Mercurial > repos > galaxyp > pyteomics_mztab2tsv

comparison test-data/1.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 This line serves as a size and separator hint for spreadsheet applications. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
2 COM Report of a minimal "Complete Quantification report" label free experiment, quantification on 2 study variables (control/treatment), 3+3 assays (replicates) reported,identifications reported.
3 MTD mzTab-version 1.0.0
4 MTD mzTab-mode Complete
5 MTD mzTab-type Quantification
6 MTD description mzTab example file for reporting a summary report of quantification data quantified on the protein level
7 MTD protein_search_engine_score[1] [MS,MS:1001171,Mascot:score,]
8 MTD psm_search_engine_score[1] [MS,MS:1001171,Mascot:score,]
9 MTD ms_run[1]-location file://C:/path/to/my/file1.mzML
10 MTD ms_run[2]-location file://C:/path/to/my/file2.mzML
11 MTD ms_run[3]-location file://C:/path/to/my/file3.mzML
12 MTD ms_run[4]-location file://C:/path/to/my/file4.mzML
13 MTD ms_run[5]-location file://C:/path/to/my/file5.mzML
14 MTD ms_run[6]-location file://C:/path/to/my/file6.mzML
15 MTD protein-quantification_unit [PRIDE, PRIDE:0000393, Relative quantification unit,]
16 MTD software[1] [MS, MS:1000752, TOPP software,]
17 MTD fixed_mod[1] [UNIMOD, UNIMOD:4, Carbamidomethyl, ]
18 MTD variable_mod[1] [UNIMOD, UNIMOD:35, Oxidation, ]
19 MTD quantification_method [MS, MS:1002038, unlabeled sample, ]
20 MTD assay[1]-quantification_reagent [MS, MS:1002038, unlabeled sample, ]
21 MTD assay[2]-quantification_reagent [MS, MS:1002038, unlabeled sample, ]
22 MTD assay[3]-quantification_reagent [MS, MS:1002038, unlabeled sample, ]
23 MTD assay[4]-quantification_reagent [MS, MS:1002038, unlabeled sample, ]
24 MTD assay[5]-quantification_reagent [MS, MS:1002038, unlabeled sample, ]
25 MTD assay[6]-quantification_reagent [MS, MS:1002038, unlabeled sample, ]
26 MTD assay[1]-ms_run_ref ms_run[1]
27 MTD assay[2]-ms_run_ref ms_run[2]
28 MTD assay[3]-ms_run_ref ms_run[3]
29 MTD assay[4]-ms_run_ref ms_run[4]
30 MTD assay[5]-ms_run_ref ms_run[5]
31 MTD assay[6]-ms_run_ref ms_run[6]
32 MTD study_variable[1]-assay_refs assay[1], assay[2], assay[3]
33 MTD study_variable[2]-assay_refs assay[4], assay[5], assay[6]
34 MTD study_variable[1]-description heat shock response of control
35 MTD study_variable[2]-description heat shock response of treatment
36
37 PRH accession description taxid species database database_version search_engine best_search_engine_score[1] search_engine_score[1]_ms_run[1] search_engine_score[1]_ms_run[2] search_engine_score[1]_ms_run[3] search_engine_score[1]_ms_run[4] search_engine_score[1]_ms_run[5] search_engine_score[1]_ms_run[6] num_psms_ms_run[1] num_psms_ms_run[2] num_psms_ms_run[3] num_psms_ms_run[4] num_psms_ms_run[5] num_psms_ms_run[6] num_peptides_distinct_ms_run[1] num_peptides_distinct_ms_run[2] num_peptides_distinct_ms_run[3] num_peptides_distinct_ms_run[4] num_peptides_distinct_ms_run[5] num_peptides_distinct_ms_run[6] num_peptides_unique_ms_run[1] num_peptides_unique_ms_run[2] num_peptides_unique_ms_run[3] num_peptides_unique_ms_run[4] num_peptides_unique_ms_run[5] num_peptides_unique_ms_run[6] ambiguity_members modifications protein_coverage protein_abundance_assay[1] protein_abundance_assay[2] protein_abundance_assay[3] protein_abundance_assay[4] protein_abundance_assay[5] protein_abundance_assay[6] protein_abundance_study_variable[1] protein_abundance_stdev_study_variable[1] protein_abundance_std_error_study_variable[1] protein_abundance_study_variable[2] protein_abundance_stdev_study_variable[2] protein_abundance_std_error_study_variable[2]
