annotate test-data/peptideshaker_reports_output_hierarchical.tabular @ 61:3ec27b4cee7c draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"

	Protein Inference	Main Accession	Description	Protein Group	Secondary Accessions	Validated Coverage [%]	Possible Coverage [%]	#Peptides	#Validated Peptides	#Unique Peptides	#PSMs	#Validated PSMs	Confidently Localized Modification Sites	#Confidently Localized Modification Sites	Ambiguously Localized Modification Sites	#Ambiguously Localized Modification Sites	Spectrum Counting NSAF	MW [kDa]	Confidence [%]	Validation	Decoy
1	Single Protein	cds.comp8310_c0_seq2	m.1138 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 22.01 EValue:2.0e-16	cds.comp8310_c0_seq2		3.69	81.0	1	1	1	1	1					0.003257328990228013	45.26545451338222	100.0	Doubtful	0
	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
1.1	cds.comp8310_c0_seq2	NLVAEESMNMLKNK	NR	FK				1	1	100.0	0	Confident
	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
1.1.1	cds.comp8310_c0_seq2	NLVAEESMNMLKNK	NH2-NLVAEESMNMLKNK-COOH			searchgui_smallspectra	small.17.17. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=17"	8.9853	811.408081054688	2+, 3+, 4+	2	1619.80111309327	1	-1.7626881884550694	0				100.0	Confident
2	Single Protein	cds.comp41890_c0_seq1	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20	cds.comp41890_c0_seq1		20.15	91.04	1	1	1	1	1					0.00819672131147541	14.802380493830709	100.0	Doubtful	0
	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
2.1	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR	LK	LG				1	1	100.0	0	Confident
	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
2.1.1	cds.comp41890_c0_seq1	PGGFAKVWANGMGDPNSGDLVWHNKSR	NH2-PGGFAKVWANGMGDPNSGDLVWHNKSR-COOH			searchgui_smallspectra	small.28.28. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=28"	16.3598	725.3583984375	2+, 3+, 4+	4	2896.38272917215	1	6.345261931182815	0				100.0	Confident
3	Related Proteins	cds.comp41779_c0_seq1	m.9429 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 30.62 EValue:7.0e-67	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	3.34	78.82	1	1	1	1	1					0.00202020202020202	69.88215380565931	100.0	Doubtful	0
	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
3.1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK	WK;WK;WK	DP;DP;DP				1	1	100.0	0	Confident
	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
3.1.1	cds.comp41779_c0_seq1,cds.comp41779_c0_seq2,cds.comp41779_c0_seq3	LDRLISATSISPEHKIDFLFK	NH2-LDRLISATSISPEHKIDFLFK-COOH			searchgui_smallspectra	small.3.3. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=3"	0.6731	810.789428710938	2+, 3+, 4+	3	2429.33184573292	0	6.00693871414815	0				100.0	Confident
4	Single Protein	cds.comp41890_c0_seq1_REVERSED	m.9546 RecName: Full=70 kDa neurofilament protein; 1051067 GO:0005882 GO:0005198 Identity: 38.58 EValue:4.0e-20-REVERSED	cds.comp41890_c0_seq1_REVERSED		8.21	90.3	1	1	1	1	1					0.008264462809917356	14.802380493830709	100.0	Doubtful	0
	Protein(s)	Sequence	AAs Before	AAs After	Variable Modifications	Fixed Modifications	Localization Confidence	#PSMs	#Validated PSMs	Confidence [%]	Decoy	Validation
4.1	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK	NK	VL				1	1	100.0	0	Confident
	Protein(s)	Sequence	Modified Sequence	Variable Modifications	Fixed Modifications	Spectrum File	Spectrum Title	RT	m/z	Measured Charge	Identification Charge	Theoretical Mass	Isotope Number	Precursor m/z Error [ppm]	Decoy	Localization Confidence	Probabilistic PTM score	D-score	Confidence [%]	Validation
4.1.1	cds.comp41890_c0_seq1_REVERSED	RYTSHEQLEGK	NH2-RYTSHEQLEGK-COOH			searchgui_smallspectra	small.46.46. File:"small.RAW", NativeID:"controllerType=0 controllerNumber=1 scan=46"	27.6339	674.841369628906	2+, 3+, 4+	2	1346.6578773639	1	5.1562724435666505	0				100.0	Confident