Result name: 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp
Result file: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.msf
Description: Ab_Quan_Tryp
Workflow based on template: Ab_Quan_Tryp
Creation date: 5/27/2019 4:49:55 PM
Created with Discoverer version: 2.3.0.523
------------------------------------------------------------------
The workflow tree:
------------------------------------------------------------------
|-(0) Spectrum Files
|-(1) Spectrum Selector
|-(2) MS Amanda 2.0
|-(3) Percolator
|-(4) IMP-apQuant
|-(5) IMP-ptmRS
|-(4) IMP-apQuant
|-(6) Minora Feature Detector
------------------------------------------------------------------
Processing node 0: Spectrum Files
------------------------------------------------------------------
Input Data:
- File Name(s) (Hidden):
E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw
E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw
------------------------------------------------------------------
Processing node 1: Spectrum Selector
------------------------------------------------------------------
1. General Settings:
- Precursor Selection: Use MS1 Precursor
- Use Isotope Pattern in Precursor Reevaluation: True
- Provide Profile Spectra: Automatic
2. Spectrum Properties Filter:
- Lower RT Limit: 0
- Upper RT Limit: 0
- First Scan: 0
- Last Scan: 0
- Lowest Charge State: 0
- Highest Charge State: 0
- Min. Precursor Mass: 350 Da
- Max. Precursor Mass: 5000 Da
- Total Intensity Threshold: 0
- Minimum Peak Count: 1
3. Scan Event Filters:
- MS Order: Is Not MS1
- Min. Collision Energy: 0
- Max. Collision Energy: 1000
- Scan Type: Is Full
4. Peak Filters:
- S/N Threshold (FT-only): 1.5
5. Replacements for Unrecognized Properties:
- Unrecognized Charge Replacements: Automatic
- Unrecognized Mass Analyzer Replacements: ITMS
- Unrecognized MS Order Replacements: MS2
- Unrecognized Activation Type Replacements: CID
- Unrecognized Polarity Replacements: +
- Unrecognized MS Resolution@200 Replacements: 60000
- Unrecognized MSn Resolution@200 Replacements: 30000
6. Precursor Pattern Extraction:
- Precursor Clipping Range Before: 2.5 Da
- Precursor Clipping Range After: 5.5 Da
------------------------------------------------------------------
Processing node 2: MS Amanda 2.0
------------------------------------------------------------------
1. Input Data:
- Protein Database:
common_contaminants.fasta
IMGT-Human-IGHV-genes_20190403_noSTOP.fasta
IMGT-Human-IGKV-genes_20190403_noSTOP.fasta
IMGT-Human-IGLV-genes_20190403_noSTOP.fasta
uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta
- Enzyme Name: Trypsin (Full)
- Missed Cleavages: 2
- MS1 tolerance: 20 ppm
- MS2 tolerance: 0.02 Da
2. Static Modifications:
- 1. Static Modification: Carbamidomethyl / +57.021 Da (C)
3. Dynamic Modifications:
- 1. Dynamic Modification: Oxidation / +15.995 Da (M)
- 24. Dynamic Protein N-Terminal Modification: Ab-Gln->pyro-Glu / -17.027 Da (Q)
- 25. Dynamic Protein N-Terminal Modification: Ab-Glu->pyro-Glu / -18.011 Da (E)
4. Additional Settings:
- Max No. of same modifs: 4
- Max No. of dynamic modifs: 4
- Max number of same neutral losses (H2O, NH3): 1
- No. of considered NLs (modifications): 2
- Max. No. modif sites: 6
- Ion Settings: b,y,H2O,NH3
- Max. Rank: 5
- Peptide Cut Off Score: 1
- Minimum Peptide Length: 5
- Maximum Peptide Length: 20
- Perform deisotoping: True
- Use monoisotopic mass: True
5. Second Search:
- Second Search: False
- Keep y1 Ion: True
- Remove water losses: True