38 COM Accession Description Taxonomie ID Species Database Version Search Engine best Mascot score Mascot score (HSPControlRep1) Mascot score (HSPControlRep2) Mascot score (HSPControlRep3) Mascot score (HSPTreatmentRep1) Mascot score (HSPTreatmentRep2) Mascot score (HSPTreatmentRep3) PSMs (HSPControlRep1) PSMs (HSPControlRep2) PSMs (HSPControlRep3) PSMs (HSPTreatmentRep4) PSMs (HSPTreatmentRep5) PSMs (HSPTreatmentRep6) Distinct Peptides (HSPControlRep1) Distinct Peptides (HSPControlRep2) Distinct Peptides (HSPControlRep3) Distinct Peptides (HSPTreatmentRep4) Distinct Peptides (HSPTreatmentRep5) Distinct Peptides (HSPTreatmentRep6) Unique Peptides (HSPControlRep1) Unique Peptides (HSPControlRep2) Unique Peptides (HSPControlRep3) Unique Peptides (HSPTreatmentRep4) Unique Peptides (HSPTreatmentRep5) Unique Peptides (HSPTreatmentRep6) Ambiguity Members Modifications Protein Coverage (fraction) Abundance (HSPTreatmentRep1) Abundance (HSPTreatmentRep2) Abundance (HSPTreatmentRep3) Abundance (HSPTreatmentRep4) Abundance (HSPTreatmentRep5) Abundance (HSPTreatmentRep6) Abundance (HSPControl) Standard Deviation (HSPControl) Standard Error (HSPControl) Abundance (HSPTreatment) Standard Deviation (HSPTreatment) Standard Error (HSPTreatment)
39 PRT P63017 Heat shock cognate 71 kDa protein 10090 Mus musculus UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 46 46 26 36 -3 -1 null 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 null 0 0.34 34.3 40.43507695 41.12124635 266.9554147 234.4 271.0324163 38.61877444 3.755870949 2.168453103 257.4626103 20.07656548 11.59121048
40 PRT P14602 Heat shock protein beta-1 10090 Mus musculus UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 100 100 -9 20 100 4 3 3 1 2 3 2 3 3 1 2 3 2 2 2 1 2 2 1 Q340U4,Q5K0U2,P8L901 0 0.12 98588.4 114212.9033 100070.7061 4709.411242 4345.7 6704.588342 104290.6698 8624.809914 4979.536326 5253.233195 1269.998146 733.2337713
41 PRT Q8K0U4 Heat shock 70 kDa protein 12A 10090 Mus musculus UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 120 120 null -2 39 36 -7 1 0 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 null 0 0.14 43.4 86.09123822 54.98032306 459.4934179 375.5 609.3477328 61.49052043 22.0776461 12.74653492 481.4470502 118.4595375 68.39264584
42 PRT Q61699 Heat shock protein 105 kDa 10090 Mus musculus UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 36 30 31 36 -2 31 24 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 null 0 0.08 3432.54 3847.349077 3838.448278 11372.30364 9587.5 10303.56594 3706.112452 236.9624883 136.8103564 10421.12319 898.190283 518.5704017
43 PRT P07901 Heat shock protein HSP 90-alpha 10090 Mus musculus UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 45 45 6 -2 35 8 3 4 3 4 3 2 4 4 3 4 3 2 4 4 3 4 3 2 4 null 12-UNIMOD:35, 98-UNIMOD:35,727-UNIMOD:35 0.21 3242354.3 3284123.069 3404460.592 633072.591 552426.4 618457.6276 3310312.654 84166.6994 48593.66656 601318.8729 42968.06623 24807.6246
44
45 PSH sequence PSM_ID accession unique database database_version search_engine search_engine_score[1] modifications spectra_ref retention_time charge exp_mass_to_charge calc_mass_to_charge pre post start end
46 COM Sequence PSM identifier accession Unqiue Database Database Version Search Engine Mascot score Modifications Spectra Reference Retention Time Charge Experimental m/z Calculated m/z Pre Post Start End
47 PSM QTQTFTTYSDNQPGVL 1 P63017 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 46 null ms_run[1]:scan=1296 1336.62 3 600.6006697 600.6197 K I 424 439
48 PSM AVVNGYSASDTVGAGFAQAK 2 Q8K0U4 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 120 null ms_run[1]:scan=1300 1327.08 2 956.9464833 956.9736 K E 261 281
49 PSM ALLRLHQECEKLK 3 Q61699 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 30 9-UNIMOD:4 ms_run[1]:scan=845 885.62 3 527.6406579 527.6362 R K 262 274
50 PSM DWYPAHSR 4 P14602 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[1]:scan=544 571.08 2 516.21 516.2383 R L 21 28
51 PSM DWYPAHSR 4 Q340U4 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[1]:scan=544 571.08 2 516.21 516.2383 K E 143 150
52 PSM DWYPAHSR 4 P16627 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[1]:scan=544 571.08 2 516.21 516.2383 R M 240 247
53 PSM MNQSNASPTLDGLFR 5 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 14 null ms_run[1]:scan=1155 1195.62 3 550.9282794 550.935 - R 1 15
54 PSM LWPFQVINEAGKPK 6 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 45 null ms_run[1]:scan=1064 1104.62 3 542.9688356 542.9716 K V 91 104
