COM Meta data section MTD mzTab-version 2.0.0-M MTD mzTab-ID mzTab-GCxGC-MS MTD description Minimal sample file for GCxGC-MS quantification of small molecules between two experiments MTD instrument[1]-name [MS, MS:1001945, Pegasus 4D, ] MTD instrument[1]-source [MS, MS:1000389, electron Ionization, ] MTD instrument[1]-analyzer[1] [MS, MS:1000084, time-of-flight, ] MTD instrument[1]-detector [MS, MS:1000114, microchannel plate detector, ] MTD software[1] [MS, MS:1001799, ChromaTOF software, 3.21] MTD software[1]-setting[1] baseline=0.2 MTD software[1]-setting[2] dbMatchTreshold=900 MTD sample[1]-species[1] [NCBITaxon, NCBITaxon:9606, Homo sapiens, ] MTD sample[1]-cell_type[1] [CL, CL:0000233, platelet, ] MTD sample[1]-description Unstimulated human blood platelets MTD sample[2]-species[1] [NCBITaxon, NCBITaxon:9606, Homo sapiens, ] MTD sample[2]-cell_type[1] [CL, CL:0000233, platelet, ] MTD sample[2]-description Unstimulated human blood platelets MTD ms_run[1]-location file://c:/data/control.mzML MTD ms_run[1]-format [MS, MS:1000584, mzML file, ] MTD ms_run[1]-id_format [MS, MS:1000776, scan number only nativeID format, ] MTD ms_run[1]-scan_polarity[1] [MS, MS:1000130, positive scan, ] MTD ms_run[2]-location file://c:/data/treatment.mzML MTD ms_run[2]-format [MS, MS:1000584, mzML file, ] MTD ms_run[2]-id_format [MS, MS:1000776, scan number only nativeID format, ] MTD ms_run[2]-scan_polarity[1] [MS, MS:1000130, positive scan, ] MTD assay[1]-sample_ref sample[1] MTD assay[1]-ms_run_ref ms_run[1] MTD assay[2]-sample_ref sample[2] MTD assay[2]-ms_run_ref ms_run[2] MTD study_variable[1] Untreated MTD study_variable[1]-assay_refs assay[1] MTD study_variable[1]-description drug response control MTD study_variable[1]-average_function [MS, MS:1002962, mean, ] MTD study_variable[1]-variation_function [MS, MS:1002885, standard error, ] MTD study_variable[2] Treated MTD study_variable[2]-assay_refs assay[2] MTD study_variable[2]-description drug response treatment MTD study_variable[2]-average_function [MS, MS:1002962, mean, ] MTD study_variable[2]-variation_function [MS, MS:1002885, standard error, ] MTD cv[1]-label MS MTD cv[1]-full_name PSI-MS controlled vocabulary MTD cv[1]-version 20-06-2018 MTD cv[1]-uri https://www.ebi.ac.uk/ols/ontologies/ms MTD cv[2]-label NCBITaxon MTD cv[2]-full_name An ontology representation of the NCBI organismal taxonomy Ontology MTD cv[2]-version 2018-03-02 MTD cv[2]-uri https://www.ebi.ac.uk/ols/ontologies/ncbitaxon MTD cv[3]-label CL MTD cv[3]-full_name The Cell Ontology is a structured controlled vocabulary for cell types in animals. MTD cv[3]-version 2017-12-11 MTD cv[3]-uri https://www.ebi.ac.uk/ols/ontologies/cl MTD cv[4]-label PRIDE MTD cv[4]-full_name PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary MTD cv[4]-version 14-06-2018 MTD cv[4]-uri https://www.ebi.ac.uk/ols/ontologies/pride MTD cv[5]-label CHEBI MTD cv[5]-full_name Chemical Entities of Biological Interest MTD cv[5]-version 08-02-2019 MTD cv[5]-uri https://www.ebi.ac.uk/ols/ontologies/chebi MTD database[1] [, ,Golm Metabolite Database, ] MTD database[1]-prefix GMD MTD database[1]-version 2.3 MTD database[1]-uri http://gmd.mpimp-golm.mpg.de/ MTD database[2] [, , no database, null] MTD database[2]-prefix null MTD database[2]-uri null MTD database[2]-version Unknown MTD derivatization_agent[1] [,,Methoxylamine hydrochloride,] MTD