category: Metadata description: 'The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis. ' links: - label: Protocol references the Study it is part of. name: Study required: 'True' properties: 1d_chromatography_type: description: Type of chromatography of the first dimension. If only 1D was used, annotate that dimension here. enum: - RPLC - bRPLC - bRPLC (pH 7.5) - bRPLC (pH 10) - SCX required: 'True' type: Enumeration 2d_chromatography_type: description: Type of chromatography for the second dimension. This will generally be RPLC. enum: - RPLC - UHPLC required: 'True' type: Enumeration acquisition_type: description: Mass spectrometry acquisition method enum: - DDA - DIA required: 'True' type: Enumeration alkylation_reagent: description: Reagent used for cysteine alkylation enum: - Iodoacetamide (IAA) - 2-chloroacetamide (TCEP) - tris(2-carboxyethyl)phosphine - Methyl Methanethiosulfonate (MMTS) required: 'True' type: Enumeration amount_on_column: description: Approximate mass with units required: 'False' type: Number amount_on_column_uom: description: Unit of Measure of amount_on_column required: 'False' type: String analytical_technique: description: General strategy used for metabolomics analysis required: False (Required for metabolomics only) type: String chromatography_dimensions_count: description: Number of discrete chromatographic dimensions used enum: - 1 - 2 required: 'True' type: Enumeration chromatography_instrument_make: description: Manufacturer of chromatography instrument required: False (Required for metabolomics only) type: String chromatography_instrument_model: description: Model of chromatography instrument required: False (Required for metabolomics only) type: String column_inner_diameter: description: Approximate diameter with units required: 'False' type: Number column_inner_diameter_uom: description: "Unit of Measure of column_inner_diameter, \xC2\xB5m" required: 'False' type: String column_length: description: Approximate length with units required: 'False' type: Integer column_length_uom: description: Unit of Measure of column_length, cm required: 'False' type: String column_type: description: Type of column used enum: - C18 - New Objective - PicoFrit SELF/P required: 'False' type: Enumeration dda_topn: description: Number of precursors sampled per cycle required: 'False' type: String dia_ims: description: Numeric value that represents the current weight of the sample, measured in milligrams. enum: - 'Yes' - 'No' required: 'False' type: Enumeration dia_multiplexing: cde_id: MS:1000501,MS:1000500 description: Uses overlapping windows (MSX) enum: - 'Yes' - 'No' required: 'True' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000501 type: Enumeration digestion_reagent: cde_id: MS:1001045 description: Enzyme or reagent used for digestion. Multiple enzymes can be separated by (;) enum: - 2-iodobenzoate - Arg-C, Asp-N - Asp-N_ambic - Chymotrypsin - CNBr, Formic_acid - Glutamyl endopeptidase - Leukocyte elastase - Lys-C, Lys-C/P - No cleavage - NoEnzyme - PepsinA - Proline endopeptidase - TrypChymo - Trypsin - Trypsin/P - Unspecific cleavage - V8-DE - V8-E - Lys-C - Trypsin required: 'True' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1001045 type: Enumeration dissociation_type: cde_id: MS:1000044 description: Gas phase dissociation type enum: - HCD - CID - ETD - ECD required: 'True' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000044 type: Enumeration document_name: description: Name of protocol document required: 'False' type: String enrichment: description: 'Protocol or reagent used for enrichment, for example: Fe3+ NTA-Agarose (Qiagen). User can select existing enrichments or add their own.' required: 'True' type: String enrichment_strategy: description: Type of peptide or protein enrichment enum: - Acetylome - Proteome - Phosphoproteome - Glycoproteome - Ubiquitylome - Metabolome - Lipidome required: 'True' type: Enumeration experiment_type: description: Type of labeling reagent used. Indicate number of channels. enum: - Label Free - iTRAQ - TMT required: 'True' type: Enumeration extraction_method: description: Method/Solution used for metabolite extraction required: False (Required for metabolomics only) type: String fractions_analyzed_count: description: Final number of fractions analyzed by mass spectrometry. For Thermo instruments, this will equal the number of data files. required: 'True' type: Integer gradient_length: description: Time with units required: 'False' type: Integer gradient_length_uom: description: Unit of Measure of gradient_length, minutes required: 'False' type: String instrument_make: description: Manufacturer of instrument enum: - Agilent - Applied Biosystems - Bruker - Dionex - Hitachi - LECO - SCIEX - Shimadzu - Thermo Fisher Scientific - Varian - Waters required: 'True' type: Enumeration instrument_model: cde_id: depends on make description: Model of instrument enum: - 1200 series LC/MSD SL - 1200 series LC/MSD VL - 6110 Quadrupole LC/MS - 6120A Quadrupole LC/MS - 6120B Quadrupole LC/MS - 6130 Quadrupole LC/MS - 6140 Quadrupole LC/MS - 6150 Quadrupole LC/MS - 6210 Time-of-Flight LC/MS - 6220 Time-of-Flight LC/MS - 6224 Time-of-Flight LC/MS - 6230A Time-of-Flight LC/MS - 6230B Time-of-Flight LC/MS - 6310 Ion Trap LC/MS - 6320 Ion Trap LC/MS - 6330 Ion Trap LC/MS - 6340 Ion Trap LC/MS - 6410 Triple Quadrupole LC/MS - 6420 Triple Quadrupole LC/MS - 6430 Triple Quadrupole LC/MS - 6460 Triple Quadrupole LC/MS - 6490 Triple Quadrupole LC/MS - 6495A Triple Quadrupole LC/MS - 6495B Triple Quadrupole LC/MS - 6510 Quadrupole Time-of-Flight LC/MS - 6520A Quadrupole Time-of-Flight LC/MS - 6520B Q-TOF LC/MS - 6530A Q-TOF LC/MS - 6530B Q-TOF LC/MS - 6538 Q-TOF LC/MS - 6540 Q-TOF LC/MS - 6542 Q-TOF LC/MS - 6545 Q-TOF LC/MS - 6550 iFunnel Q-TOF LC/MS - 6550A iFunnel Q-TOF LC/MS - 6560 Q-TOF LC/MS - 6570 Q-TOF LC/MS - 7000A Triple Quadrupole GC/MS - 7000B Triple Quadrupole GC/MS - 7800 Quadrupole ICP-MS - 8800 Triple Quadrupole ICP-MS - 4700 Proteomics Analyzer - 4800 Proteomics Analyzer - Voyager-DE PRO - Voyager-DE STR - Bruker Daltonics amaZon series - Bruker Daltonics apex series - Bruker Daltonics BioTOF series - Bruker Daltonics esquire series - Bruker Daltonics EVOQ series - Bruker Daltonics flex series - Bruker Daltonics HCT series - Bruker Daltonics maXis series - Bruker Daltonics micrOTOF series - Bruker Daltonics SCION series - Bruker Daltonics solarix series - timsTOF Pro - Citius HRT - Pegasus - Pegasus 4D - Pegasus BT - Pegasus HRT - Pegasus III - TruTOF - 2000 QTRAP - 2500 QTRAP - 3200 QTRAP - 3500 QTRAP - 4000 QTRAP - 4000 QTRAP - 4800 Plus MALDI TOF/TOF - 5800 TOF/TOF - API 100 - API 100LC - API 150EX - API 150EX Prep - API 165 - API 2000 - API 300 - API 3000 - API 3200 - API 350 - API 365 - API 4000 - API 5000 - proteomics solution 1 - Q TRAP - QSTAR - QSTAR Elite - QSTAR Pulsar - QSTAR XL - QTRAP 4500 - QTRAP 5500 - QTRAP 6500 - QTRAP 6500+m - SymBiot I - SymBiot XVI - Triple Quad 3500 - Triple Quad 4500 - Triple Quad 5500 - Triple Quad 6500 - Triple Quad 6500+ - TripleTOF 4600 - TripleTOF 5600 - TripleTOF 5600+ - TripleTOF 6600 - X500R QTOF - AXIMA Assurance Linear MALDI-TOF - AXIMA CFR MALDI-TOF - AXIMA Confidence MALDI-TOF - AXIMA Performance MALDI-TOF/TOF - AXIMA-CFR