- Remove ammonia losses: True
- Exclude first precursor: True
- Max multiple precursors: 5
6. Performance Settings:
- Protein Database Size: 200000
- Number of spectra per package: 10000
------------------------------------------------------------------
Processing node 3: Percolator
------------------------------------------------------------------
1. Target/Decoy Strategy:
- Target/Decoy Selection: Concatenated
- Validation based on: q-Value
2. Input Data:
- Maximum Delta Cn: 0.05
- Maximum Rank: 0
3. FDR Targets:
- Target FDR (Strict): 0.01
- Target FDR (Relaxed): 0.05
------------------------------------------------------------------
Processing node 4: IMP-apQuant
------------------------------------------------------------------
1. PSM Search Parameters:
- PSM Confidence Level: High
- Minimum Sequence Length: 6
- Score Name: MS Amanda: Amanda Score
- Minimum Score: 70
- Search Engine Rank: 1
- Mass Tolerance: 15 ppm
2. Integration Parameters:
- Retention Time Tolerance: 0.5
- Missing Peaks: 2
- RT Correction: True
- Use Deisotoping: False
- Tolerance for deisotoping (in Da): 0.005
- Minimum Width for Peak (in min): 0.1
- Noise Level: 10000
- LOESS Smoothing: True
- LOESS window size (in min): 0.2
- Match Between Runs: True
- Noise Level Percentage: 5
3. PhosphoRS/ptmRS Settings:
- PhosphoRS Column Name: ptmRS [4]: Best Site Probabilities
- Probability Threshold: 75
4. Performance Parameters:
- Workpackage size: 1000
- Thread count: 0
5. Confidence Parameters:
- Scoring Method: percolator
- MBR Confidence High Cutoff: 0.01
- MBR Confidence Medium Cutoff: 0.05
- Use Robust Methods: True
- Set Arealess to Low: False
- Score Components to use:
DeltaM1
DeltaM2
DeltaT1
DeltaT2
distF
F1
F2
F3
F4
N/S
RMSD
- Replacement Value: 5
- Export peak3d: False
6. Crosslink Search Parameters:
- CSM Confidence Level: High
- Mass Tolerance: 5 ppm
------------------------------------------------------------------
Processing node 5: IMP-ptmRS
------------------------------------------------------------------
1. Scoring:
- PhosphoRS Mode: False
- Report Only PTMs: True
- Use Diagnostic Ions: True
- Use Fragment Mass Tolerance of Search Node: True
- Fragment Mass Tolerance: 0.5 Da
- Consider neutral loss peaks for CID, HCD and EThcD: Automatic
- Maximum Peak Depth: 8
- Use a mass accuracy correction: False
2. Performance:
- Maximum Number of Position Isoforms: 500
- Maximum PTMs per peptide: 10
------------------------------------------------------------------
Processing node 6: Minora Feature Detector
------------------------------------------------------------------
1. Peak & Feature Detection:
- Min. Trace Length: 5
- Max. ΔRT of Isotope Pattern Multiplets [min]: 0.2
2. Feature to ID Linking:
- PSM Confidence At Least: High
------------------------------------------------------------------
Workflow messages:
------------------------------------------------------------------
05/27/2019 04:49 PM Job Execution: Processing E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.msf
05/27/2019 04:49 PM (1): Spectrum Selector: Profile spectra are not sent.
05/27/2019 04:50 PM (1): Spectrum Selector: Reading from file 1 of 2 F14: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (25381 spectra total)
05/27/2019 04:50 PM (2): MS Amanda 2.0: Starting MS Amanda search version 2.3.0.12368, Engine version 2.0.0.12368
05/27/2019 04:50 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:50 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database.
