annotate test-data/peptideshaker_reports_output_certificate.txt @ 61:3ec27b4cee7c draft default tip

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"

Project Details

1: PeptideShaker Version: 2.0.18
2: Date: Fri Apr 02 17:00:43 GMT 2021
3: Experiment: Galaxy_Experiment_2021040219001617382836
4: Sample: Not implemented
5: Replicate Number: Not implemented
6: Identification Algorithms: OMSSA, X!Tandem and MS-GF+

Database Search Parameters

1: Precursor Tolerance Unit: ppm
2: Precursor Ion m/z Tolerance: 10.0
3: Fragment Ion Tolerance Unit: Da
4: Fragment Ion m/z Tolerance: 0.5
5: Cleavage: Enzyme
6: Enzyme: Trypsin
7: Missed Cleavages: 2
8: Specificity: Specific
9: Database: input_fasta_file.fasta
10: Forward Ion: 1
11: Rewind Ion: 4
12: Fixed Modifications: 
13: Variable Modifications: 
14: Refinement Variable Modifications: 
15: Refinement Fixed Modifications: 

Input Filters

1: Minimal Peptide Length: 8
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: 4.0
2: Proteins: Total Possible TP: 4.0
3: Proteins: FDR Limit [%]: 0.0
4: Proteins: FNR Limit [%]: 0.0
5: Proteins: Confidence Limit [%]: 100.0
6: Proteins: PEP Limit [%]: 100.0
7: Proteins: Confidence Accuracy [%]: 9.223372036854776E16
8: Peptides: #Validated: 4.0
9: Peptides: Total Possible TP: 4.0
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 [%]: 9.223372036854776E16
15: PSMs: #Validated PSM: 6.0
16: PSMs: Total Possible TP: 6.0
17: PSMs: FDR Limit [%]: 0.0
18: PSMs: 0.0
19: PSMs: Confidence Limit [%]: 100.0
20: PSMs: PEP Limit [%]: 0.0
21: PSMs: Confidence Accuracy [%]: 9.223372036854776E16

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: Doubtful

Annotation Settings

1: Intensity Limit: 0.75
2: Automatic Annotation: Yes
3: Selected Ions: b, y
4: Neutral Losses: H2O, NH3
5: Neutral Losses Sequence Dependence: Yes
6: Fragment Ion m/z Tolerance: 10.0