apQuant error in PD2.3

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Erik de G

unread,
May 27, 2019, 11:20:41 AM5/27/19
to MS Amanda
Hi all,
Sorry I put this here but I cannot get any acces to the apquant/peakjuggler google group for this node.
I use PD2.3, with the MSamanda, apquant and ptmRS nodes in my workflows, as also shown on the workflow screen captures. However, I get the error below. 

Time Processing Node Level Message
5:06 PM (4): IMP-apQuant Error 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) at IMP.apQuant.Node.ApQuantNode.FilterItems[T](IEnumerable`1 rawItems, List`1 modifications, PropertyAccessor ptmrsAccessor) at IMP.apQuant.Node.ApQuantNode.DoProcessing[T](Boolean xlink)

Any clue what goes wrong?

Thank you,
Erik

Erik de G

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May 27, 2019, 11:23:29 AM5/27/19
to MS Amanda
IMP-apQuant Version 3.1.1.24322
PD2.3.0.523

Viktoria Dorfer

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May 28, 2019, 7:40:50 AM5/28/19
to MS Amanda

Hi Erik,

I have forwarded your issue to the corresponding people, they will come back to you asap!

Best regards,
Viktoria

André Lüttig

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May 28, 2019, 9:18:47 AM5/28/19
to MS Amanda
Hey Erik!

Thank you for your interest in apQuant. Could you send me a picture or a description of the parameters you used for apQuant? (When you click on the apQuant node the values which should be shown in the lefthand-side of the screen).

Best regards,
André

Erik de G

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May 28, 2019, 9:29:51 AM5/28/19
to MS Amanda
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: Written by Lukas Käll (luk...@u.washington.edu) in the
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: More nodes and documentations can be found here http://ms.imp.ac.at/?goto=pd-nodes.
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)
   at IMP.apQuant.Node.ApQuantNode.FilterItems[T](IEnumerable`1 rawItems, List`1 modifications, PropertyAccessor ptmrsAccessor)
   at IMP.apQuant.Node.ApQuantNode.DoProcessing[T](Boolean xlink)
05/27/2019 05:06 PM (4): IMP-apQuant: IMP-apQuant finished in 0:0:3
05/27/2019 05:06 PM (4): IMP-apQuant: -- Total execution of IMP-apQuant (4) took 3.8 s --
05/27/2019 05:06 PM (6): Minora Feature Detector: Start detecting lcmspeaks...
05/27/2019 05:06 PM (6): Minora Feature Detector: Running 2 jobs with 2 jobs in parallel.
05/27/2019 05:06 PM (6): Minora Feature Detector: Start F14 with 'FTMS + p NSI Full ms [350.0000-1850.0000]'
05/27/2019 05:06 PM (6): Minora Feature Detector: Start F3 with 'FTMS + p NSI Full ms [350.0000-1850.0000]'
05/27/2019 05:10 PM (6): Minora Feature Detector: Detecting LcmsPeaks took 4 min 2 s
05/27/2019 05:10 PM (6): Minora Feature Detector: Start processing F14: '190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw'.
05/27/2019 05:10 PM (6): Minora Feature Detector: Start processing F3: '190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw'.
05/27/2019 05:10 PM (6): Minora Feature Detector: Importing peaks for F14 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])...
05/27/2019 05:10 PM (6): Minora Feature Detector: Importing peaks for F3 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])...
05/27/2019 05:10 PM (6): Minora Feature Detector: F3: Found 186494 chromatographic peaks.
05/27/2019 05:10 PM (6): Minora Feature Detector: F14: Found 234305 chromatographic peaks.
05/27/2019 05:10 PM (6): Minora Feature Detector: F3: Importing auto traces...
05/27/2019 05:10 PM (6): Minora Feature Detector: F3: Imported 125889 auto traces.
05/27/2019 05:10 PM (6): Minora Feature Detector: F14: Importing auto traces...
05/27/2019 05:10 PM (6): Minora Feature Detector: F14: Imported 150740 auto traces.
05/27/2019 05:10 PM (6): Minora Feature Detector: Importing peak to spectrum links...
05/27/2019 05:12 PM (6): Minora Feature Detector: F3: Standard deviations: m/z 5.30; RT 0.10; Intensity 64.63; Fraction Missing Intensity 0.20; Shoulder Score 0.000; Peak Length Score 0.0516998891422097 took 1 min 19 s
05/27/2019 05:12 PM (6): Minora Feature Detector: F14: Standard deviations: m/z 5.46; RT 0.10; Intensity 68.38; Fraction Missing Intensity 0.19; Shoulder Score 0.000; Peak Length Score 0.0437464097347174 took 1 min 38 s
05/27/2019 05:13 PM (6): Minora Feature Detector: Found 3871 features (F3: 1806, F14: 2065)
05/27/2019 05:13 PM (6): Minora Feature Detector: Writing data took 1.9 s.
05/27/2019 05:13 PM (6): Minora Feature Detector: Creating features for PSMs took 6.9 s.
05/27/2019 05:14 PM (6): Minora Feature Detector: F3: Unidentified feature detection took 1 min 9 s
05/27/2019 05:15 PM (6): Minora Feature Detector: F14: Unidentified feature detection took 1 min 33 s
05/27/2019 05:15 PM (6): Minora Feature Detector: Found 85400 unidentified features (F3 : 37200, F14 : 48200).
05/27/2019 05:15 PM (6): Minora Feature Detector: -- Total execution of Minora Feature Detector (6) took 8 min 57 s --
05/27/2019 05:15 PM Job Execution: Finished E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.msf
05/27/2019 05:15 PM Job Execution: ----- Total Job execution took: 25 min 12 s. -----
Message has been deleted

André Lüttig

unread,
May 28, 2019, 9:38:08 AM5/28/19
to MS Amanda
Thank you! It was like I expected (we should maybe include this in the setup for apQuant with the new MS Amanda node).

Could you try to a score value named "MS Amanda 2.0: Amanda Score" in the PSM scores in the MSF Files settings? The problem is, that it tries to find the score of the MS Amanda node, which is not present in the current workflow, and this yields the error.

I have attached a picture showing where to add the value and what the value is again called.

If this doesn't help you and the error persists, feel free to write again!

Best regards,
André

André Lüttig

unread,
May 28, 2019, 10:03:28 AM5/28/19
to MS Amanda
Ah, I forgot:
Of course you need to set the parameter "Score Name" to this new value!
Otherwise the error persists.

Sorry for the inconvenience.

Best regards,
André

Erik de G

unread,
May 28, 2019, 11:26:57 AM5/28/19
to MS Amanda
Thank you for you reply.
Indeed now the quantification works, but not entirely I think.
There is a warning in the processing workflow about percolator could not be used. And then maybe related also in the consensus.