55 PSM MIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 7 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 45 null ms_run[1]:scan=2849 2876.08 2 1974.400793 1974.3984 R M 692 728
56 PSM LGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 8 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 120 23-UNIMOD:35 ms_run[1]:scan=2584 2611.08 2 1788.281997 1788.2886 K M 695 728
57 PSM TLTIVDTGIGMTK 9 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 76 11-UNIMOD:35 ms_run[1]:scan=1092 1132.62 3 450.5920214 450.583 R A 88 100
58 PSM MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNK 10 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 87 0-UNIMOD:35 ms_run[1]:scan=3157 3184.08 2 2405.587318 2405.6084 - E 1 41
59 PSM QTQTFTTYSDNQPGVL 11 P63017 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 26 null ms_run[2]:scan=1530 1336.62 3 600.6265518 600.6197 K I 424 439
60 PSM ALLRLHQECEKLK 12 Q61699 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 36 9-UNIMOD:4 ms_run[2]:scan=1079 885.62 3 527.6362432 527.6362 R K 262 274
61 PSM DWYPAHSR 13 P14602 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[2]:scan=778 571.08 2 516.21 516.2383 R L 21 28
62 PSM DWYPAHSR 13 Q340U4 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[2]:scan=778 571.08 2 516.21 516.2383 K E 143 150
63 PSM DWYPAHSR 13 P16627 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[2]:scan=778 571.08 2 516.21 516.2383 R M 240 247
64 PSM MNQSNASPTLDGLFR 14 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 40 null ms_run[2]:scan=1389 1195.62 3 550.9468571 550.935 - R 1 15
65 PSM LWPFQVINEAGKPK 15 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 16 null ms_run[2]:scan=1298 1104.62 3 542.9666503 542.9716 K V 91 104
66 PSM MIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 16 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 6 null ms_run[2]:scan=3083 2876.08 2 1974.399035 1974.3984 R M 692 728
67 PSM TLTIVDTGIGMTK 17 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 21 null ms_run[2]:scan=1326 1132.62 3 450.5400013 450.583 R A 88 100
68 PSM MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNK 18 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -5 null ms_run[2]:scan=3391 3184.08 2 2405.599817 2405.6084 - E 1 41
69 PSM QTQTFTTYSDNQPGVL 19 P63017 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 36 null ms_run[3]:scan=1062 1336.62 3 600.6484541 600.6197 K I 424 439
70 PSM AVVNGYSASDTVGAGFAQAK 20 Q8K0U4 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -2 null ms_run[3]:scan=1066 1327.08 2 956.9766608 956.9736 K E 261 281
71 PSM ALLRLHQECEKLK 21 Q61699 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 36 9-UNIMOD:4 ms_run[3]:scan=611 885.62 3 527.6486368 527.6362 R K 262 274
72 PSM MNQSNASPTLDGLFR 22 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -9 null ms_run[3]:scan=921 1195.62 3 550.9336303 550.935 - R 1 15
73 PSM MIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 23 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -2 null ms_run[3]:scan=2615 2876.08 2 1974.392219 1974.3984 R M 692 728
74 PSM LGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 24 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -3 23-UNIMOD:35 ms_run[3]:scan=2350 2611.08 2 1788.28771 1788.2886 K M 695 728
75 PSM TLTIVDTGIGMTK 25 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 37 null ms_run[3]:scan=858 1132.62 3 450.5960917 450.583 R A 88 100
76 PSM MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNK 26 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 6 12-UNIMOD:35 ms_run[3]:scan=2923 3184.08 2 2405.604605 2405.6084 - E 1 41
77 PSM QTQTFTTYSDNQPGVL 27 P63017 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -3 null ms_run[4]:scan=2731 1336.62 3 600.6123009 600.6197 K I 424 439
78 PSM AVVNGYSASDTVGAGFAQAK 28 Q8K0U4 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 39 null ms_run[4]:scan=2735 1327.08 2 956.9765302 956.9736 K E 261 281
79 PSM ALLRLHQECEKLK 29 Q61699 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -2 9-UNIMOD:4 ms_run[4]:scan=2280 885.62 3 527.6343404 527.6362 R K 262 274
