrates fixed: male, female, intersex, hermaphrodite, anonymized, not available, not applicable, pooled Biological sex of the donor true true true developmental stage characteristics EFO:0000399 human, vertebrates, invertebrates, plants, cell-lines EFO Developmental stage of the organism or donor true true false individual characteristics EFO:0000542 human free text pattern or pooled Unique identifier for the donor individual true true true cell line characteristics CLO:0000031 cell-lines CLO, BTO, EFO Name of the cell line false false false cellosaurus accession characteristics PRIDE:0000835 cell-lines Cellosaurus (CVCL_XXXX) Cellosaurus accession number for the cell line true false false cellosaurus name characteristics PRIDE:0000836 cell-lines Cellosaurus Official Cellosaurus name for the cell line true false false sampling site characteristics EFO:0000688 clinical-metadata, cell-lines UBERON, BTO Local sampling context, provenance, or original source label relative to the organism part. May be equal to the organism part or provide finer context (e.g., normal tissue adjacent to tumor, apex of left ventricle). true true false disease staging characteristics EFO:0000410 oncology-metadata NCIT, EFO Disease progression stage (stage I-IV, chronic phase, end stage). Distinct from tumor-specific staging. true true false tumor grading characteristics OBI:0600002 oncology-metadata NCIT Histological tumor grade (grade 1-4). Describes how abnormal cells look. true true false tumor stage characteristics EFO:0004925 oncology-metadata NCIT TNM staging notation (T0-4, N0-3, M0-1). Describes extent of cancer spread. true true false clinical data characteristics EFO:0030083 oncology-metadata free text Free-text clinical details (receptor status, treatment history, surgical details). Use for context not captured in structured fields. true true false clinical history characteristics EFO:0000352 oncology-metadata free text Relevant medical history information for the patient. true true false phenotype characteristics EFO:0000651 clinical-metadata PATO, EFO, free text Observable characteristics or traits (drug sensitivity, molecular markers, expression phenotypes, environmental responses). Captures how sample behaves/appears. true true false metastasis site characteristics NCIT:C172233 oncology-metadata UBERON, BTO Location where cancer has spread from primary site. true true false survival time characteristics EFO:0000714 oncology-metadata pattern: number + unit Patient survival time for survival analysis studies. true true false tumor size characteristics EFO:0004134 oncology-metadata pattern: number + unit Tumor size measurement (e.g., 2.5 cm). true true false tumor mass characteristics EFO:0007062 oncology-metadata pattern: number + unit Tumor mass/weight measurement. true true false biopsy site characteristics EFO:0000288 oncology-metadata UBERON, BTO Specific anatomical location of biopsy. true true false last follow up characteristics EFO:0007058 oncology-metadata pattern: number + unit Time of last clinical follow-up for longitudinal studies. true true false exposure duration characteristics NCIT:C83280 clinical-metadata pattern: number + time unit Duration of treatment exposure (e.g., 24 hour, 5 day) true true false genetic modification characteristics EFO:0000510 clinical-metadata EFO Method of genetic modification (knockout, knockdown, overexpression, transduction). Describes HOW modification was done. true true false compound characteristics CHEBI:24431 clinical-metadata CHEBI, NCIT, EFO Chemical compound or drug applied to sample. Use ChEBI ontology for standardization. true true false dose characteristics NCIT:C25488 clinical-metadata number + unit (e.g., 10 mg/kg, 50 uM, 100 nM). Units: mg/kg, uM, nM, mg, ug, mg/mL, ug/mL, mM Dose or concentration of compound treatment. Quantitative values preferred. true true false pre-existing condition characteristics NCIT:C54056 clinical-metadata MONDO, EFO, DOID Pre-existing medical conditions or comorbidities. true true true treatment status characteristics NCIT:C45501 clinical-metadata fixed: pre-treatment, on treatment, post-treatment, treatment naive Treatment status at time of sampling. true true false treatment response characteristics NCIT:C50995 clinical-metadata NCIT Response to treatment (complete response, partial response, progressive disease). true true false body mass index characteristics EFO:0004340 clinical-metadata numeric Body mass index (BMI) in kg/m^2. true true false smoking status characteristics NCIT:C19796 clinical-metadata NCIT (children of NCIT:C19796) Patient smoking status. true true false menopausal status characteristics NCIT:C16151 clinical-metadata fixed: