Mercurial > repos > galaxyp > pyteomics_mztab2tsv
diff test-data/2.mztab @ 0:84e4b5d4b7ad draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
| author | galaxyp |
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| date | Fri, 15 Jan 2021 15:58:54 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2.mztab Fri Jan 15 15:58:54 2021 +0000 @@ -0,0 +1,86 @@ +COM Meta data section +MTD mzTab-version 2.0.0-M +MTD mzTab-ID ISAS-2018-1234 +MTD description Minimal proposed sample file for identification and quantification of lipids +MTD publication[1] pubmed:29039908 | doi:10.1021/acs.analchem.7b03576 +MTD cv[1]-label MS +MTD cv[1]-full_name PSI-MS controlled vocabulary +MTD cv[1]-version 4.0.18 +MTD cv[1]-uri https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo +MTD cv[2]-label MSIO +MTD cv[2]-uri https://www.ebi.ac.uk/ols/ontologies/msio +MTD cv[2]-version 1.0.1 +MTD cv[2]-full_name Metabolomics Standards Initiative Ontology (MSIO) +MTD cv[3]-label UO +MTD cv[3]-full_name Units of Measurement Ontology +MTD cv[3]-version 2017-09-25 +MTD cv[3]-uri http://purl.obolibrary.org/obo/uo.owl +MTD quantification_method [MS, MS:1001838, SRM quantitation analysis, ] +MTD sample_processing[1] [MSIO, MSIO:0000148, high performance liquid chromatography, ] +MTD instrument[1]-name [MS, MS:1001911, Q Exactive , ] +MTD instrument[1]-source [MS, MS:1000073, electrospray ionization, ] +MTD instrument[1]-analyzer[1] [MS, MS:1000081, quadrupole, ] +MTD instrument[1]-analyzer[2] [MS, MS:1000484, orbitrap, ] +MTD instrument[1]-detector [MS, MS:1000624, inductive detector, ] +MTD software[1] [MS, MS:1000532, Xcalibur,2.8-280502/2.8.1.2806] +MTD software[1]-setting[1] ScheduledSRMWindow: 2 min +MTD software[1]-setting[2] CycleTime: 2 s +MTD software[2] [MS, MS:1000922, Skyline, 3.5.0.9319] +MTD software[2]-setting[1] MSMSmassrange: (50.0, 1800.0) +MTD sample[1] QEx-1273-prm-sp1 +MTD sample[1]-description Sphingolipids with concentration reported as picomolar per mg of protein, abundances are reported after calibration correction. +MTD ms_run[1]-location file:///C:/data/QEx-1273-prm-sp1.mzML +MTD ms_run[1]-format [MS, MS:1000584, mzML file, ] +MTD ms_run[1]-id_format [MS, MS:1000768, Thermo nativeID format, ] +MTD ms_run[1]-scan_polarity[1] [MS, MS:1000130, positive scan, ] +MTD ms_run[1]-instrument_ref instrument[1] +MTD assay[1] Description of assay 1 +MTD assay[1]-sample_ref sample[1] +MTD assay[1]-ms_run_ref ms_run[1] +MTD study_variable[1] Sphingolipid SRM Quantitation +MTD study_variable[1]-assay_refs assay[1] +MTD study_variable[1]-description sphingolipid srm quantitation +MTD study_variable[1]-average_function [MS, MS:1002883, median, ] +MTD study_variable[1]-variation_function [MS, MS:1002885, standard error, ] +MTD small_molecule-quantification_unit [UO, UO:0000072, picomolal, ] +MTD small_molecule_feature-quantification_unit [UO, UO:0000072, picomolal, ] +MTD small_molecule-identification_reliability [MS, MS:1002896, compound identification confidence level, ] +MTD database[1] [,, Pubchem, ] +MTD database[1]-prefix PUBCHEM-CPD +MTD database[1]-version 02.12.2017 +MTD database[1]-uri https://www.ncbi.nlm.nih.gov/pccompound +MTD database[2] [,, LipidMaps, ] +MTD database[2]-prefix LM +MTD database[2]-version 2017-12 +MTD database[2]-uri http://www.lipidmaps.org/ +MTD database[3] [,, LipidCreator Transitions, ] +MTD database[3]-prefix LCTR +MTD database[3]-version 2018-07 +MTD database[3]-uri