80 PSM MNQSNASPTLDGLFR 30 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 20 null ms_run[4]:scan=2590 1195.62 3 550.9284574 550.935 - R 1 15
81 PSM LWPFQVINEAGKPK 31 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -3 null ms_run[4]:scan=2499 1104.62 3 542.9715699 542.9716 K V 91 104
82 PSM MIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 32 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 35 null ms_run[4]:scan=4284 2876.08 2 1974.40429 1974.3984 R M 692 728
83 PSM LGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 33 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 0 23-UNIMOD:35 ms_run[4]:scan=4019 2611.08 2 1788.289062 1788.2886 K M 695 728
84 PSM MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNK 34 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 11 0-UNIMOD:35 ms_run[4]:scan=4592 3184.08 2 2405.57421 2405.6084 - E 1 41
85 PSM QTQTFTTYSDNQPGVL 35 P63017 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -1 null ms_run[5]:scan=2031 1336.62 3 600.5900228 600.6197 K I 424 439
86 PSM AVVNGYSASDTVGAGFAQAK 36 Q8K0U4 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 36 null ms_run[5]:scan=2035 1327.08 2 956.9477197 956.9736 K E 261 281
87 PSM ALLRLHQECEKLK 37 Q61699 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 31 9-UNIMOD:4 ms_run[5]:scan=1580 885.62 3 527.6254449 527.6362 R K 262 274
88 PSM DWYPAHSR 38 P14602 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[5]:scan=1279 571.08 2 516.21 516.2383 R L 21 28
89 PSM DWYPAHSR 38 Q340U4 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[5]:scan=1279 571.08 2 516.21 516.2383 K E 143 150
90 PSM DWYPAHSR 38 P16627 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 100 null ms_run[5]:scan=1279 571.08 2 516.21 516.2383 R M 240 247
91 PSM MNQSNASPTLDGLFR 39 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 32 null ms_run[5]:scan=1890 1195.62 3 550.9120992 550.935 - R 1 15
92 PSM LWPFQVINEAGKPK 40 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 21 null ms_run[5]:scan=1799 1104.62 3 542.9599424 542.9716 K V 91 104
93 PSM TLTIVDTGIGMTK 41 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 8 11-UNIMOD:35 ms_run[5]:scan=1827 1132.62 3 450.5534561 450.583 R A 88 100
94 PSM MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNK 42 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -5 0-UNIMOD:35 ms_run[5]:scan=3892 3184.08 2 2405.594573 2405.6084 - E 1 41
95 PSM AVVNGYSASDTVGAGFAQAK 43 Q8K0U4 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] -7 null ms_run[6]:scan=1331 1327.08 2 956.9880766 956.9736 K E 261 281
96 PSM ALLRLHQECEKLK 44 Q61699 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 24 9-UNIMOD:4 ms_run[6]:scan=876 885.62 3 527.64539 527.6362 R K 262 274
97 PSM DWYPAHSR 45 P14602 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 4 null ms_run[6]:scan=575 571.08 2 516.21 516.2383 R L 21 28
98 PSM DWYPAHSR 45 Q340U4 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 40 null ms_run[6]:scan=575 571.08 2 516.21 516.2383 K E 143 150
99 PSM DWYPAHSR 45 P16627 0 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 9 null ms_run[6]:scan=575 571.08 2 516.21 516.2383 R M 240 247
100 PSM MNQSNASPTLDGLFR 46 P14602 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 32 null ms_run[6]:scan=1186 1195.62 3 550.9319012 550.935 - R 1 15
101 PSM MIKLGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 47 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 3 null ms_run[6]:scan=2880 2876.08 2 1974.377816 1974.3984 R M 692 728
102 PSM LGLGIDEDDPTVDDTSAAVTEEMPPLEGDDDTSR 48 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 29 23-UNIMOD:35 ms_run[6]:scan=2615 2611.08 2 1788.294771 1788.2886 K M 695 728
103 PSM TLTIVDTGIGMTK 49 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 39 11-UNIMOD:35 ms_run[6]:scan=1123 1132.62 3 450.6038036 450.583 R A 88 100
104 PSM MPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNK 50 P07901 1 UniProtKB 2013_08 [MS,MS:1001207,Mascot,] 33 0-UNIMOD:35 ms_run[6]:scan=3188 3184.08 2 2405.605739 2405.6084 - E 1 41