05/27/2019 04:50 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:50 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:50 PM (2): MS Amanda 2.0: Loading database
05/27/2019 04:50 PM (2): MS Amanda 2.0: Loading database done
05/27/2019 04:50 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:50 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:50 PM (2): MS Amanda 2.0: Loading database
05/27/2019 04:50 PM (2): MS Amanda 2.0: Loading database done
05/27/2019 04:50 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:50 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:50 PM (2): MS Amanda 2.0: Loading database
05/27/2019 04:50 PM (2): MS Amanda 2.0: Loading database done
05/27/2019 04:50 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:50 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/27/2019 04:50 PM (2): MS Amanda 2.0: Scored 15165 peptide hits and 14314 decoy peptide hits in 16.76 sec
05/27/2019 04:50 PM (2): MS Amanda 2.0: Stored 8163 PSMs for 6435 spectra
05/27/2019 04:51 PM (2): MS Amanda 2.0: Stored 8304 decoy PSMs for 6354 spectra
05/27/2019 04:52 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:52 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database.
05/27/2019 04:52 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:52 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:52 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:52 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:52 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:52 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:52 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:52 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/27/2019 04:53 PM (2): MS Amanda 2.0: Scored 19912 peptide hits and 16420 decoy peptide hits in 95.90 sec
05/27/2019 04:53 PM (2): MS Amanda 2.0: Stored 9769 PSMs for 8476 spectra
05/27/2019 04:54 PM (2): MS Amanda 2.0: Stored 9428 decoy PSMs for 8019 spectra
05/27/2019 04:54 PM (1): Spectrum Selector: Sent 20756 spectra from file F14.
05/27/2019 04:54 PM (1): Spectrum Selector: Reading from file 2 of 2 F3: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (27076 spectra total)
05/27/2019 04:56 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:56 PM (2): MS Amanda 2.0: Searching 10756 spectra in common_contaminants.fasta and decoy database.
05/27/2019 04:56 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:56 PM (2): MS Amanda 2.0: Searching 10756 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:56 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:56 PM (2): MS Amanda 2.0: Searching 10756 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:56 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:56 PM (2): MS Amanda 2.0: Searching 10756 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:56 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:56 PM (2): MS Amanda 2.0: Searching 10756 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/27/2019 04:57 PM (2): MS Amanda 2.0: Scored 15558 peptide hits and 14698 decoy peptide hits in 24.26 sec
05/27/2019 04:57 PM (2): MS Amanda 2.0: Stored 8403 PSMs for 6748 spectra
05/27/2019 04:57 PM (2): MS Amanda 2.0: Stored 8445 decoy PSMs for 6670 spectra
05/27/2019 04:58 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:58 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database.
05/27/2019 04:58 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:58 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:59 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:59 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 04:59 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 04:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/27/2019 05:00 PM (2): MS Amanda 2.0: Scored 20211 peptide hits and 17330 decoy peptide hits in 86.17 sec
05/27/2019 05:00 PM (2): MS Amanda 2.0: Stored 9985 PSMs for 8692 spectra
05/27/2019 05:01 PM (2): MS Amanda 2.0: Stored 9713 decoy PSMs for 8336 spectra
05/27/2019 05:02 PM (1): Spectrum Selector: Sent 22334 spectra from file F3.
05/27/2019 05:02 PM (1): Spectrum Selector: Sent 43090 spectra from 2 files (processing time: 2 min 8 s).
05/27/2019 05:02 PM (1): Spectrum Selector: -- Total execution of Spectrum Selector (1) took 12 min 20 s --
05/27/2019 05:02 PM (2): MS Amanda 2.0: Storing spectra took 1 min 52 s.
05/27/2019 05:02 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 05:02 PM (2): MS Amanda 2.0: Searching 2334 spectra in common_contaminants.fasta and decoy database.
05/27/2019 05:02 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 05:02 PM (2): MS Amanda 2.0: Searching 2334 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 05:02 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 05:02 PM (2): MS Amanda 2.0: Searching 2334 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 05:02 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 05:02 PM (2): MS Amanda 2.0: Searching 2334 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/27/2019 05:02 PM (2): MS Amanda 2.0: Identifying Peptides
05/27/2019 05:02 PM (2): MS Amanda 2.0: Searching 2334 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/27/2019 05:02 PM (2): MS Amanda 2.0: Scored 3021 peptide hits and 2311 decoy peptide hits in 10.10 sec
05/27/2019 05:02 PM (2): MS Amanda 2.0: Stored 1404 PSMs for 1246 spectra
05/27/2019 05:02 PM (2): MS Amanda 2.0: Stored 1375 decoy PSMs for 1182 spectra
05/27/2019 05:02 PM (2): MS Amanda 2.0: Finalizing search results...