pre-menopausal, peri-menopausal, post-menopausal Menopausal status for female patients. true true false histologic subtype characteristics NCIT:C19790 oncology-metadata NCIT Breast cancer molecular subtype (luminal A, luminal B, HER2-enriched, triple-negative). true true false single cell isolation protocol characteristics EFO:0010214 single-cell fixed: FACS, cellenONE, microfluidics, laser capture microdissection, manual picking, nanoPOTS, droplet microfluidics, acoustic droplet ejection Method used to isolate single cells true true false cell identifier characteristics EFO:0010197 single-cell free text pattern Unique identifier for the single cell false true false cell viability characteristics CMPO:0000013 single-cell fixed: live, viable, dead, unknown Viability status of the cell at isolation true true false cell cycle phase characteristics GO:0022403 single-cell fixed: G1, S, G2, G2/M, M, G0, not determined Cell cycle phase of the isolated cell true true false enrichment marker characteristics PRIDE:0000940 single-cell free text Markers used for cell sorting/enrichment true true false genotype characteristics EFO:0000513 single-cell, invertebrates, clinical-metadata free text Known genetic variant, mutation, or genotype of the subject true true false strain or breed characteristics GENO:0000112 vertebrates, invertebrates, plants free text Strain, breed, cultivar, or ecotype of the organism true true false mhc protein complex characteristics GO:0042611 immunopeptidomics fixed: MHC class I protein complex, MHC class II protein complex, non-classical MHC protein complex, mutant MHC protein complex, MHC protein complex with serotype MHC protein complex targeted for immunopeptidome enrichment (MRO terms under GO:0042611) false false false immunopeptidome enrichment method characteristics PRIDE:0000586 immunopeptidomics fixed: immunoaffinity purification, immunoaffinity purification (iodoacetamide), mild acid elution, detergent lysis Method used to enrich MHC-bound peptides false false false mhc typing characteristics PRIDE:0000893 immunopeptidomics IPD-MHC nomenclature (https://www.ebi.ac.uk/ipd/mhc/); IPD-IMGT/HLA for human MHC allelic composition of the sample following IPD-MHC nomenclature true true false mhc typing method characteristics PRIDE:0000894 immunopeptidomics fixed: NGS-based typing (NCIT:C101293), sequence-based typing (NCIT:C130180), PCR-SSO (NCIT:C130181), PCR-SSP (NCIT:C130179), PCR-based genotyping (NCIT:C17003), predicted from RNA-seq, inferred from mass spectrometry, inbred strain (known genotype) Method used to determine MHC alleles true true false enrichment process characteristics EFO:0009090 sample-metadata, crosslinking PRIDE, EFO (children of EFO:0009090) Enrichment strategy applied to the sample (phosphopeptide, crosslinked peptide, glycopeptide enrichment, etc.) true true false crosslink distance characteristics PRIDE:0000948 crosslinking pattern: number + Å Maximum distance constraint provided by the crosslinker true true false crosslinking reaction time characteristics PRIDE:0000949 crosslinking pattern: number + time unit Duration of the crosslinking reaction true true false crosslinking temperature characteristics PRIDE:0000950 crosslinking pattern: number + °C Temperature at which crosslinking was performed true true false environmental sample type characteristics PRIDE:0000993 metaproteomics, human-gut, soil, water ENVO, EFO Type of environmental sample analyzed false false false environmental medium characteristics PRIDE:0000994 metaproteomics, human-gut, soil, water ENVO Environmental material from which the sample was obtained true true false sample collection method characteristics PRIDE:0000997 metaproteomics, human-gut, soil, water free text Method used to collect the environmental sample true true false geographic location characteristics PRIDE:0000995 metaproteomics, human-gut, soil, water GAZ Geographic location where sample was collected true true false collection date characteristics PRIDE:0000996 metaproteomics, human-gut, soil, water ISO 8601 date Date when sample was collected true true false depth characteristics PRIDE:0000711 metaproteomics, human-gut, soil, water pattern: number + m/cm/mm Depth at which sample was collected true true false altitude characteristics PRIDE:0000712 metaproteomics, human-gut, soil, water pattern: number + m Altitude or elevation of sampling site true true false temperature characteristics PRIDE:0000703 metaproteomics, human-gut, soil, water pattern: number + °C Temperature at sampling location true true false ph characteristics PRIDE:0000746 metaproteomics, human-gut, soil, water numeric pH at sampling location true true false microbiome source