https://lifs.isas.de/lipidcreator +COM MTD colunit-small_molecule retention_time=[UO, UO:0000010, second, ] +MTD colunit-small_molecule_evidence opt_global_mass_error=[UO, UO:0000169, parts per million, ] +MTD id_confidence_measure[1] [MS, MS:1002890, fragmentation score, ] +MTD external_study_uri[1] file:///C:/data/prm.sky.zip + +COM "MzTab 2.0.0-M ""proposed"" specification" +COM Summary rows. +COM Evidences (e.g. multiple modifications, adducts incl. charge variants are summarized). +COM For most use cases this summary lines may be sufficient. +COM Negative and positive scan polarities are currently not explicitly included, this is still under debate in the mzTAB community. +SMH SML_ID SMF_ID_REFS chemical_name database_identifier chemical_formula smiles inchi 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] opt_global_lipid_category opt_global_lipid_species opt_global_lipid_best_id_level +SML 1 1 | 2 | 3 | 4 Cer(d18:1/24:0) LM:LMSP02010012 C42H83NO3 CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC InChI=1S/C42H83NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,40-41,44-45H,3-34,36,38-39H2,1-2H3,(H,43,46)/b37-35+/t40-,41+/m0/s1 http://www.lipidmaps.org/data/LMSDRecord.php?LM_ID=LMSP02010012 649.6373 [M+H]+ 2 [,, qualifier ions exact mass,] 0.958 4.448784E-05 4.448784E-05 0 Sphingolipids Cer 42:1 Cer d18:1/24:0 + +COM MS feature rows , used to report m/z and individual abundance information for quantification +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] opt_global_quantifiers_SMF_ID_REFS +SMF 1 1 null [M+H]1+ null 650.6432 1 821.2341 756.0000 954.0000 4.448784E-05 3 +SMF 2 2 null null null 252.2677 1 821.2341 756.0000 954.0000 6.673176E-06 null +SMF 3 3 null null null 264.2689 1 821.2341 756.0000 954.0000 1.3346352E-05 null +SMF 4 4 null null null 282.2788 1 821.2341 756.0000 954.0000 9.831813E-06 null + +COM Evidence rows for parent / fragment ions. +COM Primary use case: report single hits from spectral library or accurate mass searches without quantification. -> Qualification +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 opt_global_mass_error spectra_ref identification_method ms_level id_confidence_measure[1] rank opt_global_qualifiers_evidence_grouping_ID_REFS +SME 1 1 LM:LMSP0501AB02 C42H83NO3 CCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)/C=C/CCCCCCCCCCCCC InChI=1S/C42H83NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h35,37,40-41,44-45H,3-34,36,38-39H2,1-2H3,(H,43,46)/b37-35+/t40-,41+/m0/s1 LacCer d18:1/12:0 http://www.lipidmaps.org/data/LMSDRecord.php?LM_ID=LMSP02010012 null [M+H]1+ 650.6432 1 650.6446 -2.1517 ms_run[1]:controllerType=0 controllerNumber=1 scan=731 [,, qualifier ions exact mass,] [MS,MS:1000511, ms level, 1] 0.958 1 2 +SME 2 2 LCTR:LCTR0809812 C17H33N null null Cer d18:1/24:0 W' - CHO null null null 252.2677 1 252.2686 -3.5676 ms_run[1]:controllerType=0 controllerNumber=1 scan=732 [,, exact mass, ] [MS,MS:1000511, ms level, 2] 0.9780 1 null +SME 3 2 LCTR:LCTR0871245 C18H33N null null Cer d18:1/24:0 W'' null null null 264.2689 1 264.2686 -1.1352 ms_run[1]:controllerType=0 controllerNumber=1 scan=732 [,, exact mass, ] [MS,MS:1000511, ms level, 2] 0.7500 1 null +SME 4 2 LCTR:LCTR0809711 C18H35NO null null Cer d18:1/24:0 W' null null null 282.2788 1 282.2791 -1.0628 ms_run[1]:controllerType=0 controllerNumber=1 scan=732 [,, exact mass, ] [MS,MS:1000511, ms level, 2] 0.8760 1 null \ No newline at end of file