05/27/2019 05:03 PM (2): MS Amanda 2.0: -- Total search time was 7 min 51 s --
05/27/2019 05:05 PM (3): Percolator: Creating input file for MS Amanda 2.0 (2) took 1 min 34 s.
05/27/2019 05:05 PM (3): Percolator: The input file contains 20034 PSMs, 13632 decoy PSMs and 32 features.
05/27/2019 05:05 PM (3): Percolator: Generated percolator input for concatenated mode
05/27/2019 05:05 PM (3): Percolator: Percolator version 3.02.1, Build Date Aug 14 2018 00:44:01
05/27/2019 05:05 PM (3): Percolator: Copyright (c) 2006-9 University of Washington. All rights reserved.
05/27/2019 05:05 PM (3): Percolator: Department of Genome Sciences at the University of Washington.
05/27/2019 05:05 PM (3): Percolator: Issued command:
05/27/2019 05:05 PM (3): Percolator: C:\Program Files\Thermo\Proteome Discoverer 2.3\Tools\Percolator\percolator.exe -s -X C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job32\Percol(3)\output.xml -Z -I auto -k C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job32\Percol(3)\input.xml
05/27/2019 05:05 PM (3): Percolator: Started Mon May 27 17:05:25 2019
05/27/2019 05:05 PM (3): Percolator: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
05/27/2019 05:05 PM (3): Percolator: Reading pin-xml input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job32\Percol(3)\input.xml
05/27/2019 05:05 PM (3): Percolator: enzyme=Trypsin
05/27/2019 05:05 PM (3): Percolator: Features:
05/27/2019 05:05 PM (3): Percolator: CharmeRTCombinedScore Delta Cn From Second PSM Binomial Score Isolation Interference [%] MH+ [Da] Delta Mass [Da] Delta Mass [ppm] Absolute Delta Mass [Da] Absolute Delta Mass [ppm] Peptide Length Is z=1 Is z=2 Is z=3 Is z=4 Is z=5 Is z>5 # Missed Cleavages Log Peptides Matched Log Total Intensity Fraction Matched Intensity [%] Fragment Coverage Series A, B, C [%] Fragment Coverage Series X, Y, Z [%] Log Matched Fragment Series Intensities A, B, C Log Matched Fragment Series Intensities X, Y, Z Longest Sequence Series A, B, C Longest Sequence Series X, Y, Z IQR Fragment Delta Mass [Da] IQR Fragment Delta Mass [ppm] Mean Fragment Delta Mass [Da] Mean Fragment Delta Mass [ppm] Mean Absolute Fragment Delta Mass [Da] Mean Absolute Fragment Delta Mass [ppm]
05/27/2019 05:05 PM (3): Percolator: Concatenated search input detected, skipping both target-decoy competition and mix-max.
05/27/2019 05:05 PM (3): Percolator: Train/test set contains 20034 positives and 13632 negatives, size ratio=1.46963 and pi0=1
05/27/2019 05:05 PM (3): Percolator: Selecting Cpos by cross-validation.
05/27/2019 05:05 PM (3): Percolator: Selecting Cneg by cross-validation.
05/27/2019 05:05 PM (3): Percolator: Split 1: Selected feature 26 as initial direction. Could separate 3380 training set positives with q<0.01 in that direction.
05/27/2019 05:05 PM (3): Percolator: Split 2: Selected feature 26 as initial direction. Could separate 3427 training set positives with q<0.01 in that direction.
05/27/2019 05:05 PM (3): Percolator: Split 3: Selected feature 26 as initial direction. Could separate 3489 training set positives with q<0.01 in that direction.
