Mercurial > repos > galaxyp > pyteomics_mztab2tsv

comparison test-data/2.mztab @ 0:84e4b5d4b7ad draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"
author galaxyp
date Fri, 15 Jan 2021 15:58:54 +0000
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-1:000000000000 0:84e4b5d4b7ad
1 COM Meta data section
2 MTD mzTab-version 2.0.0-M
3 MTD mzTab-ID ISAS-2018-1234
4 MTD description Minimal proposed sample file for identification and quantification of lipids
5 MTD publication[1] pubmed:29039908 | doi:10.1021/acs.analchem.7b03576
6 MTD cv[1]-label MS
7 MTD cv[1]-full_name PSI-MS controlled vocabulary
8 MTD cv[1]-version 4.0.18
9 MTD cv[1]-uri https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo
10 MTD cv[2]-label MSIO
11 MTD cv[2]-uri https://www.ebi.ac.uk/ols/ontologies/msio
12 MTD cv[2]-version 1.0.1
13 MTD cv[2]-full_name Metabolomics Standards Initiative Ontology (MSIO)
14 MTD cv[3]-label UO
15 MTD cv[3]-full_name Units of Measurement Ontology
16 MTD cv[3]-version 2017-09-25
17 MTD cv[3]-uri http://purl.obolibrary.org/obo/uo.owl
18 MTD quantification_method [MS, MS:1001838, SRM quantitation analysis, ]
19 MTD sample_processing[1] [MSIO, MSIO:0000148, high performance liquid chromatography, ]
20 MTD instrument[1]-name [MS, MS:1001911, Q Exactive , ]
21 MTD instrument[1]-source [MS, MS:1000073, electrospray ionization, ]
22 MTD instrument[1]-analyzer[1] [MS, MS:1000081, quadrupole, ]
23 MTD instrument[1]-analyzer[2] [MS, MS:1000484, orbitrap, ]
24 MTD instrument[1]-detector [MS, MS:1000624, inductive detector, ]
25 MTD software[1] [MS, MS:1000532, Xcalibur,2.8-280502/2.8.1.2806]
26 MTD software[1]-setting[1] ScheduledSRMWindow: 2 min
27 MTD software[1]-setting[2] CycleTime: 2 s
28 MTD software[2] [MS, MS:1000922, Skyline, 3.5.0.9319]
29 MTD software[2]-setting[1] MSMSmassrange: (50.0, 1800.0)
30 MTD sample[1] QEx-1273-prm-sp1
31 MTD sample[1]-description Sphingolipids with concentration reported as picomolar per mg of protein, abundances are reported after calibration correction.
32 MTD ms_run[1]-location file:///C:/data/QEx-1273-prm-sp1.mzML
33 MTD ms_run[1]-format [MS, MS:1000584, mzML file, ]
34 MTD ms_run[1]-id_format [MS, MS:1000768, Thermo nativeID format, ]
35 MTD ms_run[1]-scan_polarity[1] [MS, MS:1000130, positive scan, ]
36 MTD ms_run[1]-instrument_ref instrument[1]
37 MTD assay[1] Description of assay 1
38 MTD assay[1]-sample_ref sample[1]
39 MTD assay[1]-ms_run_ref ms_run[1]
40 MTD study_variable[1] Sphingolipid SRM Quantitation
41 MTD study_variable[1]-assay_refs assay[1]
42 MTD study_variable[1]-description sphingolipid srm quantitation
43 MTD study_variable[1]-average_function [MS, MS:1002883, median, ]
44 MTD study_variable[1]-variation_function [MS, MS:1002885, standard error, ]
45 MTD small_molecule-quantification_unit [UO, UO:0000072, picomolal, ]
46 MTD small_molecule_feature-quantification_unit [UO, UO:0000072, picomolal, ]
47 MTD small_molecule-identification_reliability [MS, MS:1002896, compound identification confidence level, ]
48 MTD database[1] [,, Pubchem, ]
49 MTD database[1]-prefix PUBCHEM-CPD
50 MTD database[1]-version 02.12.2017
51 MTD database[1]-uri https://www.ncbi.nlm.nih.gov/pccompound
52 MTD database[2] [,, LipidMaps, ]
53 MTD database[2]-prefix LM
54 MTD database[2]-version 2017-12
55 MTD database[2]-uri http://www.lipidmaps.org/
56 MTD database[3] [,, LipidCreator Transitions, ]
57 MTD database[3]-prefix LCTR
58 MTD database[3]-version 2018-07
59 MTD database[3]-uri https://lifs.isas.de/lipidcreator
60 COM MTD colunit-small_molecule retention_time=[UO, UO:0000010, second, ]
61 MTD colunit-small_molecule_evidence opt_global_mass_error=[UO, UO:0000169, parts per million, ]
62 MTD id_confidence_measure[1] [MS, MS:1002890, fragmentation score, ]
63 MTD external_study_uri[1] file:///C:/data/prm.sky.zip
64
65 COM "MzTab 2.0.0-M ""proposed"" specification"
66 COM Summary rows.
67 COM Evidences (e.g. multiple modifications, adducts incl. charge variants are summarized).
68 COM For most use cases this summary lines may be sufficient.
69 COM Negative and positive scan polarities are currently not explicitly included, this is still under debate in the mzTAB community.
70 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
71 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
72
73 COM MS feature rows , used to report m/z and individual abundance information for quantification
74 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
75 SMF 1 1 null [M+H]1+ null 650.6432 1 821.2341 756.0000 954.0000 4.448784E-05 3
76 SMF 2 2 null null null 252.2677 1 821.2341 756.0000 954.0000 6.673176E-06 null
77 SMF 3 3 null null null 264.2689 1 821.2341 756.0000 954.0000 1.3346352E-05 null
78 SMF 4 4 null null null 282.2788 1 821.2341 756.0000 954.0000 9.831813E-06 null
79
80 COM Evidence rows for parent / fragment ions.
81 COM Primary use case: report single hits from spectral library or accurate mass searches without quantification. -> Qualification
82 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
83 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
84 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
85 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
86 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