derivatization_agent[2] [CHEBI, CHEBI:85064, N-methyl-N-(trimethylsilyl)trifluoroacetamide,] MTD small_molecule-identification_reliability [MS, MS:1002896, compound identification confidence level, ] MTD id_confidence_measure[1] [MS, MS:1002890, fragmentation score, ] MTD small_molecule-quantification_unit [PRIDE, PRIDE:0000330, Arbitrary quantification unit, ] MTD small_molecule_feature-quantification_unit [PRIDE, PRIDE:0000330, Arbitrary quantification unit, ] MTD quantification_method [,,baseline-corrected intensity quantification,] MTD custom[1] [MS, MS:1000901, retention time normalization standard, n-alkanes C10–C36] COM Small molecule summary rows (similar to Protein section). COM Evidences (e.g. multiple modifications, adducts incl. charge variants are summarized). COM For most use cases this summary lines might be sufficient. SMH SML_ID SMF_ID_REFS database_identifier chemical_formula smiles inchi chemical_name uri theoretical_neutral_mass adduct_ions reliability best_id_confidence_measure best_id_confidence_value abundance_assay[1] abundance_study_variable[1] abundance_variation_study_variable[1] abundance_assay[2] abundance_study_variable[2] abundance_variation_study_variable[2] SML 1 1 | 2 GMD:cd7993ea-ad14-452a-a907-33376cc98790 C18H36O2 CCCCCCCCCCCCCCCCCC(O)=O InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20) Octadecanoic acid http://identifiers.org/gmd/cd7993ea-ad14-452a-a907-33376cc98790 284.478 [M+H]1+ 2 [MS, MS:1002890, fragmentation score, ] 978 805.16 805.16 0 589.9 589.9 0 COM Small molecule feature rows (only reported in Complete Quantification files and if feature information like e.g. mass traces are important) SFH SMF_ID SME_ID_REFS SME_ID_REF_ambiguity_code adduct_ion isotopomer exp_mass_to_charge charge retention_time_in_seconds retention_time_in_seconds_start retention_time_in_seconds_end abundance_assay[1] abundance_assay[2] opt_global_retention_time_nd opt_global_retention_time_nd_window_start opt_global_retention_time_nd_window_end SMF 1 1 null [M+H]1+ null 285.484 1 1564.47 1559.45 1564.48 805.16 805.16 1562 | 2.47 1557 | 2.45 1562 | 2.48 SMF 2 2 null [M+H]1+ null 285.484 1 1564.48 1554.45 1569.47 589.9 589.9 1562 | 2.48 1552 | 2.45 1567| 2.47 COM Small molecule evidence rows for parent ions. Analog to PSM. COM Primary use case: report single hits from spectral library or accurate mass searches without quantification. SEH SME_ID evidence_input_id database_identifier chemical_formula smiles inchi chemical_name uri derivatized_form adduct_ion exp_mass_to_charge charge theoretical_mass_to_charge spectra_ref identification_method ms_level id_confidence_measure[1] rank SME 1 ms_run[1]:scan=8 GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3 C18H36O2 CCCCCCCCCCCCCCCCCC(O)=O InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20) Octadecanoic acid (1TMS) http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3 [CHEBI, CHEBI:51088, trimethylsilyl group, 1] [M+H]+ 356.6588 1 356.659 ms_run[1]:scan=8 [,, ChromaTOF database search,] [MS, MS:1000511, ms level, 1] 957 1 SME 2 ms_run[2]:scan=23 GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3 C18H36O2 CCCCCCCCCCCCCCCCCC(O)=O InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20) Octadecanoic acid (1TMS) http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3 [CHEBI, CHEBI:51088, trimethylsilyl group, 1] [M+H]+ 356.6589 1 356.659 ms_run[2]:scan=23 [,, ChromaTOF database search,] [MS, MS:1000511, ms level, 1] 972 1