characteristics PRIDE:0000986 metaproteomics, human-gut, soil, water free text Source of the microbiome being studied true true false mock community characteristics PRIDE:0000987 metaproteomics, human-gut, soil, water free text Identifier or name of mock community standard used true true false mock community composition characteristics PRIDE:0000988 metaproteomics, human-gut, soil, water free text Description of mock community composition true true false host organism characteristics PRIDE:0000998 human-gut NCBITaxon Host organism for host-associated microbiome samples false true false host subject id characteristics PRIDE:0000680 human-gut free text pattern De-identified unique identifier for the host subject true true false host disease status characteristics PRIDE:0000682 human-gut MONDO, DOID Host disease diagnoses true true false host body site characteristics PRIDE:0000685 human-gut UBERON, BTO Body site where sample was obtained true true false host age characteristics PRIDE:0000681 human-gut pattern: {Number}{Unit} (Y/M/W/D) Age of host at the time of sampling true true false host sex characteristics PRIDE:0000999 human-gut fixed: male, female, intersex Sex of the host organism true true false host body-mass index characteristics PRIDE:0000695 human-gut numeric Body mass index (weight/height^2) true true false host height characteristics PRIDE:0000688 human-gut pattern: number + cm/m Height of the host true true false host total mass characteristics PRIDE:0000687 human-gut pattern: number + kg/g Total mass of the host true true false ethnicity characteristics PRIDE:0000696 human-gut free text Ethnicity of the host true true false host diet characteristics PRIDE:0000689 human-gut free text Diet type of the host true true false special diet characteristics PRIDE:0000679 human-gut free text Special dietary restrictions true true false host last meal characteristics PRIDE:0000690 human-gut free text Content of last meal and time since feeding true true false gastrointestinal tract disorder characteristics PRIDE:0000677 human-gut free text History of GI tract disorders true true false liver disorder characteristics PRIDE:0000678 human-gut free text History of liver disorders true true false antibiotic treatment characteristics PRIDE:0001000 human-gut free text Recent antibiotic exposure of the host true true false ihmc medication code characteristics PRIDE:0000683 human-gut free text Medication codes (IHMC) true true false host body product characteristics PRIDE:0000686 human-gut free text Substance produced by the body where sample was obtained true true false host body temperature characteristics PRIDE:0000694 human-gut pattern: number + °C Core body temperature at sample collection true true false soil type characteristics PRIDE:0001001 soil ENVO Soil classification type true true false soil horizon characteristics PRIDE:0001002 soil fixed: O horizon, A horizon, B horizon, C horizon, E horizon, R horizon Soil horizon from which sample was collected true true false land use characteristics PRIDE:0000713 soil free text Land use type at sampling site true true false vegetation characteristics PRIDE:0001003 soil free text Dominant vegetation at sampling site true true false total organic carbon characteristics PRIDE:0000749 soil pattern: number + mg/kg/g/kg/% Total organic carbon content true true false total nitrogen characteristics PRIDE:0000751 soil pattern: number + mg/kg/g/kg/% Total nitrogen content true true false water content characteristics PRIDE:0000727 soil pattern: number + g/g/% Water content of soil sample true true false soil texture measurement characteristics PRIDE:0000744 soil free text Soil texture measurement (sand/silt/clay percentages) true true false current vegetation characteristics PRIDE:0000714 soil ENVO Current vegetation type at sampling site true true false crop rotation characteristics PRIDE:0000718 soil free text Crop rotation history true true false water body type characteristics PRIDE:0001004 water ENVO Type of water body from which sample was collected true true false salinity characteristics PRIDE:0000701 water pattern: number + PSU/ppt/g/L or descriptive term Salinity measurement true true false dissolved oxygen characteristics PRIDE:0000788 water pattern: number + mg/L or descriptive term Dissolved oxygen concentration true true false chlorophyll characteristics PRIDE:0000775 water pattern: number + ug/L/mg/L Chlorophyll concentration if measured true true false sampling depth zone characteristics PRIDE:0001005 water fixed: epipelagic, mesopelagic, bathypelagic, abyssopelagic, hadopelagic, benthic, surface Ecological depth zone of the sampling site true true false turbidity