See the output below:

================================================================================
Consensus Step Workflow
================================================================================
Result name: APQUANTTEST2_19EDG05_aDn7iso-13d
Result file: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\APQUANTTEST2_19EDG05_aDn7iso-13d.pdResult
Description: Result filtered for high confident peptides.
Workflow based on template: CWF_Erik_Quan_AllPep_Intensity
Creation date: 5/28/2019 4:08:54 PM
Created with Discoverer version: 2.3.0.523


------------------------------------------------------------------
The workflow tree:
------------------------------------------------------------------

  |-(0) MSF Files
    |-(1) PSM Grouper
      |-(2) Peptide Validator
        |-(3) Peptide and Protein Filter
          |-(4) Protein Scorer
            |-(5) Protein Grouping
              |-(6) Peptide in Protein Annotation
              |-(12) IMP-apQuant Peptide and Protein Quantifier
            |-(7) Protein FDR Validator
    |-(8) Feature Mapper
      |-(9) Precursor Ions Quantifier

Post-processing nodes:
--------------------------------

  |-(10) Display Settings

------------------------------------------------------------------
Processing node 0: MSF Files
------------------------------------------------------------------
1. Storage Settings:
- Spectra to Store:  Identified or Quantified
- Feature Traces to Store:  All

2. Merging of Identified Peptide and Proteins:
- Merge Mode:  Globally by Search Engine Type

3. FASTA Title Line Display:
- Reported FASTA Title Lines:  All
- Title Line Rule:  standard

4. PSM Filters:
- Maximum Delta Cn:  0.05
- Maximum Rank:  0
- Maximum Delta Mass:  0 ppm
- 1. Score:  MS Amanda: Amanda Score
- 1. Threshold:  60

Hidden Parameters:
- MSF File(s):  E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp-(2).msf

------------------------------------------------------------------
Processing node 1: PSM Grouper
------------------------------------------------------------------
1. Peptide Group Modifications:
- Site Probability Threshold:  75

------------------------------------------------------------------
Processing node 2: Peptide Validator
------------------------------------------------------------------
1. General Validation Settings:
- Validation Mode:  Automatic (Control peptide level error rate if possible)
- Target FDR (Strict) for PSMs:  0.01
- Target FDR (Relaxed) for PSMs:  0.05
- Target FDR (Strict) for Peptides:  0.01
- Target FDR (Relaxed) for Peptides:  0.05

2. Specific Validation Settings:
- Validation Based on:  q-Value
- Target/Decoy Selection for PSM Level FDR Calculation Based on Score:  Automatic
- Reset Confidences for Nodes without Decoy Search (Fixed score thresholds):  False

------------------------------------------------------------------
Processing node 3: Peptide and Protein Filter
------------------------------------------------------------------
1. Peptide Filters:
- Peptide Confidence At Least:  High
- Keep Lower Confident PSMs:  True
- Minimum Peptide Length:  4
- Remove Peptides Without Protein Reference:  False

2. Protein Filters:
- Minimum Number of Peptide Sequences:  1
- Count Only Rank 1 Peptides:  True
- Count Peptides Only for Top Scored Protein:  False

------------------------------------------------------------------
Processing node 4: Protein Scorer
------------------------------------------------------------------
No parameters

------------------------------------------------------------------
Processing node 5: Protein Grouping
------------------------------------------------------------------
1. Protein Grouping:
- Apply strict parsimony principle:  False

------------------------------------------------------------------
Processing node 6: Peptide in Protein Annotation
------------------------------------------------------------------
1. Flanking Residues:
- Annotate Flanking Residues of the Peptide:  False
- Number Flanking Residues in Connection Tables:  1

2. Modifications in Peptide:
- Protein Modifications Reported:  For All Proteins

3. Modifications in Protein:
- Modification Sites Reported:  All And Specific
- Minimum PSM Confidence:  High
- Report Only PTMs:  False

4. Positions in Protein:
- Protein Positions for Peptides:  For All Proteins

------------------------------------------------------------------
Processing node 12: IMP-apQuant Peptide and Protein Quantifier
------------------------------------------------------------------
1. Protein Area:
- ID Confidence Level:  High
- MBR Confidence Level:  High
- Use shared peptides for:  all proteins
- Grouping Method:  average
- Peptides to use for Protein Area::  top x per sample

2. Peptide Area:
- Minimum Area:  50000
- Confidence to use:  highest
- Check for overlaps:  True
- Check for overlaps C13:  True

3. Modifications to use:
- Use all modifications for Quantification:  True

4. iBAQ Parameters:
- Enzyme Name:  Trypsin (Full)
- Min peptide length:  6

5. Top X Parameters:
- Usage of peptides:  average
- # peps for protein aera:  3

------------------------------------------------------------------
Processing node 7: Protein FDR Validator
------------------------------------------------------------------
1. Confidence Thresholds:
- Target FDR (Strict):  0.01
- Target FDR (Relaxed):  0.05

------------------------------------------------------------------
Processing node 8: Feature Mapper
------------------------------------------------------------------
1. Chromatographic Alignment:
- Perform RT Alignment:  False
- Maximum RT Shift [min]:  10
- Mass Tolerance:  10 ppm
- Parameter Tuning:  Coarse

2. Feature Linking and Mapping:
- RT Tolerance [min]:  0
- Mass Tolerance:  0 ppm
- Min. S/N Threshold:  5

------------------------------------------------------------------
Processing node 9: Precursor Ions Quantifier
------------------------------------------------------------------
1. General Quantification Settings:
- Peptides to Use:  All
- Consider Protein Groups for Peptide Uniqueness:  False
- Reject Quan Results with Missing Channels:  False

2. Precursor Quantification:
- Precursor Abundance Based On:  Intensity
- Min. # Replicate Features [%]:  0

3. Normalization and Scaling:
- Normalization Mode:  Total Peptide Amount
- Proteins For Normalization:  common_contaminants.fasta
- Scaling Mode:  None

4. Exclude Peptides from Protein Quantification:
- For Normalization:  Use All Peptides
- For Protein Roll-Up:  Use All Peptides
- For Pairwise Ratios:  Exclude Modified

5. Quan Rollup and Hypothesis Testing:
- Protein Abundance Calculation:  Top N Average
- N for Top N:  3
- Protein Ratio Calculation:  Pairwise Ratio Based
- Maximum Allowed Fold Change:  100
- Imputation Mode:  None
- Hypothesis Test:  t-test (Background Based)

6. Quan Ratio Distributions:
- 1st Fold Change Threshold:  2
- 2nd Fold Change Threshold:  4
- 3rd Fold Change Threshold:  6
- 4th Fold Change Threshold:  8
- 5th Fold Change Threshold:  10

