================================================================================ Consensus Step Workflow ================================================================================ Result name: 19EDG05-06_aDn7_SERISO Result file: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn7_SERISO.pdResult Description: Result filtered for high confident peptides. Workflow based on template: CWF_Erik_Quan_AllPep_Intensity Creation date: 6/14/2019 1:54:55 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 2.0: Amanda Score - 1. Threshold: 60 Hidden Parameters: - MSF File(s) (Hidden): E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn2-4_SERISO-Tryp-(2).msf E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo-(2).msf E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C-(1).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: ------------------------------------------------------------------ 06/14/2019 02:41 PM Job Execution: Processing E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn7_SERISO.pdResult 06/14/2019 02:41 PM (0): MSF Files: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn2-4_SERISO-Tryp-(2).msf 06/14/2019 02:41 PM (0): MSF Files: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo-(2).msf 06/14/2019 02:41 PM (0): MSF Files: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C-(1).msf 06/14/2019 02:41 PM (0): MSF Files: All 3 files are ready for processing. 06/14/2019 02:41 PM (0): MSF Files: Errors reported in at least one input processing workflow (check processing summary). 06/14/2019 02:41 PM (0): MSF Files: Start transferring results of 3 msf files... 06/14/2019 02:42 PM (0): MSF Files: Transferred 13583 Proteins to result file in 1 min 3 s. 06/14/2019 02:43 PM (0): MSF Files: Transferred 13050 Decoy Proteins to result file in 1 min 16 s. 06/14/2019 02:45 PM (0): MSF Files: Added 33673 Mass Spectra to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 276635 traces to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 2 Input Files to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 37722 PSMs to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 37182 Decoy PSMs to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 43090 MS/MS Spectrum Info to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 6 Specialized Traces to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 3294 apQuant Features to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 2 apQuant Alignment to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 3294 apQuant Decoy Features to result file. 06/14/2019 02:45 PM (0): MSF Files: Added 89284 LCMS Features to result file. 06/14/2019 02:46 PM (0): MSF Files: Added 417261 LCMS Peaks to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 34924 Mass Spectra to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 316282 traces to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 2 Input Files to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 41488 PSMs to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 41136 Decoy PSMs to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 44002 MS/MS Spectrum Info to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 6 Specialized Traces to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 1972 apQuant Features to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 2 apQuant Alignment to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 1972 apQuant Decoy Features to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 103984 LCMS Features to result file. 06/14/2019 02:47 PM (0): MSF Files: Added 480679 LCMS Peaks to result file. 06/14/2019 02:48 PM (0): MSF Files: Added 26123 Mass Spectra to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 332692 traces to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 2 Input Files to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 32952 PSMs to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 32224 Decoy PSMs to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 39079 MS/MS Spectrum Info to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 6 Specialized Traces to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 115281 LCMS Features to result file. 06/14/2019 02:49 PM (0): MSF Files: Added 535179 LCMS Peaks to result file. 06/14/2019 02:50 PM (0): MSF Files: Copying data took 9 min 14 s. 06/14/2019 02:51 PM (0): MSF Files: Finding unique sequences took 7.2 s. 06/14/2019 02:51 PM (0): MSF Files: Filtering PSMs took 12.8 s. 06/14/2019 02:51 PM (0): MSF Files: Filter 0/3303 Proteins (3303 excluded) took: 17.9 s 06/14/2019 02:51 PM (0): MSF Files: Filter 0/3568 Decoy Proteins (3568 excluded) took: 16.8 s 06/14/2019 02:51 PM (0): MSF Files: Filtering proteins took 34.7 s. 06/14/2019 02:52 PM (0): MSF Files: -- Total execution of MSF Files (0) took 10 min 42 s -- 06/14/2019 02:52 PM (1): PSM Grouper: Grouping 'PSMs' 06/14/2019 02:52 PM (1): PSM Grouper: Found 17867 Peptide Groups. 06/14/2019 02:52 PM (1): PSM Grouper: Grouping 'Decoy PSMs' 06/14/2019 02:52 PM (1): PSM Grouper: Found 14835 Decoy Peptide Groups. 