characteristics PRIDE:0000827 water pattern: number + NTU/FNU Turbidity measurement true true false alkalinity characteristics PRIDE:0000760 water pattern: number + mg/L/meq/L Alkalinity measurement true true false nitrate characteristics PRIDE:0000796 water pattern: number + mg/L/umol/L Nitrate concentration true true false phosphate characteristics PRIDE:0000805 water pattern: number + mg/L/umol/L Phosphate concentration true true false conductivity characteristics PRIDE:0000776 water pattern: number + uS/cm/mS/cm/S/m Electrical conductivity of water sample true true false total dissolved solids characteristics PRIDE:0001007 water pattern: number + mg/L/g/L Total dissolved solids true true false light intensity characteristics PRIDE:0000792 water pattern: number + lux/umol/m2/s Light intensity at sampling depth true true false current characteristics PRIDE:0001006 water pattern: number + m/s/cm/s/knots Water current velocity true true false perturbation characteristics PRIDE:0000700 human-gut, soil free text Type of perturbation applied true true false chemical administration characteristics PRIDE:0000684 human-gut, soil free text Chemical compounds administered true true false proteomics data acquisition method comment PRIDE:0000659 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition PRIDE Mass spectrometry acquisition method false false false label comment PRIDE:0000514 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition PRIDE Labeling strategy used for quantification false false false instrument comment MS:1000031 ms-proteomics, affinity-proteomics MS, PRIDE Mass spectrometer instrument used false false false cleavage agent details comment MS:1001044 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition MS (PSI-MS) Enzyme or chemical used for protein digestion false true false fraction identifier comment MS:1000858 base, ms-proteomics, affinity-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition integer Fraction number for fractionated samples false false false technical replicate comment MS:1001808 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition integer Identifier for the technical replicate false false false data file comment MS:1003083 base, ms-proteomics, human, cell-lines, single-cell, immunopeptidomics, crosslinking, metaproteomics, dia-acquisition file name Name of the primary/canonical raw data file (e.g. .raw, .wiff, .d). For vendor formats that ship multiple files (e.g. AB Sciex .wiff + .wiff.scan), use comment[associated data file] for the secondary files. false false false associated data file comment ms-proteomics, dia-acquisition file name Name of an auxiliary file required to read the primary data file (e.g. AB Sciex .wiff.scan companion to a .wiff). Multiple columns are allowed when several auxiliary files are needed. Pending accession from PRIDE-Archive/pride-ontology#180. true true false associated file uri comment PRIDE:0000403 ms-proteomics, dia-acquisition URI URI to retrieve the auxiliary file referenced by comment[associated data file]. Multiple columns are allowed when several auxiliary files are needed. true true false modification parameters comment MS:1001055 ms-proteomics, dia-acquisition Unimod, PSI-MOD Post-translational modifications searched true true false precursor mass tolerance comment PRIDE:0000575 ms-proteomics, dia-acquisition pattern: number + ppm/Da Precursor mass tolerance for database search true true false fragment mass tolerance comment PRIDE:0000576 ms-proteomics, dia-acquisition pattern: number + ppm/Da Fragment mass tolerance for database search true true false ms min mz comment PRIDE:0000476 ms-proteomics, dia-acquisition numeric (m/z) MS method-defined minimum precursor m/z setting used to acquire the data true true false ms max mz comment PRIDE:0000477 ms-proteomics, dia-acquisition numeric (m/z) MS method-defined maximum precursor m/z setting used to acquire the data true true false ms min charge comment PRIDE:0000472 ms-proteomics, dia-acquisition integer MS method-defined minimum precursor charge state setting used to acquire the data true true false ms max charge comment PRIDE:0000473 ms-proteomics, dia-acquisition integer MS method-defined maximum precursor charge state setting used to acquire the data true true false ms min rt comment PRIDE:0000474 ms-proteomics, dia-acquisition numeric (minutes) LC method-defined minimum retention time setting used to acquire the data true true false ms max rt comment PRIDE:0000475 ms-proteomics, dia-acquisition numeric (minutes) LC method-defined maximum retention time setting used to acquire the data true true false ms min im comment PRIDE:0000841 ms-proteomics, dia-acquisition numeric (1/K0 or