------------------------------------------------------------------
Processing node 10: Display Settings
------------------------------------------------------------------
1. General:
- Filter Set:
###   Filter Set MasterProteinFilter.filterset contains the following filters:
###   Row Filter for TargetProtein:
###   Master is equal to Master
###
'magellan filter set' 1 'MasterProteinFilter.filterset'  FiltersetProperties 1  'LastFileName' 'C:\Users\frank.berg\Desktop\MasterProteinFilter.filterset' Filter 'TargetProtein' 1 NARY_AND 1 = FilterConditionProperties 1  'NamedComparableFilterCondition/DisplayPropertyHint' 'Master' property 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein' constant 'Thermo.PD.EntityDataFramework.MasterProteinAssessment, Thermo.Magellan.EntityDataFramework' 'IsMasterProtein'


------------------------------------------------------------------
Workflow messages:
------------------------------------------------------------------
05/28/2019 04:29 PM Job Execution: Processing E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\APQUANTTEST2_19EDG05_aDn7iso-13d.pdResult
05/28/2019 04:29 PM (0): MSF Files: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp-(2).msf
05/28/2019 04:29 PM (0): MSF Files: All 1 files are ready for processing.
05/28/2019 04:29 PM (0): MSF Files: Warnings reported in at least one input processing workflow (check processing summary).
05/28/2019 04:29 PM (0): MSF Files: Start transferring results of 1 msf files...
05/28/2019 04:29 PM (0): MSF Files: Transferred 7225 Proteins to result file in 2.1 s.
05/28/2019 04:29 PM (0): MSF Files: Transferred 6854 Decoy Proteins to result file in 2 s.
05/28/2019 04:29 PM (0): MSF Files: Added 33666 Mass Spectra to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 276635 traces to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 2 Input Files to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 37724 PSMs to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 37265 Decoy PSMs to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 43090 MS/MS Spectrum Info to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 6 Specialized Traces to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 3010 apQuant Features to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 2 apQuant Alignment to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 3010 apQuant Decoy Features to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 89271 LCMS Features to result file.
05/28/2019 04:29 PM (0): MSF Files: Added 417261 LCMS Peaks to result file.
05/28/2019 04:29 PM (0): MSF Files: Copying data took 48.6 s.
05/28/2019 04:29 PM (0): MSF Files: Finding unique sequences took 1.8 s.
05/28/2019 04:29 PM (0): MSF Files: File (E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp-(2).msf): No search node found that produces results for this score filter: Node: 'MS Amanda' Score: 'Amanda Score' Threshold: '60'.
05/28/2019 04:29 PM (0): MSF Files: Filtering proteins took 165.4 ms.
05/28/2019 04:30 PM (0): MSF Files: -- Total execution of MSF Files (0) took 1 min 1 s --
05/28/2019 04:30 PM (1): PSM Grouper: Grouping 'PSMs'
05/28/2019 04:30 PM (1): PSM Grouper: Found 10345 Peptide Groups.
05/28/2019 04:30 PM (1): PSM Grouper: Grouping 'Decoy PSMs'
05/28/2019 04:30 PM (1): PSM Grouper: Found 9325 Decoy Peptide Groups.
05/28/2019 04:30 PM (1): PSM Grouper: -- Total execution of PSM Grouper (1) took 14.9 s --
05/28/2019 04:30 PM (2): Peptide Validator: Start PSM and Peptide validation in 'Automatic (Control peptide level error rate if possible)' mode...
05/28/2019 04:30 PM (2): Peptide Validator: Updated PSM confidences in 1 s.
05/28/2019 04:30 PM (2): Peptide Validator: Use svm score for 'peptide' qvality run.
05/28/2019 04:30 PM (2): Peptide Validator: Updated peptide confidences using qvality in 5.4 s.
05/28/2019 04:30 PM (2): Peptide Validator: Calculating Mascot thresholds.
05/28/2019 04:30 PM (2): Peptide Validator: -- Total execution of Peptide Validator (2) took 6.6 s --
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter Peptide Groups
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter 1100/10345 Peptide Groups (9245 excluded) and 6565/20034 PSMs (13469 excluded) took 1.4 s
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filtering Proteins
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter 755/7225 Proteins (6470 excluded) took 471.3 ms
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter Decoy Peptide Groups
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter 10/9325 Decoy Peptide Groups (9315 excluded) and 19/13632 Decoy PSMs (13613 excluded) took 1.8 s
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filtering Decoy Proteins
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter 10/6854 Decoy Proteins (6844 excluded) took 360.9 ms
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter Proteins
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Filter Decoy Proteins
05/28/2019 04:30 PM (3): Peptide and Protein Filter: Updating counts took 10.8 s.
05/28/2019 04:30 PM (3): Peptide and Protein Filter: -- Total execution of Peptide and Protein Filter (3) took 15.6 s --
05/28/2019 04:30 PM (4): Protein Scorer: Calculating Coverage and Counts
05/28/2019 04:30 PM (4): Protein Scorer: Calculated counts and coverages in 1.9 s.
05/28/2019 04:30 PM (4): Protein Scorer: Scoring target proteins
05/28/2019 04:30 PM (4): Protein Scorer: Scored 755 proteins in 1.8 s.
05/28/2019 04:30 PM (4): Protein Scorer: Scoring decoy proteins
05/28/2019 04:30 PM (4): Protein Scorer: Scored 10 decoy proteins in 131.3 ms.
05/28/2019 04:30 PM (4): Protein Scorer: -- Total execution of Protein Scorer (4) took 3.9 s --
05/28/2019 04:30 PM (5): Protein Grouping: Retrieving 294 protein groups took 45.8 ms.
05/28/2019 04:30 PM (5): Protein Grouping: Storing, updating and connecting protein groups, PSMs and peptides took 12.6 s.
05/28/2019 04:30 PM (5): Protein Grouping: Found 294 protein groups.