05/27/2019 05:05 PM (3): Percolator: Found 5148 test set positives with q<0.01 in initial direction
05/27/2019 05:05 PM (3): Percolator: Reading in data and feature calculation took 8.526 cpu seconds or 9 seconds wall clock time.
05/27/2019 05:05 PM (3): Percolator: ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 1: Estimated 6301 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 2: Estimated 6493 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 3: Estimated 6525 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 4: Estimated 6558 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 5: Estimated 6574 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 6: Estimated 6580 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 7: Estimated 6583 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 8: Estimated 6584 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 9: Estimated 6590 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Iteration 10: Estimated 6590 PSMs with q<0.01
05/27/2019 05:05 PM (3): Percolator: Learned normalized SVM weights for the 3 cross-validation splits:
05/27/2019 05:05 PM (3): Percolator: Split1 Split2 Split3 FeatureName
05/27/2019 05:05 PM (3): Percolator: 0.3559 0.0089 -0.3295 CharmeRTCombinedScore
05/27/2019 05:05 PM (3): Percolator: 0.3616 0.0615 0.3112 Delta Cn From Second PSM
05/27/2019 05:05 PM (3): Percolator: 3.6969 3.9415 4.2524 Binomial Score
05/27/2019 05:05 PM (3): Percolator: 0.0994 0.0815 0.0674 Isolation Interference [%]
05/27/2019 05:05 PM (3): Percolator: -0.1703 -0.2710 -0.5441 MH+ [Da]
05/27/2019 05:05 PM (3): Percolator: 0.4451 -0.1239 0.3285 Delta Mass [Da]
05/27/2019 05:05 PM (3): Percolator: -0.2145 0.5731 -0.2872 Delta Mass [ppm]
05/27/2019 05:05 PM (3): Percolator: 0.0593 -0.3462 -1.0731 Absolute Delta Mass [Da]
05/27/2019 05:05 PM (3): Percolator: -0.5269 0.1493 0.7226 Absolute Delta Mass [ppm]
05/27/2019 05:05 PM (3): Percolator: 0.7139 0.7042 1.1771 Peptide Length
05/27/2019 05:05 PM (3): Percolator: 0.0000 0.0000 0.0000 Is z=1
05/27/2019 05:05 PM (3): Percolator: -0.3579 -0.2634 -0.4201 Is z=2
05/27/2019 05:05 PM (3): Percolator: 0.3533 0.2582 0.3703 Is z=3
05/27/2019 05:05 PM (3): Percolator: -0.0134 -0.0097 0.1127 Is z=4
05/27/2019 05:05 PM (3): Percolator: 0.1418 0.1199 0.1825 Is z=5
05/27/2019 05:05 PM (3): Percolator: 0.0153 0.0174 0.0195 Is z>5
05/27/2019 05:05 PM (3): Percolator: -0.5959 -0.6830 -0.6234 # Missed Cleavages
05/27/2019 05:05 PM (3): Percolator: 0.0000 0.0000 0.0000 Log Peptides Matched
05/27/2019 05:05 PM (3): Percolator: -0.0129 -0.0272 0.1754 Log Total Intensity
05/27/2019 05:05 PM (3): Percolator: -0.1060 -0.0082 0.0797 Fraction Matched Intensity [%]
05/27/2019 05:05 PM (3): Percolator: -0.7441 -0.4088 -0.5837 Fragment Coverage Series A, B, C [%]
05/27/2019 05:05 PM (3): Percolator: 0.4545 -0.1878 0.3328 Fragment Coverage Series X, Y, Z [%]
05/27/2019 05:05 PM (3): Percolator: 0.1533 0.1374 0.0468 Log Matched Fragment Series Intensities A, B, C
05/27/2019 05:05 PM (3): Percolator: -0.8425 -0.8714 -0.9545 Log Matched Fragment Series Intensities X, Y, Z
05/27/2019 05:05 PM (3): Percolator: 0.1477 -0.4996 -0.2605 Longest Sequence Series A, B, C
05/27/2019 05:05 PM (3): Percolator: 0.8447 1.3034 1.0883 Longest Sequence Series X, Y, Z
05/27/2019 05:05 PM (3): Percolator: 0.4419 -0.2119 0.3820 IQR Fragment Delta Mass [Da]
05/27/2019 05:05 PM (3): Percolator: -0.0097 -0.3833 -0.6509 IQR Fragment Delta Mass [ppm]
05/27/2019 05:05 PM (3): Percolator: 0.1695 0.0045 -0.8683 Mean Fragment Delta Mass [Da]
05/27/2019 05:05 PM (3): Percolator: -0.2400 -0.0551 0.5314 Mean Fragment Delta Mass [ppm]
05/27/2019 05:05 PM (3): Percolator: -1.9740 -1.4565 -2.4635 Mean Absolute Fragment Delta Mass [Da]
05/27/2019 05:05 PM (3): Percolator: 0.1977 -0.0143 0.5456 Mean Absolute Fragment Delta Mass [ppm]
05/27/2019 05:05 PM (3): Percolator: -2.8111 -3.1942 -3.5846 m0
05/27/2019 05:05 PM (3): Percolator: Found 6487 test set PSMs with q<0.01.