plus - AXIMA-QIT - Shimadzu MALDI-7090 - LCMS-2010A - LCMS-2010EV - LCMS-2020 - LCMS-8040 - LCMS-8045 - LCMS-8050 - LCMS-8060 - LCMS-9030 - LCMS-IT-TOF - Accela PDA - DFS - DSQ II - Element 2 - Element GD - Element XR - Exactive - Exactive Plus - GC IsoLink - ISQ - ITQ 1100 - ITQ 700 - ITQ 900 - LTQ - LTQ FT - LTQ FT Ultra - LTQ Orbitrap - LTQ Orbitrap Classic - LTQ Orbitrap Discovery - LTQ Orbitrap Elite - LTQ Orbitrap Velos - LTQ Orbitrap XL - LTQ Orbitrap XL ETD - LTQ Velos - LTQ Velos ETD - LTQ XL - LTQ XL ETD - LXQ - MALDI LTQ Orbitrap - MALDI LTQ XL - Orbitrap Fusion - Orbitrap Fusion ETD - Orbitrap Fusion Lumos - Q Exactive - Q Exactive HF - Q Exactive HF-X - Q Exactive Plus - Surveyor PDA - TSQ 8000 Evo - TSQ 9000 - TSQ Altis - TSQ Endura - TSQ Quantis - TSQ Quantiva - TSQ Quantum Access - TSQ Quantum Ultra - TSQ Quantum Ultra AM - TSQ Vantage - Velos Plus - explorer - HiRes ESI - HiRes MALDI - OMEGA - OMEGA-2001 - ultima - '3100' - Acquity TQD - ACQUITY UPLC - Acquity UPLC FLR - ACQUITY UPLC H-Class - ACQUITY UPLC H-Class Bio - ACQUITY UPLC I-Class - Acquity UPLC PDA - ACQUITY UPLC Systems with 2D Technology - Auto Spec Ultima NT - GCT - GCT Premier - IsoPrime - IsoProbe T - M@LDI L - M@LDI LR - MALDI Synapt G2-S HDMS - MALDI Synapt G2-S MS - MALDI SYNAPT G2-Si - MALDI Synapt HDMS - MALDI Synapt MS - nanoACQUITY UPLC - nanoACQUITY UPLC System with 1D Technology - nanoACQUITY UPLC with HDX Technology - NG-5400 - Platform ICP - Q-Tof micro - Q-Tof Premier - Q-Tof Ultima - quattro micro - Quattro micro GC - Quattro Ultima - SQ Detector 2 - Synapt G2 HDMS - Synapt G2 MS - Synapt G2-S HDMS - Synapt G2-S MS - SYNAPT G2-Si - Synapt HDMS - Synapt MS - TRIZAIC UPLC nanoTile - Xevo G2 Q-Tof - Xevo G2 Tof - Xevo G2 XS Tof - Xevo G2-S QTof - Xevo G2-S Tof - Xevo Q-Tof - Xevo TQ MS - Xevo TQ-S - Xevo TQD - 220 GC/MS Ion Trap System - 240 GC/MS Ion Trap System - 6200 Series Accurate-Mass Time-of-Flight (TOF) LC/MS - 6400 Series Triple Quadrupole LC/MS - 7000 Triple Quadrupole GC/MS System - 7200 GC/Q-TOF - EVOQ Elite - EVOQ Qube - maXis 4G - maXis impact - microOTOF focus II - microOTOF-Q II - solariX - Pipeline - MALDI 4800 - FTMS - LTQ Velos Pro - LTQ-FT - LTQ-OT - Orbitrap Elite - Orbitrap Velos - TSQ Quantum - Acquity SQD - API-US - Bio-Q - EMD 1000 - LCT - LCT Premier - LCT Premier XE - MALDI L - MALDI LR - MALDI micro MX - MALDI R - MALDI Synapt G2 HDMS - MALDI Synapt G2 MS - Micro - Platform - Platform II - Platform LCZ - PLC - Premier - Quattro - Quattro II - Quattro LC - Quattro Premier - Quattro Premier XE - Quattro Ultima Pt - TofSpec - TofSpec 2E - TofSpec E - TofSpec SE - Xevo QTof - ZMD - ZQ - Orbitrap Lumos - Thermo Orbitrap Q Exactive HF-X - Thermo Orbitrap Fusion Lumos required: 'True' term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000031 type: Enumeration internal_standards: description: Reference material used for standardization/QC required: 'False' type: String ionization_mode: description: Method of ionization used in Mass Spec such as Electron Impact (EI) or Electrospray Ionization (ESI) required: 'False' type: String isobaric_labeling_reagent: description: Reagent set used for isobaric labeling enum: - iTRAQ4 - iTRAQ8 - TMT6 - TMT10 - TMT11 - TMT16 - TMT18 - '180' - AQUA - ICAT - ICPL - SILAC required: 'True' type: Enumeration label_free_quantitation: cde_id: MS:1001834 description: Type of label free data analysis strategy proposed for this data enum: - Label-free protein level quantitation - Label-free peptide level quantitation - Label-free protein group level quantitation - Label-free raw feature quantitation - Label-free gene level quantitation