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

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 49b21b01937067ffc7cf088e615d68177644640b"

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