Vs/cm2) MS method-defined minimum ion mobility setting used to acquire the data true true false ms max im comment PRIDE:0000842 ms-proteomics, dia-acquisition numeric (1/K0 or Vs/cm2) MS method-defined maximum ion mobility setting used to acquire the data true true false ms2 min mz comment PRIDE:0001011 ms-proteomics {number}m/z MS method-defined minimum product ion (MS2) m/z setting true true false ms2 max mz comment PRIDE:0001012 ms-proteomics {number}m/z MS method-defined maximum product ion (MS2) m/z setting true true false ms3 min mz comment PRIDE:0001013 ms-proteomics {number}m/z MS method-defined minimum product ion (MS3) m/z setting true true false ms3 max mz comment PRIDE:0001014 ms-proteomics {number}m/z MS method-defined maximum product ion (MS3) m/z setting true true false ms1 scan range comment PRIDE:0001008 ms-proteomics {number}m/z-{number}m/z m/z scan range for MS1 spectra as an interval true true false ms2 scan range comment PRIDE:0001009 ms-proteomics {number}m/z-{number}m/z m/z scan range for MS2 spectra as an interval true true false ms3 scan range comment PRIDE:0001010 ms-proteomics {number}m/z-{number}m/z m/z scan range for MS3 spectra as an interval true true false sample type characteristics PRIDE:0000895 sample-metadata, single-cell, affinity-proteomics PRIDE (children of PRIDE:0000895): study sample, single cell, environmental sample, reference, bridge, carrier, pooled, empty, negative control, positive control, bulk control, buffer control, plate control, quality control sample, calibrator, standard Classification of the sample role in the experiment. Distinguishes study samples under investigation from controls, references, and other roles in multiplexed or plate-based experiments. true true false passage number characteristics EFO:0007061 cell-lines integer or range Passage number of the cell line true true false biorepository characteristics NCIT:C48800 cell-lines free text Repository or source from which the cell line was obtained true true false cell line authentication characteristics PRIDE:0000955 cell-lines free text Method used to authenticate the cell line identity true true false cells per well characteristics UO:0000317 single-cell integer Number of cells per well/reaction (single-cell proteomics; use 1 for true single cells) true true false tissue mass characteristics OBA:2045411 sample-metadata pattern: number + mg/g Mass of tissue used for extraction true true false antibody enrichment characteristics PRIDE:0000954 immunopeptidomics free text Antibody clone used for MHC immunoprecipitation true true false elution conditions comment OBI:0302905 ms-proteomics free text Conditions used for peptide elution from MHC complexes true true false chemical cross-linking coupled with ms comment PRIDE:0000430 crosslinking fixed: cross-linking mass spectrometry MS-based cross-linking methodology used false false false cross-linker comment XLMOD:00004 crosslinking XLMOD key-value format Cross-linker compound with structured properties false false false crosslinker concentration comment PRIDE:0000951 crosslinking pattern: number + mM/uM Concentration of crosslinking reagent used true true false crosslinker to protein ratio comment PRIDE:0000952 crosslinking ratio pattern Molar ratio of crosslinker to protein true true false quenching reagent comment PRIDE:0000953 crosslinking free text Reagent used to quench the crosslinking reaction true true false crosslink enrichment method comment PRIDE:0000838 crosslinking PRIDE, MS (ontology validator, examples: size exclusion chromatography, strong cation exchange chromatography, high-pH reversed-phase chromatography, FAIMS) Method used to enrich crosslinked peptides true true false metagenome accession comment PRIDE:0000956 metaproteomics, human-gut, soil, water accession pattern Accession number for matched metagenome data true true false sample storage characteristics PRIDE:0000730 metaproteomics, human-gut, soil, water free text Storage conditions for the sample before analysis true true false biomass estimation characteristics PRIDE:0000990 metaproteomics, human-gut, soil, water free text Estimated microbial biomass in the sample true true false host contamination characteristics PRIDE:0000991 metaproteomics, human-gut, soil, water free text Level of host protein contamination if known true true false contaminant database comment PRIDE:0000992 metaproteomics, human-gut, soil, water free text Contaminant database(s) used in database search true true false expected organism list comment PRIDE:0000989 metaproteomics, human-gut, soil, water free text Semicolon-separated list of organisms expected in mock community true true false scan window lower limit