05/27/2019 05:05 PM (3): Percolator: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
05/27/2019 05:05 PM (3): Percolator: Calculating q values.
05/27/2019 05:05 PM (3): Percolator: Final list yields 1040 target peptides with q<0.01.
05/27/2019 05:05 PM (3): Percolator: Calculating posterior error probabilities (PEPs).
05/27/2019 05:05 PM (3): Percolator: Processing took 21.66 cpu seconds or 21 seconds wall clock time.
05/27/2019 05:05 PM (3): Percolator: PSMId score q-value posterior_error_prob peptide proteinIds
05/27/2019 05:06 PM (3): Percolator: 6490/63 high confident target/decoy peptides were found for MS Amanda 2.0 (2).
05/27/2019 05:06 PM (3): Percolator: 596/290 medium confident target/decoy peptides were found for MS Amanda 2.0 (2).
05/27/2019 05:06 PM (3): Percolator: -- Total execution of Percolator (64Bit) for MS Amanda 2.0 (2) took 2 min 15 s --
05/27/2019 05:06 PM (5): IMP-ptmRS: Starting IMP-ptmRS node 2.0, IMP-ptmRS 2.2.5967.19588 - based on phosphoRS3 Taus T. et al., J. Proteome Res. 2011, 10, 5354-62
05/27/2019 05:06 PM (5): IMP-ptmRS: Scoring with ptmRS (2.2.5967.19588) for MS Amanda 2.0 (2) with a fragment ion mass tolerance of 0.02 m/z allowing a maximum of 10 PTMs with neutral loss and 500 isoforms per peptide.
05/27/2019 05:06 PM (5): IMP-ptmRS: Site localization is not performed for MS Amanda 2.0 (2), because no appropriate PTM is specified as dynamic modification in the search.
05/27/2019 05:06 PM (5): IMP-ptmRS: -- Total execution of IMP-ptmRS (5) took 246.8 ms --
05/27/2019 05:06 PM (4): IMP-apQuant: 8 Processors found
05/27/2019 05:06 PM (4): IMP-apQuant: Start IMP-apQuant Version 3.1.1.24322
05/27/2019 05:06 PM (4): IMP-apQuant: Reading TargetPeptideSpectrumMatch
05/27/2019 05:06 PM (4): IMP-apQuant: Done
05/27/2019 05:06 PM (4): IMP-apQuant: creating file in E:\Work\data_MS_plus_raw\19EDG05\raw
05/27/2019 05:06 PM (4): IMP-apQuant: Collecting Modifications
05/27/2019 05:06 PM (4): IMP-apQuant: Filtering Items
05/27/2019 05:06 PM (4): IMP-apQuant: IMP-apQuant bailed out. Error Message: Object reference not set to an instance of an object., Stacktrace: at IMP.apQuant.Node.ApQuantNode.FilterItems[T](IEnumerable`1 rawItems)