05/28/2019 04:30 PM (5): Protein Grouping: Retrieving 10 decoy protein groups took 1.1 ms.
05/28/2019 04:31 PM (5): Protein Grouping: Storing, updating and connecting protein groups, PSMs and peptides took 6.1 s.
05/28/2019 04:31 PM (5): Protein Grouping: Found 10 decoy protein groups.
05/28/2019 04:31 PM (5): Protein Grouping: -- Total execution of Protein Grouping (5) took 20.9 s --
05/28/2019 04:31 PM (6): Peptide in Protein Annotation: Start retrieving flanking residues and positions...
05/28/2019 04:31 PM (6): Peptide in Protein Annotation: Annotated PSMs/peptides for 755 proteins.
05/28/2019 04:31 PM (6): Peptide in Protein Annotation: Start annotating peptide groups with flanking residues and positions...
05/28/2019 04:31 PM (6): Peptide in Protein Annotation: Annotate Peptide Groups items
05/28/2019 04:31 PM (6): Peptide in Protein Annotation: Start calculating protein coverage...
05/28/2019 04:31 PM (6): Peptide in Protein Annotation: -- Total execution of Peptide in Protein Annotation (6) took 12.4 s --
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Starting IMP-apQuant Quantifier version: 3.1.1.24321
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Connecting tables
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Calculating overlaps
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Add overlaps to QuanResults
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Finished calculating overlaps
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Quantifying peptides
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Write data to TargetPeptideGroup table
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Quantifying Proteins
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Combining peptide areas
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: Quantification failed
The value must be lower than or equal to 2.
Parameter name: position
Actual value was 3.
   at Thermo.Magellan.Utilities.ArgumentHelper.AssertValueLowerThanOrEqualTo[T](T arg, String argName, T upperLimit)
   at Thermo.Magellan.EntityDataFramework.DataDistributionMap`1.SetValue(DataDistributionValue distributionValue, Int32 position, Nullable`1 value)
   at IMP.apQuant.Quantifier.AqQuantifierNode.QuantifyProteins(Dictionary`2 pepAreaDictionary, Dictionary`2 pepIdDictionary, List`1 mySamples)
   at IMP.apQuant.Quantifier.AqQuantifierNode.Start()
05/28/2019 04:31 PM (12): IMP-apQuant Peptide and Protein Quantifier: IMP-apQuant Quantifier finished in 00:00:08
05/28/2019 04:31 PM (7): Protein FDR Validator: Apply confidences based on protein scores of 755 proteins.
05/28/2019 04:31 PM (7): Protein FDR Validator: Calculating Sum PEP Score for Proteins
05/28/2019 04:31 PM (7): Protein FDR Validator: Calculating Sum PEP Score for Decoy Proteins
05/28/2019 04:31 PM (7): Protein FDR Validator: -- Total execution of Protein FDR Validator (7) took 3.9 s --
05/28/2019 04:31 PM (8): Feature Mapper: Alignment is turned off by user, alignment is not performed.
05/28/2019 04:31 PM (8): Feature Mapper: Using RT tolerance of 1.00 min and mass tolerance of 6.0 ppm for mapping
05/28/2019 04:31 PM (8): Feature Mapper: Mapping 1 Fraction(s)
05/28/2019 04:31 PM (8): Feature Mapper: Mapping Fraction 1 of 1
05/28/2019 04:32 PM (8): Feature Mapper: Mapping 1 Fraction(s) took 49.4 s
05/28/2019 04:32 PM (8): Feature Mapper: -- Performing cross file mapping took 50 s. --
05/28/2019 04:32 PM (8): Feature Mapper: Storing Top Apex RT for Peptide Groups
05/28/2019 04:32 PM (8): Feature Mapper: Storing Top Apex RT for Peptide Groups took 1.6 s
05/28/2019 04:32 PM (8): Feature Mapper: -- Total execution of Feature Mapper (8) took 54 s --
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Validating LCMS features
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Validating Consensus Features
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Validation of quantification results took 8.6 s
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Updating spectrum match areas
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Classify quan usage of PSMs
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Classifying Peptide Groups quan usage
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Classifying Peptide Groups quan usage for 1100 items took 658.8 ms
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Calculating Peptide Group Abundances
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Classifying Protein Quan Usage
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Calculating Protein Abundances
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Start normalization of abundance values...
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Calculating normalization took 3 s
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Calculating Normalized Peptide Group Abundances
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Calculating Normalized Protein Abundances
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Calculating and applying normalization took 4.4 s
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Cannot calculate quan ratios, because no ratios are specified.
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Precursor Ion Quantification took 21.2 s.
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: Preparing spectrum visualization took 732.1 ms.
05/28/2019 04:32 PM (9): Precursor Ions Quantifier: -- Total execution of Precursor Ions Quantifier (9) took 22 s --
05/28/2019 04:32 PM (10): Display Settings: Applying display filter and layout
05/28/2019 04:32 PM (10): Display Settings: -- Total execution of Display Settings (10) took 52.1 ms --
05/28/2019 04:32 PM Job Execution: Finalizing file took 8.8 s.
05/28/2019 04:32 PM Job Execution: Finished E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\APQUANTTEST2_19EDG05_aDn7iso-13d.pdResult
05/28/2019 04:32 PM Job Execution: ----- Total Job execution took: 3 min 53 s. -----