comment MS:1000501 dia-acquisition numeric m/z Lower m/z limit of the DIA scan window true true false scan window upper limit comment MS:1000500 dia-acquisition numeric m/z Upper m/z limit of the DIA scan window true true false isolation window width comment MS:1000792 dia-acquisition numeric m/z Width of the isolation window in m/z units true true false collision energy comment MS:1000045 ms-proteomics, crosslinking, dia-acquisition pattern: {value} {unit} where value is number with optional %, unit is NCE or eV. Stepped: {value} {unit};{value} {unit} Collision energy used for fragmentation. Examples: 30 NCE, 30% NCE, 27 eV, 25 NCE;27 NCE;30 NCE true true false dissociation method comment MS:1000044 ms-proteomics, crosslinking, dia-acquisition MS, PRIDE (children of MS:1000044) Fragmentation method used true true false ms2 mass analyzer comment MS:1000443 ms-proteomics, dia-acquisition MS (PSI-MS) Mass analyzer used for MS2 acquisition true true false dia method comment PRIDE:0000450 dia-acquisition PRIDE Specific DIA method variant used true true false fractionation method comment PRIDE:0000550 ms-proteomics PRIDE (children of PRIDE:0000550) Peptide fractionation method used before MS analysis true true false sdrf version comment PRIDE:0000839 base semver (vX.Y.Z) Version of the SDRF-Proteomics specification used to annotate this file false false false sdrf template comment PRIDE:0000832 base pattern (NT=name;VV=vX.Y.Z or name vX.Y.Z) Template name and version used for annotation. Multiple templates can be specified using multiple columns. false false false sdrf annotation tool comment PRIDE:0000840 base pattern (NT=name;VV=vX.Y.Z or name vX.Y.Z or manual curation) Software tool or method used to generate or annotate the SDRF file false false false sdrf validation hash comment base free text Hash value for SDRF validation integrity checking true true false pooled sample characteristics NCIT:C165587 sample-metadata fixed: not pooled, pooled; or pattern: SN=sample1;SN=sample2 Whether the sample is a pooled sample combining material from multiple biological sources true true false biosample accession number characteristics NCIT:C175889 sample-metadata accession (SAMN/SAMEA/SAMD) BioSample accession number for the sample true true false reduction reagent comment PRIDE:0000607 ms-proteomics PRIDE, MS Chemical reagent used for disulfide bond reduction true true false alkylation reagent comment PRIDE:0000598 ms-proteomics PRIDE, MS Chemical reagent used for cysteine alkylation true true false depletion characteristics PRIDE:0000020 ms-proteomics fixed: no depletion, depletion, not applicable Whether abundant protein depletion was performed true true false sample preparation batch comment ms-proteomics, single-cell free text Batch identifier for sample preparation (plate, chip, processing batch) true true false lc batch comment ms-proteomics free text Liquid chromatography batch identifier for batch effect tracking true true false acquisition date comment ms-proteomics ISO 8601 date Date of MS data acquisition true true false culture medium characteristics OBI:0000079 cell-lines NCIT Culture medium used to grow the cell line true true false sample storage temperature characteristics PRIDE:0000705 cell-lines pattern: number + °C Storage temperature of the cell line true true false cell diameter characteristics OBA:0000048 single-cell pattern: number + um/μm Physical diameter of the isolated cell true true false forward scatter characteristics PRIDE:0000937 single-cell numeric Forward scatter (FSC) value from flow cytometry - proxy for cell size true true false side scatter characteristics PRIDE:0000938 single-cell numeric Side scatter (SSC) value from flow cytometry - proxy for cell granularity true true false carrier channel comment PRIDE:0000901 single-cell TMT/TMTpro channel label TMT channel used for the carrier proteome in multiplexed SCP true true false reference channel comment PRIDE:0000899 single-cell TMT/TMTpro channel label TMT channel used for the reference sample for normalization true true false spatial coordinates characteristics PRIDE:0000939 single-cell pattern: X=number;Y=number X,Y coordinates for spatially resolved single-cell proteomics true true false tissue section comment NCIT:C158415 single-cell free text Tissue section identifier for spatially resolved single-cell proteomics true true false facs nozzle size comment PRIDE:0000981 single-cell pattern: number + um/μm Nozzle diameter used for FACS-based single cell isolation true true false facs sorting mode comment PRIDE:0000982 single-cell fixed: single cell, purity, yield, 4-way purity Sorting mode used during FACS isolation true true false microfluidics