required: 'True' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1001834 type: Enumeration labeled_quantitation: cde_id: MS:1002009 description: Type of labeling used enum: - AminoxyTMT - DiART - DiLeu - Glyco-TMT - Hydrazide TMT - IodoTMT - IPTL - iTRAQ - iTRAQH - TMT required: 'True' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1002009 type: Enumeration ms1_resolution: cde_id: MS:1000011 description: MS1 resolution, typically at 400 m/z required: 'False' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000011 type: Integer ms2_resolution: cde_id: MS:1000011 description: MS2 resolution, typically at 400 m/z required: 'False' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000011 type: Integer normalized_collision_energy: cde_id: MS:1000138 description: Normalized collisions energy (%) required: 'False' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1000138 type: Integer particle_size: description: Approximate size with units required: 'False' type: Number particle_size_uom: description: Unit of Measure of particle_size required: 'False' type: String particle_type: description: Manufacturer or brand name of particle if applicable required: 'False' type: String polarity: description: Ion polarity mode(s) used during chromatography enum: - positive - negative - postive/negative required: False (Required for metabolomics only) type: Enumeration program_id: key: 'yes' type: String program_submitter_id: key: 'yes' type: String protocol_date: description: Date protocol was created or updated required: 'False' type: Date protocol_id: key: 'yes' type: String protocol_name: description: External analytical sample protocol name required: 'False' type: String protocol_submitter_id: key: 'yes' type: String quantitation_strategy: cde_id: MS:1001833 description: General strategy used for differential analysis enum: - Absolute quantitation analysis - Isobaric label quantitation analysis - LC-MS label-free quantitation analysis - Metabolic labeling 14N / 15N quantitation analysis - MS1 label-based analysis - MS2 tag-based analysis - SILAC quantitation analysis - Spectral counting analysis - SRM quantitation analysis - MS2-based label-free quantitation required: 'True' source: PSI MS term_url: https://www.ebi.ac.uk/ols4/ontologies/ms/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMS_1001833 type: Enumeration reconstitution_solvent: description: Solvent used to reconstitute samples after evaporation required: 'False' type: String reconstitution_solvent_volume: description: Volume of the reconstitution solvent used required: 'False' type: Number reconstitution_volume_uom: description: Unit of measure of the reconstitution_solvent_volume required: 'False' type: String reporter_ion_ms_level: description: MS level at which fragmentation spectra should be analyzed for reporter ions enum: - MS2 - MS3 required: 'True' type: Enumeration serial_number: description: A serial number is a unique identifier, usually assigned by the manufacturer, to uniquely identify the instrument. This is especially useful if you are uploading raw data to PDC from multiple instruments in your lab. The serial number is usually located on the back side of the instrument. If a serial number is not available, you may also assign an alphanumeric tag that uniquely identifies the instrument. required: 'True' type: String starting_amount: description: Mass with units required: 'False' type: Number starting_amount_uom: description: Unit of Measure of starting_amount enum: - "\xB5g" - mg required: 'False' type: Enumeration title: Protocol type: object uniqueKeys: - - protocol_id - protocol_submitter_id