================================================================================
Processing Step A: Workflow
================================================================================
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-(2).msf
Description: Ab_Quan_Tryp

Workflow based on template: Ab_Quan_Tryp
Creation date: 5/28/2019 4:08:50 PM
- Score Name:  MS Amanda 2.0: Amanda Score
05/28/2019 04:08 PM Job Execution: Processing E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp-(2).msf
05/28/2019 04:08 PM (1): Spectrum Selector: Profile spectra are not sent.
05/28/2019 04:08 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)
05/28/2019 04:09 PM (2): MS Amanda 2.0: Starting MS Amanda search version 2.3.0.12368, Engine version 2.0.0.12368
05/28/2019 04:09 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database.
05/28/2019 04:09 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:09 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:09 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:09 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/28/2019 04:09 PM (2): MS Amanda 2.0: Scored 15165 peptide hits and 14314 decoy peptide hits in 15.54 sec
05/28/2019 04:09 PM (2): MS Amanda 2.0: Stored 8163 PSMs for 6435 spectra
05/28/2019 04:09 PM (2): MS Amanda 2.0: Stored 8304 decoy PSMs for 6354 spectra
05/28/2019 04:10 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:10 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database.
05/28/2019 04:10 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:10 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:10 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:10 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:10 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:10 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:10 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:10 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/28/2019 04:11 PM (2): MS Amanda 2.0: Scored 19912 peptide hits and 16420 decoy peptide hits in 38.38 sec
05/28/2019 04:11 PM (2): MS Amanda 2.0: Stored 9769 PSMs for 8476 spectra
05/28/2019 04:11 PM (2): MS Amanda 2.0: Stored 9428 decoy PSMs for 8019 spectra
05/28/2019 04:11 PM (1): Spectrum Selector: Sent 20756 spectra from file F14.
05/28/2019 04:11 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)
05/28/2019 04:12 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:12 PM (2): MS Amanda 2.0: Searching 10756 spectra in common_contaminants.fasta and decoy database.
05/28/2019 04:12 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:12 PM (2): MS Amanda 2.0: Searching 10756 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:12 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:12 PM (2): MS Amanda 2.0: Searching 10756 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:12 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:12 PM (2): MS Amanda 2.0: Searching 10756 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:12 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:12 PM (2): MS Amanda 2.0: Searching 10756 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/28/2019 04:12 PM (2): MS Amanda 2.0: Scored 15558 peptide hits and 14698 decoy peptide hits in 48.51 sec
05/28/2019 04:12 PM (2): MS Amanda 2.0: Stored 8403 PSMs for 6748 spectra
05/28/2019 04:13 PM (2): MS Amanda 2.0: Stored 8445 decoy PSMs for 6670 spectra
05/28/2019 04:14 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:14 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database.
05/28/2019 04:14 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:14 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:14 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:14 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:14 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:14 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:14 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:14 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/28/2019 04:15 PM (2): MS Amanda 2.0: Scored 20211 peptide hits and 17330 decoy peptide hits in 55.53 sec
05/28/2019 04:15 PM (2): MS Amanda 2.0: Stored 9985 PSMs for 8692 spectra
05/28/2019 04:15 PM (2): MS Amanda 2.0: Stored 9713 decoy PSMs for 8336 spectra
05/28/2019 04:15 PM (1): Spectrum Selector: Sent 22334 spectra from file F3.
05/28/2019 04:15 PM (1): Spectrum Selector: Sent 43090 spectra from 2 files (processing time: 1 min 6 s).
05/28/2019 04:15 PM (1): Spectrum Selector: -- Total execution of Spectrum Selector (1) took 6 min 43 s --
05/28/2019 04:15 PM (2): MS Amanda 2.0: Storing spectra took 1 min 17 s.
05/28/2019 04:15 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:15 PM (2): MS Amanda 2.0: Searching 2334 spectra in common_contaminants.fasta and decoy database.
05/28/2019 04:15 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:15 PM (2): MS Amanda 2.0: Searching 2334 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:15 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:15 PM (2): MS Amanda 2.0: Searching 2334 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:15 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:15 PM (2): MS Amanda 2.0: Searching 2334 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database.
05/28/2019 04:15 PM (2): MS Amanda 2.0: Identifying Peptides
05/28/2019 04:15 PM (2): MS Amanda 2.0: Searching 2334 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database.
05/28/2019 04:15 PM (2): MS Amanda 2.0: Scored 3021 peptide hits and 2311 decoy peptide hits in 7.49 sec
05/28/2019 04:15 PM (2): MS Amanda 2.0: Stored 1404 PSMs for 1246 spectra
05/28/2019 04:15 PM (2): MS Amanda 2.0: Stored 1375 decoy PSMs for 1182 spectra
05/28/2019 04:15 PM (2): MS Amanda 2.0: Finalizing search results...
05/28/2019 04:16 PM (2): MS Amanda 2.0: -- Total search time was 4 min 31 s --
05/28/2019 04:17 PM (3): Percolator: Creating input file for MS Amanda 2.0 (2) took 55.4 s.
05/28/2019 04:17 PM (3): Percolator: The input file contains 20034 PSMs, 13632 decoy PSMs and 32 features.
05/28/2019 04:17 PM (3): Percolator: Generated percolator input for concatenated mode
05/28/2019 04:17 PM (3): Percolator: Percolator version 3.02.1, Build Date Aug 14 2018 00:44:01
05/28/2019 04:17 PM (3): Percolator: Copyright (c) 2006-9 University of Washington. All rights reserved.
05/28/2019 04:17 PM (3): Percolator: Written by Lukas Käll (luk...@u.washington.edu) in the
05/28/2019 04:17 PM (3): Percolator: Department of Genome Sciences at the University of Washington.
05/28/2019 04:17 PM (3): Percolator: Issued command:
05/28/2019 04:17 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\Job36\Percol(3)\output.xml -Z -I auto -k C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job36\Percol(3)\input.xml
05/28/2019 04:17 PM (3): Percolator: Started Tue May 28 16:17:41 2019
05/28/2019 04:17 PM (3): Percolator: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
05/28/2019 04:17 PM (3): Percolator: Reading pin-xml input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job36\Percol(3)\input.xml
