annotate test-data/peptide_shaker_certificate_result2.tabular @ 22:e3be595c0bf5 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d

Project Details1: PeptideShaker Version: 0.37.4-beta
2: Date: Sat Feb 14 20:04:49 CET 2015
3: Experiment: Galaxy_Experiment_2015021420041423940686
4: Sample: Sample_2015021420041423940686
5: Replicate Number: 1
6: Identification Algorithms: X!Tandem and MS-GF+
Database Search Parameters

1: Precursor Accuracy Unit: ppm
2: Precursor Ion m/z Tolerance: 100.0
3: Fragment Ion m/z Tolerance: 0.5
4: Enzyme: Trypsin
5: Number of Missed Cleavages: Not implemented
6: Database: input_database.fasta
7: Forward Ion: b
8: Rewind Ion: y
9: Fixed Modifications: carbamidomethyl c
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
11: Refinement Variable Modifications: 
12: Refinement Fixed Modifications: 
Input Filters

1: Minimal Peptide Length: 1
2: Maximal Peptide Length: 30
3: Precursor m/z Tolerance: 10.0
4: Precursor m/z Tolerance Unit: Yes
5: Unrecognized Modifications Discarded: No
Validation Summary

1: #Validated Proteins: 0.0
2: Protein Total: 0.0
3Protein FDR Limit: 1.0 %
4: Protein FNR Limit: 0.0 %
5: Protein Confidence Limit: -1.0 %
6: Protein PEP Limit: 101.0 %
7: Protein Confidence Accuracy: 0.0 %
8: #Validated Peptides: 0.0
9: Peptide Total: 0.0
10: Peptide FDR Limit: 1.0 %
11: Peptide FNR Limit: 0.0 %
12: Peptide Confidence Limit: -1.0 %
13: Peptide PEP Limit: 101.0 %
14: Peptide Confidence Accuracy: 0.0 %
15: #Validated PSM: 0.0
16: PSM Total: 0.0
17: PSM FDR Limit: 1.0 %
18: PSM FNR Limit: 0.0 %
19: PSM Confidence Limit: -1.0 %
20: PSM PEP Limit: 101.0 %
21: PSM Confidence Accuracy: 0.0 %
Postranslational Modification Scoring Settings

1: A-score: No
2: Accounting for Neutral Losses: No
3: False Location Rate: 1.0
Spectrum Counting Parameters

1: Method: NSAF
2: Validated Matches Only: Yes
Annotation Settings

1: Intensity Limit: 0.75
2: Automatic Annotation: Yes
3: Selected Ions: b, y
4: Neutral Losses: NH3, H2O
5: Neutral Losses Sequence Dependence: Yes
6: Selected Charges: 1, 2
7: Fragment Ion m/z Tolerance: 0.5