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comparison test-data/peptide_shaker_certificate_result2.tabular @ 20:2cafc729b2ae draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
author iracooke
date Sun, 31 May 2015 09:05:57 -0400
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19:7e61179c5952 20:2cafc729b2ae
1 Project Details1: PeptideShaker Version: 0.37.4-beta
2 2: Date: Sat Feb 14 20:04:49 CET 2015
3 3: Experiment: Galaxy_Experiment_2015021420041423940686
4 4: Sample: Sample_2015021420041423940686
5 5: Replicate Number: 1
6 6: Identification Algorithms: X!Tandem and MS-GF+
7 Database Search Parameters
8
9 1: Precursor Accuracy Unit: ppm
10 2: Precursor Ion m/z Tolerance: 100.0
11 3: Fragment Ion m/z Tolerance: 0.5
12 4: Enzyme: Trypsin
13 5: Number of Missed Cleavages: Not implemented
14 6: Database: input_database.fasta
15 7: Forward Ion: b
16 8: Rewind Ion: y
17 9: Fixed Modifications: carbamidomethyl c
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
19 11: Refinement Variable Modifications:
20 12: Refinement Fixed Modifications:
21 Input Filters
22
23 1: Minimal Peptide Length: 1
24 2: Maximal Peptide Length: 30
25 3: Precursor m/z Tolerance: 10.0
26 4: Precursor m/z Tolerance Unit: Yes
27 5: Unrecognized Modifications Discarded: No
28 Validation Summary
29
30 1: #Validated Proteins: 0.0
31 2: Protein Total: 0.0
32 3Protein FDR Limit: 1.0 %
33 4: Protein FNR Limit: 0.0 %
34 5: Protein Confidence Limit: -1.0 %
35 6: Protein PEP Limit: 101.0 %
36 7: Protein Confidence Accuracy: 0.0 %
37 8: #Validated Peptides: 0.0
38 9: Peptide Total: 0.0
39 10: Peptide FDR Limit: 1.0 %
40 11: Peptide FNR Limit: 0.0 %
41 12: Peptide Confidence Limit: -1.0 %
42 13: Peptide PEP Limit: 101.0 %
43 14: Peptide Confidence Accuracy: 0.0 %
44 15: #Validated PSM: 0.0
45 16: PSM Total: 0.0
46 17: PSM FDR Limit: 1.0 %
47 18: PSM FNR Limit: 0.0 %
48 19: PSM Confidence Limit: -1.0 %
49 20: PSM PEP Limit: 101.0 %
50 21: PSM Confidence Accuracy: 0.0 %
51 Postranslational Modification Scoring Settings
52
53 1: A-score: No
54 2: Accounting for Neutral Losses: No
55 3: False Location Rate: 1.0
56 Spectrum Counting Parameters
57
58 1: Method: NSAF
59 2: Validated Matches Only: Yes
60 Annotation Settings
61
62 1: Intensity Limit: 0.75
63 2: Automatic Annotation: Yes
64 3: Selected Ions: b, y
65 4: Neutral Losses: NH3, H2O
66 5: Neutral Losses Sequence Dependence: Yes
67 6: Selected Charges: 1, 2
68 7: Fragment Ion m/z Tolerance: 0.5