05/28/2019 04:17 PM (3): Percolator: enzyme=Trypsin
05/28/2019 04:17 PM (3): Percolator: Features:
05/28/2019 04:17 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] 
05/28/2019 04:17 PM (3): Percolator: Concatenated search input detected, skipping both target-decoy competition and mix-max.
05/28/2019 04:17 PM (3): Percolator: Train/test set contains 20034 positives and 13632 negatives, size ratio=1.46963 and pi0=1
05/28/2019 04:17 PM (3): Percolator: Selecting Cpos by cross-validation.
05/28/2019 04:17 PM (3): Percolator: Selecting Cneg by cross-validation.
05/28/2019 04:17 PM (3): Percolator: Split 1: Selected feature 26 as initial direction. Could separate 3380 training set positives with q<0.01 in that direction.
05/28/2019 04:17 PM (3): Percolator: Split 2: Selected feature 26 as initial direction. Could separate 3427 training set positives with q<0.01 in that direction.
05/28/2019 04:17 PM (3): Percolator: Split 3: Selected feature 26 as initial direction. Could separate 3489 training set positives with q<0.01 in that direction.
05/28/2019 04:17 PM (3): Percolator: Found 5148 test set positives with q<0.01 in initial direction
05/28/2019 04:17 PM (3): Percolator: Reading in data and feature calculation took 4.884 cpu seconds or 5 seconds wall clock time.
05/28/2019 04:17 PM (3): Percolator: ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 1: Estimated 6301 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 2: Estimated 6493 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 3: Estimated 6525 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 4: Estimated 6558 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 5: Estimated 6574 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 6: Estimated 6580 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 7: Estimated 6583 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 8: Estimated 6584 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 9: Estimated 6590 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Iteration 10: Estimated 6590 PSMs with q<0.01
05/28/2019 04:17 PM (3): Percolator: Learned normalized SVM weights for the 3 cross-validation splits:
05/28/2019 04:17 PM (3): Percolator: Split1 Split2 Split3 FeatureName
05/28/2019 04:17 PM (3): Percolator: 0.3559 0.0089 -0.3295 CharmeRTCombinedScore
05/28/2019 04:17 PM (3): Percolator: 0.3616 0.0615 0.3112 Delta Cn From Second PSM
05/28/2019 04:17 PM (3): Percolator: 3.6969 3.9415 4.2524 Binomial Score
05/28/2019 04:17 PM (3): Percolator: 0.0994 0.0815 0.0674 Isolation Interference [%]
05/28/2019 04:17 PM (3): Percolator: -0.1703 -0.2710 -0.5441 MH+ [Da]
05/28/2019 04:17 PM (3): Percolator: 0.4451 -0.1239 0.3285 Delta Mass [Da]
05/28/2019 04:17 PM (3): Percolator: -0.2145 0.5731 -0.2872 Delta Mass [ppm]
05/28/2019 04:17 PM (3): Percolator: 0.0593 -0.3462 -1.0731 Absolute Delta Mass [Da]
05/28/2019 04:17 PM (3): Percolator: -0.5269 0.1493 0.7226 Absolute Delta Mass [ppm]
05/28/2019 04:17 PM (3): Percolator: 0.7139 0.7042 1.1771 Peptide Length
05/28/2019 04:17 PM (3): Percolator: 0.0000 0.0000 0.0000 Is z=1
05/28/2019 04:17 PM (3): Percolator: -0.3579 -0.2634 -0.4201 Is z=2
05/28/2019 04:17 PM (3): Percolator: 0.3533 0.2582 0.3703 Is z=3
05/28/2019 04:17 PM (3): Percolator: -0.0134 -0.0097 0.1127 Is z=4
05/28/2019 04:17 PM (3): Percolator: 0.1418 0.1199 0.1825 Is z=5
05/28/2019 04:17 PM (3): Percolator: 0.0153 0.0174 0.0195 Is z>5
05/28/2019 04:17 PM (3): Percolator: -0.5959 -0.6830 -0.6234 # Missed Cleavages
05/28/2019 04:17 PM (3): Percolator: 0.0000 0.0000 0.0000 Log Peptides Matched
05/28/2019 04:17 PM (3): Percolator: -0.0129 -0.0272 0.1754 Log Total Intensity
05/28/2019 04:17 PM (3): Percolator: -0.1060 -0.0082 0.0797 Fraction Matched Intensity [%]
05/28/2019 04:17 PM (3): Percolator: -0.7441 -0.4088 -0.5837 Fragment Coverage Series A, B, C [%]
05/28/2019 04:17 PM (3): Percolator: 0.4545 -0.1878 0.3328 Fragment Coverage Series X, Y, Z [%]
05/28/2019 04:17 PM (3): Percolator: 0.1533 0.1374 0.0468 Log Matched Fragment Series Intensities A, B, C
05/28/2019 04:17 PM (3): Percolator: -0.8425 -0.8714 -0.9545 Log Matched Fragment Series Intensities X, Y, Z
05/28/2019 04:17 PM (3): Percolator: 0.1477 -0.4996 -0.2605 Longest Sequence Series A, B, C
05/28/2019 04:17 PM (3): Percolator: 0.8447 1.3034 1.0883 Longest Sequence Series X, Y, Z
05/28/2019 04:17 PM (3): Percolator: 0.4419 -0.2119 0.3820 IQR Fragment Delta Mass [Da]
05/28/2019 04:17 PM (3): Percolator: -0.0097 -0.3833 -0.6509 IQR Fragment Delta Mass [ppm]
05/28/2019 04:17 PM (3): Percolator: 0.1695 0.0045 -0.8683 Mean Fragment Delta Mass [Da]
05/28/2019 04:17 PM (3): Percolator: -0.2400 -0.0551 0.5314 Mean Fragment Delta Mass [ppm]
05/28/2019 04:17 PM (3): Percolator: -1.9740 -1.4565 -2.4635 Mean Absolute Fragment Delta Mass [Da]
05/28/2019 04:17 PM (3): Percolator: 0.1977 -0.0143 0.5456 Mean Absolute Fragment Delta Mass [ppm]
05/28/2019 04:17 PM (3): Percolator: -2.8111 -3.1942 -3.5846 m0
05/28/2019 04:17 PM (3): Percolator: Found 6487 test set PSMs with q<0.01.
05/28/2019 04:17 PM (3): Percolator: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
05/28/2019 04:17 PM (3): Percolator: Calculating q values.
05/28/2019 04:17 PM (3): Percolator: Final list yields 1040 target peptides with q<0.01.
05/28/2019 04:17 PM (3): Percolator: Calculating posterior error probabilities (PEPs).
05/28/2019 04:17 PM (3): Percolator: Processing took 11.5 cpu seconds or 11 seconds wall clock time.
05/28/2019 04:17 PM (3): Percolator: PSMId score q-value posterior_error_prob peptide proteinIds
05/28/2019 04:18 PM (3): Percolator: 6490/63 high confident target/decoy peptides were found for MS Amanda 2.0 (2).
05/28/2019 04:18 PM (3): Percolator: 596/290 medium confident target/decoy peptides were found for MS Amanda 2.0 (2).
05/28/2019 04:18 PM (3): Percolator: -- Total execution of Percolator (64Bit) for MS Amanda 2.0 (2) took 1 min 17 s --
05/28/2019 04:18 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
05/28/2019 04:18 PM (5): IMP-ptmRS: More nodes and documentations can be found here http://ms.imp.ac.at/?goto=pd-nodes.
05/28/2019 04:18 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.
05/28/2019 04:18 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.
05/28/2019 04:18 PM (5): IMP-ptmRS: -- Total execution of IMP-ptmRS (5) took 184.2 ms --
05/28/2019 04:18 PM (4): IMP-apQuant: 8 Processors found
05/28/2019 04:18 PM (4): IMP-apQuant: Start IMP-apQuant Version 3.1.1.24322
05/28/2019 04:18 PM (4): IMP-apQuant: Reading TargetPeptideSpectrumMatch
05/28/2019 04:18 PM (4): IMP-apQuant: Done
05/28/2019 04:18 PM (4): IMP-apQuant: creating file in E:\Work\data_MS_plus_raw\19EDG05\raw
05/28/2019 04:18 PM (4): IMP-apQuant: Collecting Modifications
05/28/2019 04:18 PM (4): IMP-apQuant: Filtering Items
05/28/2019 04:18 PM (4): IMP-apQuant: Calculating Alignment
05/28/2019 04:18 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw
05/28/2019 04:18 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw
05/28/2019 04:18 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (3124 items)
