Mercurial > repos > galaxyp > peptideshaker

comparison test-data/peptide_shaker_certificate_result2.txt @ 30:ad60446b1e93 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
author galaxyp
date Fri, 13 Jan 2017 14:15:42 -0500
parents dfaea053e32f
children
comparison
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29:78fad25eff17 30:ad60446b1e93
1 Project Details1: PeptideShaker Version: 0.39.1 1 Project Details1: PeptideShaker Version: 1.13.6
2 2: Date: Thu Jun 04 20:07:16 CEST 2015 2 2: Date: Fri Jan 13 11:06:50 CST 2017
3 3: Experiment: Galaxy_Experiment_2015060420071433441234 3 3: Experiment: Galaxy_Experiment_2017011311051484327131
4 4: Sample: Sample_2015060420071433441234 4 4: Sample: Sample_2017011311051484327131
5 5: Replicate Number: 1 5 5: Replicate Number: 1
6 6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+ and Comet 6 6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+, Comet and MyriMatch
7 Database Search Parameters 7 Database Search Parameters
8 8
9 1: Precursor Accuracy Unit: ppm 9 1: Precursor Tolerance Unit: ppm
10 2: Precursor Ion m/z Tolerance: 100.0 10 2: Precursor Ion m/z Tolerance: 100.0
11 3: Fragment Ion m/z Tolerance: 0.5 11 3: Fragment Ion Tolerance Unit: Da
12 4: Enzyme: Trypsin 12 4: Fragment Ion m/z Tolerance: 0.5
13 5: Number of Missed Cleavages: Not implemented 13 5: Enzyme: Trypsin
14 6: Database: input_database.fasta 14 6: Maximum Missed Cleavages: 2
15 7: Forward Ion: b 15 7: Database: input_database.fasta
16 8: Rewind Ion: y 16 8: Forward Ion: b
17 9: Fixed Modifications: carbamidomethyl c 17 9: Rewind Ion: y
18 10: Variable Modifications: oxidation of m, acetylation of protein n-term, pyro-cmc, pyro-glu from n-term e, pyro-glu from n-term q 18 10: Fixed Modifications: Carbamidomethylation of C
19 11: Refinement Variable Modifications: 19 11: Variable Modifications: Oxidation of M, Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C
20 12: Refinement Fixed Modifications: 20 12: Refinement Variable Modifications:
21 13: Refinement Fixed Modifications:
21 Input Filters 22 Input Filters
22 23
23 1: Minimal Peptide Length: 1 24 1: Minimal Peptide Length: 1
24 2: Maximal Peptide Length: 30 25 2: Maximal Peptide Length: 30
25 3: Precursor m/z Tolerance: 10.0 26 3: Precursor m/z Tolerance: 10.0
26 4: Precursor m/z Tolerance Unit: Yes 27 4: Precursor m/z Tolerance Unit: Yes
27 5: Unrecognized Modifications Discarded: No 28 5: Unrecognized Modifications Discarded: Yes
28 Validation Summary 29 Validation Summary
29 30
30 1: #Validated Proteins: 0.0 31 1: Proteins: #Validated: 2.0
31 2: Protein Total: 0.0 32 2: Proteins: Total Possible TP: 2.0
32 3Protein FDR Limit: 1.0 % 33 3: Proteins: FDR Limit [%]: 0.0
33 4: Protein FNR Limit: 0.0 % 34 4: Proteins: FNR Limit [%]: 0.0
34 5: Protein Confidence Limit: -1.0 % 35 5: Proteins: Confidence Limit [%]: 100.0
35 6: Protein PEP Limit: 101.0 % 36 6: Proteins: PEP Limit [%]: 0.0
36 7: Protein Confidence Accuracy: 0.0 % 37 7: Proteins: Confidence Accuracy [%]: 0.0
37 8: #Validated Peptides: 0.0 38 8: Peptides: #Validated: 16.0
38 9: Peptide Total: 0.0 39 9: Peptides: Total Possible TP: 16.0
39 10: Peptide FDR Limit: 1.0 % 40 10: Peptides: FDR Limit [%]: 0.0
40 11: Peptide FNR Limit: 0.0 % 41 11: Peptides: FNR Limit [%]: 0.0
41 12: Peptide Confidence Limit: -1.0 % 42 12: Peptides: Confidence Limit [%]: 100.0
42 13: Peptide PEP Limit: 101.0 % 43 13: Peptides: PEP Limit [%]: 0.0
43 14: Peptide Confidence Accuracy: 0.0 % 44 14: Peptides: Confidence Accuracy [%]: 0.0
44 15: #Validated PSM: 0.0 45 15: PSMs: #Validated PSM: 42.0
45 16: PSM Total: 0.0 46 16: PSMs: Total Possible TP: 42.0
46 17: PSM FDR Limit: 1.0 % 47 17: PSMs: FDR Limit [%]: 0.0
47 18: PSM FNR Limit: 0.0 % 48 18: PSMs: FNR Limit [%]: 0.0
48 19: PSM Confidence Limit: -1.0 % 49 19: PSMs: Confidence Limit [%]: 100.0
49 20: PSM PEP Limit: 101.0 % 50 20: PSMs: PEP Limit [%]: 0.0
50 21: PSM Confidence Accuracy: 0.0 % 51 21: PSMs: Confidence Accuracy [%]: 0.0
51 Postranslational Modification Scoring Settings 52 PTM Scoring Settings
52 53
53 1: A-score: No 54 1: Probabilistic Score: PhosphoRS
54 2: Accounting for Neutral Losses: No 55 2: Accounting for Neutral Losses: No
55 3: False Location Rate: 1.0 56 3: Threshold: 95.0
56 Spectrum Counting Parameters 57 Spectrum Counting Parameters
57 58
58 1: Method: NSAF 59 1: Method: NSAF
59 2: Validated Matches Only: Yes 60 2: Validated Matches Only: No
60 Annotation Settings 61 Annotation Settings
61 62
62 1: Intensity Limit: 0.75 63 1: Intensity Limit: 0.75
63 2: Automatic Annotation: Yes 64 2: Automatic Annotation: Yes
64 3: Selected Ions: b, y 65 3: Selected Ions: y, b
65 4: Neutral Losses: H2O, NH3 66 4: Neutral Losses: H2O, NH3, CH4OS
66 5: Neutral Losses Sequence Dependence: Yes 67 5: Neutral Losses Sequence Dependence: Yes
67 6: Fragment Ion m/z Tolerance: 0.5 68 6: Fragment Ion m/z Tolerance: 0.5