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comparison test-data/peptideshaker_reports_output_certificate.txt @ 55:bb0130ff73ce draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
author galaxyp
date Fri, 15 Jan 2021 14:06:27 +0000
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children 07ff622ec007
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54:7fdd9119cc4f 55:bb0130ff73ce
1
2 Project Details
3
4 1: PeptideShaker Version: 2.0.2
5 2: Date: Thu Nov 19 10:47:40 CET 2020
6 3: Experiment: Galaxy_Experiment_2020111910471605779259
7 4: Sample: Not implemented
8 5: Replicate Number: Not implemented
9 6: Identification Algorithms: OMSSA, X!Tandem and MS-GF+
10
11 Database Search Parameters
12
13 1: Precursor Tolerance Unit: ppm
14 2: Precursor Ion m/z Tolerance: 10.0
15 3: Fragment Ion Tolerance Unit: Da
16 4: Fragment Ion m/z Tolerance: 0.5
17 5: Cleavage: Enzyme
18 6: Enzyme: Trypsin
19 7: Missed Cleavages: 2
20 8: Specificity: Specific
21 9: Database: input_fasta_file.fasta
22 10: Forward Ion: 1
23 11: Rewind Ion: 4
24 12: Fixed Modifications:
25 13: Variable Modifications:
26 14: Refinement Variable Modifications:
27 15: Refinement Fixed Modifications:
28
29 Input Filters
30
31 1: Minimal Peptide Length: 8
32 2: Maximal Peptide Length: 30
33 3: Precursor m/z Tolerance: 10.0
34 4: Precursor m/z Tolerance Unit: Yes
35 5: Unrecognized Modifications Discarded: Yes
36
37 Validation Summary
38
39 1: Proteins: #Validated: 4.0
40 2: Proteins: Total Possible TP: 4.0
41 3: Proteins: FDR Limit [%]: 0.0
42 4: Proteins: FNR Limit [%]: 0.0
43 5: Proteins: Confidence Limit [%]: 100.0
44 6: Proteins: PEP Limit [%]: 100.0
45 7: Proteins: Confidence Accuracy [%]: 9.223372036854776E16
46 8: Peptides: #Validated: 4.0
47 9: Peptides: Total Possible TP: 4.0
48 10: Peptides: FDR Limit [%]: 0.0
49 11: Peptides: FNR Limit [%]: 0.0
50 12: Peptides: Confidence Limit [%]: 100.0
51 13: Peptides: PEP Limit [%]: 0.0
52 14: Peptides: Confidence Accuracy [%]: 9.223372036854776E16
53 15: PSMs: #Validated PSM: 6.0
54 16: PSMs: Total Possible TP: 6.0
55 17: PSMs: FDR Limit [%]: 0.0
56 18: PSMs: 0.0
57 19: PSMs: Confidence Limit [%]: 100.0
58 20: PSMs: PEP Limit [%]: 0.0
59 21: PSMs: Confidence Accuracy [%]: 9.223372036854776E16
60
61 PTM Scoring Settings
62
63 1: Probabilistic Score: PhosphoRS
64 2: Accounting for Neutral Losses: No
65 3: Threshold: 95.0
66
67 Spectrum Counting Parameters
68
69 1: Method: NSAF
70 2: Validated Matches Only: Doubtful
71
72 Annotation Settings
73
74 1: Intensity Limit: 0.75
75 2: Automatic Annotation: Yes
76 3: Selected Ions: b, y
77 4: Neutral Losses: H2O, NH3
78 5: Neutral Losses Sequence Dependence: Yes
79 6: Fragment Ion m/z Tolerance: 10.0