annotate test-data/peptide_shaker_certificate_result2.txt @ 42:9e20c34298e3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0ce31532e2d232c87298f3aa73d02fc201fa108d

Project Details1: PeptideShaker Version: 1.13.6
2: Date: Fri Jan 13 11:06:50 CST 2017
3: Experiment: Galaxy_Experiment_2017011311051484327131
4: Sample: Sample_2017011311051484327131
5: Replicate Number: 1
6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+, Comet and MyriMatch
Database Search Parameters

1: Precursor Tolerance Unit: ppm
2: Precursor Ion m/z Tolerance: 100.0
3: Fragment Ion Tolerance Unit: Da
4: Fragment Ion m/z Tolerance: 0.5
5: Enzyme: Trypsin
6: Maximum Missed Cleavages: 2
7: Database: input_database.fasta
8: Forward Ion: b
9: Rewind Ion: y
10: Fixed Modifications: Carbamidomethylation of C
11: Variable Modifications: Oxidation of M, Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C
12: Refinement Variable Modifications: 
13: 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: Yes
Validation Summary

1: Proteins: #Validated: 2.0
2: Proteins: Total Possible TP: 2.0
3: Proteins: FDR Limit [%]: 0.0
4: Proteins: FNR Limit [%]: 0.0
5: Proteins: Confidence Limit [%]: 100.0
6: Proteins: PEP Limit [%]: 0.0
7: Proteins: Confidence Accuracy [%]: 0.0
8: Peptides: #Validated: 16.0
9: Peptides: Total Possible TP: 16.0
10: Peptides: FDR Limit [%]: 0.0
11: Peptides: FNR Limit [%]: 0.0
12: Peptides: Confidence Limit [%]: 100.0
13: Peptides: PEP Limit [%]: 0.0
14: Peptides: Confidence Accuracy [%]: 0.0
15: PSMs: #Validated PSM: 42.0
16: PSMs: Total Possible TP: 42.0
17: PSMs: FDR Limit [%]: 0.0
18: PSMs: FNR Limit [%]: 0.0
19: PSMs: Confidence Limit [%]: 100.0
20: PSMs: PEP Limit [%]: 0.0
21: PSMs: Confidence Accuracy [%]: 0.0
PTM Scoring Settings

1: Probabilistic Score: PhosphoRS
2: Accounting for Neutral Losses: No
3: Threshold: 95.0
Spectrum Counting Parameters

1: Method: NSAF
2: Validated Matches Only: No
Annotation Settings

1: Intensity Limit: 0.75
2: Automatic Annotation: Yes
3: Selected Ions: y, b
4: Neutral Losses: H2O, NH3, CH4OS
5: Neutral Losses Sequence Dependence: Yes
6: Fragment Ion m/z Tolerance: 0.5