05/28/2019 04:18 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (3012 items)
05/28/2019 04:18 PM (4): IMP-apQuant: Worker 0 Finished Processing 38 items
05/28/2019 04:18 PM (4): IMP-apQuant: Worker 1 Finished Processing 38 items
05/28/2019 04:18 PM (4): IMP-apQuant: Worker 2 Finished Processing 40 items
05/28/2019 04:18 PM (4): IMP-apQuant: Collecting Traces
05/28/2019 04:18 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw
05/28/2019 04:18 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw
05/28/2019 04:18 PM (4): IMP-apQuant: Creating items
05/28/2019 04:18 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (3922 items)
05/28/2019 04:19 PM (4): IMP-apQuant: Creating items
05/28/2019 04:19 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (3858 items)
05/28/2019 04:19 PM (4): IMP-apQuant: Worker 1 Finished Processing 500 items
05/28/2019 04:21 PM (4): IMP-apQuant: Worker 0 Finished Processing 543 items
05/28/2019 04:21 PM (4): IMP-apQuant: Worker 2 Finished Processing 462 items
05/28/2019 04:21 PM (4): IMP-apQuant: Creating items
05/28/2019 04:21 PM (4): IMP-apQuant: Creating items
05/28/2019 04:21 PM (4): IMP-apQuant: Finished writing
05/28/2019 04:21 PM (4): IMP-apQuant: Collecting Decoy Traces 1505
05/28/2019 04:21 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw
05/28/2019 04:21 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw
05/28/2019 04:21 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (3628 items)
05/28/2019 04:22 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (3599 items)
05/28/2019 04:22 PM (4): IMP-apQuant: Worker 1 Finished Processing 505 items
05/28/2019 04:22 PM (4): IMP-apQuant: Worker 0 Finished Processing 500 items
05/28/2019 04:22 PM (4): IMP-apQuant: Worker 2 Finished Processing 500 items
05/28/2019 04:22 PM (4): IMP-apQuant: Finished writing
05/28/2019 04:22 PM (4): IMP-apQuant: Calculating Areas
05/28/2019 04:22 PM (4): IMP-apQuant: It took me 00:04:40.6726286 seconds to finish the task
05/28/2019 04:22 PM (4): IMP-apQuant: Calculating Scores
05/28/2019 04:22 PM (4): IMP-apQuant: Calculating Scores
05/28/2019 04:22 PM (4): IMP-apQuant: Reading features from table
05/28/2019 04:22 PM (4): IMP-apQuant: Creating Percolator input
05/28/2019 04:22 PM (4): IMP-apQuant: Starting Percolator
05/28/2019 04:22 PM (4): IMP-apQuant: Percolator version 3.01, Build Date Nov 16 2016 08:44:38
05/28/2019 04:22 PM (4): IMP-apQuant: Copyright (c) 2006-9 University of Washington. All rights reserved.
05/28/2019 04:22 PM (4): IMP-apQuant: Written by Lukas Käll (luk...@u.washington.edu) in the
05/28/2019 04:22 PM (4): IMP-apQuant: Department of Genome Sciences at the University of Washington.
05/28/2019 04:22 PM (4): IMP-apQuant: Issued command:
05/28/2019 04:22 PM (4): IMP-apQuant: C:\Program Files\Thermo\Proteome Discoverer 2.3\Tools\apQuant\percolator.exe C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job36\IMPapQ(4)\percoInput.txt -m C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job36\IMPapQ(4)\percoOutput_Target.txt -M C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job36\IMPapQ(4)\percoOutput_Decoy.txt -U -Y
05/28/2019 04:22 PM (4): IMP-apQuant: Started Tue May 28 16:22:48 2019
05/28/2019 04:22 PM (4): IMP-apQuant: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
05/28/2019 04:22 PM (4): IMP-apQuant: Reading tab-delimited input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job36\IMPapQ(4)\percoInput.txt
05/28/2019 04:22 PM (4): IMP-apQuant: Features:
05/28/2019 04:22 PM (4): IMP-apQuant: DeltaT1 DeltaT2 DeltaM1 DeltaM2 
05/28/2019 04:22 PM (4): IMP-apQuant: Exception caught: ERROR: Reading tab file, the peptide sequence NaN with PSM id T1 is too short.
05/28/2019 04:22 PM (4): IMP-apQuant:
05/28/2019 04:22 PM (4): IMP-apQuant: Finished Percolator
05/28/2019 04:22 PM (4): IMP-apQuant: Percolator could not process the dataset. Falling back to other method. See the verbose output for more information
05/28/2019 04:22 PM (4): IMP-apQuant: Calculating Scores
05/28/2019 04:22 PM (4): IMP-apQuant: IMP-apQuant finished in 0:4:48
05/28/2019 04:22 PM (4): IMP-apQuant: -- Total execution of IMP-apQuant (4) took 4 min 48 s --
05/28/2019 04:22 PM (6): Minora Feature Detector: Start detecting lcmspeaks...
05/28/2019 04:22 PM (6): Minora Feature Detector: Running 2 jobs with 2 jobs in parallel.
05/28/2019 04:22 PM (6): Minora Feature Detector: Start F14 with 'FTMS + p NSI Full ms [350.0000-1850.0000]'
05/28/2019 04:22 PM (6): Minora Feature Detector: Start F3 with 'FTMS + p NSI Full ms [350.0000-1850.0000]'
05/28/2019 04:24 PM (6): Minora Feature Detector: Detecting LcmsPeaks took 1 min 48 s
05/28/2019 04:24 PM (6): Minora Feature Detector: Start processing F14: '190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw'.
05/28/2019 04:24 PM (6): Minora Feature Detector: Start processing F3: '190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw'.
05/28/2019 04:24 PM (6): Minora Feature Detector: Importing peaks for F14 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])...
05/28/2019 04:24 PM (6): Minora Feature Detector: Importing peaks for F3 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])...
05/28/2019 04:24 PM (6): Minora Feature Detector: F3: Found 186494 chromatographic peaks.
05/28/2019 04:24 PM (6): Minora Feature Detector: F14: Found 234305 chromatographic peaks.
05/28/2019 04:24 PM (6): Minora Feature Detector: F3: Importing auto traces...
05/28/2019 04:24 PM (6): Minora Feature Detector: F3: Imported 125889 auto traces.
05/28/2019 04:24 PM (6): Minora Feature Detector: F14: Importing auto traces...
05/28/2019 04:25 PM (6): Minora Feature Detector: F14: Imported 150740 auto traces.
05/28/2019 04:25 PM (6): Minora Feature Detector: Importing peak to spectrum links...
05/28/2019 04:26 PM (6): Minora Feature Detector: F3: Standard deviations: m/z 5.30; RT 0.10; Intensity 64.63; Fraction Missing Intensity 0.20; Shoulder Score 0.000; Peak Length Score 0.0516998891422097 took 57.5 s
05/28/2019 04:26 PM (6): Minora Feature Detector: F14: Standard deviations: m/z 5.46; RT 0.10; Intensity 68.38; Fraction Missing Intensity 0.19; Shoulder Score 0.000; Peak Length Score 0.0437464097347174 took 1 min 39 s
05/28/2019 04:27 PM (6): Minora Feature Detector: Found 3871 features (F3: 1806, F14: 2065)
05/28/2019 04:27 PM (6): Minora Feature Detector: Writing data took 1.6 s.
05/28/2019 04:27 PM (6): Minora Feature Detector: Creating features for PSMs took 5 s.
05/28/2019 04:28 PM (6): Minora Feature Detector: F3: Unidentified feature detection took 50.4 s
05/28/2019 04:28 PM (6): Minora Feature Detector: F14: Unidentified feature detection took 1 min 0 s
05/28/2019 04:28 PM (6): Minora Feature Detector: Found 85400 unidentified features (F3 : 37200, F14 : 48200).
05/28/2019 04:29 PM (6): Minora Feature Detector: -- Total execution of Minora Feature Detector (6) took 6 min 7 s --
05/28/2019 04:29 PM Job Execution: Finished E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp-(2).msf
05/28/2019 04:29 PM Job Execution: ----- Total Job execution took: 20 min 6 s. -----

