Mercurial > repos > galaxyp > peptideshaker

annotate test-data/peptide_shaker_certificate_result2.txt @ 20:2375ad43661f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
author galaxyp
date Fri, 13 Jan 2017 14:15:29 -0500
parents ef4ac2d49ff0
children
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1 Project Details1: PeptideShaker Version: 1.13.6
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2 2: Date: Fri Jan 13 11:06:50 CST 2017
2375ad43661f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
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3 3: Experiment: Galaxy_Experiment_2017011311051484327131
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4 4: Sample: Sample_2017011311051484327131
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5 5: Replicate Number: 1
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6 6: Identification Algorithms: OMSSA, X!Tandem, MS-GF+, Comet and MyriMatch
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7 Database Search Parameters
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9 1: Precursor Tolerance Unit: ppm
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10 2: Precursor Ion m/z Tolerance: 100.0
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11 3: Fragment Ion Tolerance Unit: Da
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12 4: Fragment Ion m/z Tolerance: 0.5
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13 5: Enzyme: Trypsin
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14 6: Maximum Missed Cleavages: 2
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15 7: Database: input_database.fasta
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16 8: Forward Ion: b
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17 9: Rewind Ion: y
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18 10: Fixed Modifications: Carbamidomethylation of C
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19 11: Variable Modifications: Oxidation of M, Acetylation of protein N-term, Pyrolidone from E, Pyrolidone from Q, Pyrolidone from carbamidomethylated C
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20 12: Refinement Variable Modifications:
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21 13: Refinement Fixed Modifications:
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22 Input Filters
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24 1: Minimal Peptide Length: 1
9d12b1d3c4ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 04b529c9366e6b77f45bfaa44c1a7fac5772f5b9
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25 2: Maximal Peptide Length: 30
9d12b1d3c4ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 04b529c9366e6b77f45bfaa44c1a7fac5772f5b9
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26 3: Precursor m/z Tolerance: 10.0
9d12b1d3c4ef planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 04b529c9366e6b77f45bfaa44c1a7fac5772f5b9
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27 4: Precursor m/z Tolerance Unit: Yes
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28 5: Unrecognized Modifications Discarded: Yes
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29 Validation Summary
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31 1: Proteins: #Validated: 2.0
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32 2: Proteins: Total Possible TP: 2.0
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33 3: Proteins: FDR Limit [%]: 0.0
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34 4: Proteins: FNR Limit [%]: 0.0
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35 5: Proteins: Confidence Limit [%]: 100.0
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36 6: Proteins: PEP Limit [%]: 0.0
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37 7: Proteins: Confidence Accuracy [%]: 0.0
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38 8: Peptides: #Validated: 16.0
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39 9: Peptides: Total Possible TP: 16.0
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40 10: Peptides: FDR Limit [%]: 0.0
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41 11: Peptides: FNR Limit [%]: 0.0
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42 12: Peptides: Confidence Limit [%]: 100.0
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43 13: Peptides: PEP Limit [%]: 0.0
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44 14: Peptides: Confidence Accuracy [%]: 0.0
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45 15: PSMs: #Validated PSM: 42.0
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46 16: PSMs: Total Possible TP: 42.0
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47 17: PSMs: FDR Limit [%]: 0.0
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48 18: PSMs: FNR Limit [%]: 0.0
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49 19: PSMs: Confidence Limit [%]: 100.0
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50 20: PSMs: PEP Limit [%]: 0.0
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51 21: PSMs: Confidence Accuracy [%]: 0.0
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52 PTM Scoring Settings
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53
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54 1: Probabilistic Score: PhosphoRS
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55 2: Accounting for Neutral Losses: No
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56 3: Threshold: 95.0
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57 Spectrum Counting Parameters
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59 1: Method: NSAF
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60 2: Validated Matches Only: No
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61 Annotation Settings
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63 1: Intensity Limit: 0.75
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64 2: Automatic Annotation: Yes
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65 3: Selected Ions: y, b
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66 4: Neutral Losses: H2O, NH3, CH4OS
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67 5: Neutral Losses Sequence Dependence: Yes
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68 6: Fragment Ion m/z Tolerance: 0.5