chip type comment PRIDE:0000983 single-cell free text Type and manufacturer of the microfluidics chip used for single cell isolation true true false lcm microscope model comment PRIDE:0000984 single-cell free text Model of the laser capture microdissection microscope used for cell isolation true true false nanopots chip version comment PRIDE:0000985 single-cell free text Version of the nanoPOTS chip used for single cell sample preparation true true false treatment characteristics EFO:0000727 sample-metadata, plants NCIT, EFO Treatment or perturbation applied to the sample (drug, stimulus, environmental stress) true true false synthetic peptide characteristics PRIDE:0000495 sample-metadata synthetic, not synthetic Whether the sample is a synthetic peptide library or biological material true true false spiked compound characteristics PRIDE:0000496 sample-metadata pattern: CT=type;QY=quantity;PS=sequence;AC=accession;CN=name;CV=vendor Spiked-in compound details (peptides, proteins, mixtures for standards or RT alignment) true true false weight characteristics EFO:0004324 clinical-metadata pattern: number + unit (kg, g, lb) Body weight of the subject true true false height characteristics EFO:0004339 clinical-metadata pattern: number + unit (cm, m) Height of the subject true true false sampling time characteristics EFO:0000689 sample-metadata pattern: number + time unit Time at which the sample was collected true true false dukes stage characteristics NCIT:C16475 oncology-metadata fixed: A, B, C, D Dukes staging for colorectal cancer true true false ann arbor stage characteristics NCIT:C16282 oncology-metadata pattern: (I-IV)(A/B)(E/S) Ann Arbor staging for lymphoma true true false gleason score characteristics NCIT:C28091 oncology-metadata pattern: sum or components (e.g., 3+4) Gleason score for prostate cancer grading true true false weiss grade characteristics NCIT:C160679 oncology-metadata fixed: low, high Weiss scoring system for adrenal cortical carcinoma true true false mitotic rate characteristics NCIT:C62401 oncology-metadata pattern: count or count/HPF Number of mitoses per high-power field true true false growth condition characteristics EFO:0000523 plants free text Growth conditions for the plant (photoperiod, temperature, growth medium) true true false platform comment affinity-proteomics PRIDE Affinity proteomics platform used (e.g., Olink Explore HT, SomaScan Assay 7K) false false false panel name comment affinity-proteomics free text Name of the commercial panel used true true false panel version comment affinity-proteomics free text Version of the assay panel true true false quantification unit comment PRIDE:0000392 affinity-proteomics fixed: NPX, RFU Unit of quantification for the assay (NPX for Olink, RFU for SomaScan) true true false plate comment affinity-proteomics free text Plate identifier for batch effect analysis true true false sample matrix characteristics affinity-proteomics UBERON, BTO Type of biological matrix used as input (serum, plasma, CSF, urine) true true false normalization method comment affinity-proteomics free text Normalization method applied to quantification values true true false olink panel comment olink free text Specific Olink panel name (Target 96 Inflammation, Explore 3072) false false false olink platform comment olink fixed: Olink Target 96, Olink Explore 384, Olink Explore HT, Olink Reveal Olink platform version false false false npx normalization comment olink fixed: plate control normalized, intensity normalized, bridge normalized, not normalized Normalization method applied to NPX values true true false olink lot number comment olink free text Reagent lot number for traceability true true false somascan menu comment somascan fixed: SomaScan 1.1K, SomaScan 1.3K, SomaScan 5K, SomaScan 7K, SomaScan 11K SomaScan assay menu (number of aptamers/proteins measured) false false false somascan platform comment somascan fixed: SomaScan Assay, SomaScan Assay v4, SomaScan Assay v4.1 SomaScan instrument/platform version false false false somascan lot number comment somascan free text Reagent lot number for traceability true true false dilution comment OBI:0002483 somascan pattern: 0.005%, 0.5%, 20%, 40% Sample dilution factor used in SomaScan assay true true false xenograft characteristics EFO:0003942 human, vertebrates free text Indicates if sample is a patient-derived xenograft (PDX). Metadata (age, sex) must refer to the original patient, not the host organism. true true false mass characteristics PRIDE:0000505 sample-metadata pattern: number + unit (e.g., 1 ug, 500 ng, 10 fmol) Injected mass of the sample. Used for spiked-in experiments and quantitative comparisons. true true false