André Lüttig

unread,
May 31, 2019, 2:44:21 AM5/31/19
to MS Amanda
Hey Erik,

The issue with percolator shouldn't be that big, as when it's not working it falls back to the non-percolator scoring methods.
More interesting is the bug in your consensus step, since this is the one not giving you the protein areas. Could you maybe update your apQuant to the newest version and try to rerun your workflow, since we had a lot of version changes in the last few weeks? You can download it from here: http://ms.imp.ac.at/index.php?action=apQuant.

Best regards,
André

Erik de G

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Jun 3, 2019, 9:42:06 AM6/3/19
to MS Amanda
Hi Andre,
Percolator is one of the reasons to choose for apquant. Can you give a reason(s) why this is not working? see verbose below.

Gr
Erik

TimeProcessing NodeLevelMessage
12:51 PM(4): IMP-apQuantVerbose
12:51 PM(4): IMP-apQuantVerboseException caught: ERROR: Reading tab file, the peptide sequence NaN with PSM id T19 is too short.
12:51 PM(4): IMP-apQuantVerboseDeltaT1 DeltaT2 DeltaM1 DeltaM2 RMSD F1 F2 F3 F4 distF N/S Score
12:51 PM(4): IMP-apQuantVerboseFeatures:
12:51 PM(4): IMP-apQuantVerboseReading tab-delimited input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job57\IMPapQ(4)\percoInput.txt
12:51 PM(4): IMP-apQuantVerbose
Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10
12:51 PM(4): IMP-apQuantVerboseStarted Mon Jun 03 12:51:50 2019
12:51 PM(4): IMP-apQuantVerboseC:\Program Files\Thermo\Proteome Discoverer 2.3\Tools\apQuant\percolator.exe C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job57\IMPapQ(4)\percoInput.txt -m C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job57\IMPapQ(4)\percoOutput_Target.txt -M C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job57\IMPapQ(4)\percoOutput_Decoy.txt -U -Y
12:51 PM(4): IMP-apQuantVerboseIssued command:
12:51 PM(4): IMP-apQuantVerbose
Department of Genome Sciences at the University of Washington.
12:51 PM(4): IMP-apQuantVerbose
Written by Lukas Käll (luk...@u.washington.edu) in the
12:51 PM(4): IMP-apQuantVerbose
Copyright (c) 2006-9 University of Washington. All rights reserved.
12:51 PM(4): IMP-apQuantVerbose
Percolator version 3.01, Build Date Nov 16 2016 08:44:38
Message has been deleted

Erik de G

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Jun 14, 2019, 7:32:43 AM6/14/19
to MS Amanda
This problem was solved with installing a new bugfixed installation.
However, I cannot get the XIC trace view for each quanresult. How can I see this? I would really like to see it and compare it with the default PD XIC, because I see quite some discrepancies between PD quan and apquan...

Greetings,
Erik


On Monday, May 27, 2019 at 5:20:41 PM UTC+2, Erik de G wrote:

André Lüttig

unread,
Jun 17, 2019, 2:40:47 AM6/17/19
to MS Amanda
Dear Erik,

don't you have the "Show XIC" button as shown in the picture below? If not, can you check your Output, if there was any error or warning regarding apQuant (or at all)?

Best,
André





Erik de G

unread,
Jun 17, 2019, 9:55:15 AM6/17/19
to MS Amanda
Hi Andre,

See attachment, there is no button, also not in the extra columns. Maybe it is due to the RT alignment that did not work on all raw files. Maybe grouping is not compatible with apquant (I have different enzyme digestions in the same group, that will obviously show a bad RT alignment).

Greetings,
Erik
apquant.png
results-summary.txt

André Lüttig

unread,
Jun 17, 2019, 10:01:28 AM6/17/19
to MS Amanda
There seems to be a problem in your Consensus Output, apQuant threw an exception before it could reach the point where it creates the buttons. Did you Re-Process the whole workflow or only the consensus?
Normally your grouping and your multiple processing steps shouldn't pose a problem, since we're using it here quite often as well.

Is there any chance you could send me your .pdResult file to have look at it? Maybe this could help narrow down the problem.

Kind regards,
André
Message has been deleted

André Lüttig

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Jun 19, 2019, 5:33:37 AM6/19/19
to MS Amanda
I also just saw, that there was an error in your Processing Step C, as ptmRS was not executed and apQuant threw an error thinking it was executed where it actually wasn't. So couls you maybe either remove ptmRS from this workflow or specify a PTM as dynamic modification in your search?
The exact error messages are at the end of this post, so you know what I meant. It also probably has not much to do with the error you posted, but it's still worth to mention.

Best regards,
André

06/14/2019 02:13 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.
06/14/2019 02:13 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.
06/14/2019 02:13 PM	(5): IMP-ptmRS:	-- Total execution of IMP-ptmRS (5) took 323.2 ms --
06/14/2019 02:13 PM	(4): IMP-apQuant:	8 Processors found
06/14/2019 02:13 PM	(4): IMP-apQuant:	Start IMP-apQuant Version 3.1.1.16751
06/14/2019 02:13 PM	(4): IMP-apQuant:	Reading TargetPeptideSpectrumMatch
06/14/2019 02:13 PM	(4): IMP-apQuant:	Done
06/14/2019 02:13 PM	(4): IMP-apQuant:	creating file in E:\Work\data_MS_plus_raw\19EDG05\raw
06/14/2019 02:13 PM	(4): IMP-apQuant:	Collecting Modifications
06/14/2019 02:13 PM	(4): IMP-apQuant:	Filtering Items
06/14/2019 02:13 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)
   at IMP.apQuant.Node.ApQuantNode.FilterItems[T](IEnumerable`1 rawItems, List`1 modifications, PropertyAccessor ptmrsAccessor)
   at IMP.apQuant.Node.ApQuantNode.DoProcessing[T](Boolean xlink)
06/14/2019 02:13 PM	(4): IMP-apQuant:	IMP-apQuant finished in 0:0:3
06/14/2019 02:13 PM	(4): IMP-apQuant:	-- Total execution of IMP-apQuant (4) took 3.3 s --
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