06/14/2019 02:52 PM (1): PSM Grouper: -- Total execution of PSM Grouper (1) took 43.1 s -- 06/14/2019 02:52 PM (2): Peptide Validator: Start PSM and Peptide validation in 'Automatic (Control peptide level error rate if possible)' mode... 06/14/2019 02:53 PM (2): Peptide Validator: Updated PSM confidences in 2.8 s. 06/14/2019 02:53 PM (2): Peptide Validator: Use svm score for 'peptide' qvality run. 06/14/2019 02:53 PM (2): Peptide Validator: Updated peptide confidences using qvality in 10.4 s. 06/14/2019 02:53 PM (2): Peptide Validator: Calculating Mascot thresholds. 06/14/2019 02:53 PM (2): Peptide Validator: -- Total execution of Peptide Validator (2) took 13.4 s -- 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter Peptide Groups 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter 2163/17867 Peptide Groups (15704 excluded) and 12604/37198 PSMs (24594 excluded) took 6.6 s 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filtering Proteins 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter 1076/10280 Proteins (9204 excluded) took 2.9 s 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter Decoy Peptide Groups 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter 20/14835 Decoy Peptide Groups (14815 excluded) and 35/22530 Decoy PSMs (22495 excluded) took 1.9 s 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filtering Decoy Proteins 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter 21/9482 Decoy Proteins (9461 excluded) took 531.2 ms 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter Proteins 06/14/2019 02:53 PM (3): Peptide and Protein Filter: Filter Decoy Proteins 06/14/2019 02:54 PM (3): Peptide and Protein Filter: Updating counts took 1 min 21 s. 06/14/2019 02:54 PM (3): Peptide and Protein Filter: -- Total execution of Peptide and Protein Filter (3) took 1 min 35 s -- 06/14/2019 02:54 PM (4): Protein Scorer: Calculating Coverage and Counts 06/14/2019 02:55 PM (4): Protein Scorer: Calculated counts and coverages in 23.6 s. 06/14/2019 02:55 PM (4): Protein Scorer: Scoring target proteins 06/14/2019 02:55 PM (4): Protein Scorer: Scored 1076 proteins in 13.8 s. 06/14/2019 02:55 PM (4): Protein Scorer: Scoring decoy proteins 06/14/2019 02:55 PM (4): Protein Scorer: Scored 21 decoy proteins in 198.2 ms. 06/14/2019 02:55 PM (4): Protein Scorer: -- Total execution of Protein Scorer (4) took 38 s -- 06/14/2019 02:55 PM (5): Protein Grouping: Retrieving 488 protein groups took 60.2 ms. 06/14/2019 02:56 PM (5): Protein Grouping: Storing, updating and connecting protein groups, PSMs and peptides took 1 min 6 s. 06/14/2019 02:56 PM (5): Protein Grouping: Found 488 protein groups. 06/14/2019 02:56 PM (5): Protein Grouping: Retrieving 20 decoy protein groups took 6.2 ms. 06/14/2019 02:56 PM (5): Protein Grouping: Storing, updating and connecting protein groups, PSMs and peptides took 2.7 s. 06/14/2019 02:56 PM (5): Protein Grouping: Found 20 decoy protein groups. 06/14/2019 02:57 PM (5): Protein Grouping: -- Total execution of Protein Grouping (5) took 1 min 37 s -- 06/14/2019 02:57 PM (6): Peptide in Protein Annotation: Start retrieving flanking residues and positions... 06/14/2019 02:58 PM (6): Peptide in Protein Annotation: Annotated PSMs/peptides for 1076 proteins. 06/14/2019 02:58 PM (6): Peptide in Protein Annotation: Start annotating peptide groups with flanking residues and positions... 06/14/2019 02:58 PM (6): Peptide in Protein Annotation: Annotate Peptide Groups items 06/14/2019 02:58 PM (6): Peptide in Protein Annotation: Start calculating protein coverage... 06/14/2019 02:58 PM (6): Peptide in Protein Annotation: -- Total execution of Peptide in Protein Annotation (6) took 1 min 33 s -- 06/14/2019 02:58 PM (12): IMP-apQuant Peptide and Protein Quantifier: Starting IMP-apQuant Quantifier version: 3.1.1.28153 06/14/2019 02:58 PM (12): IMP-apQuant Peptide and Protein Quantifier: Connecting tables 06/14/2019 02:58 PM (12): IMP-apQuant Peptide and Protein Quantifier: Calculating overlaps 06/14/2019 02:59 PM (12): IMP-apQuant Peptide and Protein Quantifier: Add overlaps to QuanResults 06/14/2019 02:59 PM (12): IMP-apQuant Peptide and Protein Quantifier: Finished calculating overlaps 06/14/2019 02:59 PM (12): IMP-apQuant Peptide and Protein Quantifier: Quantifying peptides 06/14/2019 02:59 PM (12): IMP-apQuant Peptide and Protein Quantifier: Write data to TargetPeptideGroup table 06/14/2019 03:00 PM (12): IMP-apQuant Peptide and Protein Quantifier: Quantifying Proteins 06/14/2019 03:00 PM (12): IMP-apQuant Peptide and Protein Quantifier: Combining peptide areas 06/14/2019 03:00 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() 06/14/2019 03:00 PM (12): IMP-apQuant Peptide and Protein Quantifier: IMP-apQuant Quantifier finished in 00:01:30 06/14/2019 03:00 PM (7): Protein FDR Validator: Apply confidences based on protein scores of 1076 proteins. 06/14/2019 03:00 PM (7): Protein FDR Validator: Calculating Sum PEP Score for Proteins 06/14/2019 03:00 PM (7): Protein FDR Validator: Calculating Sum PEP Score for Decoy Proteins 06/14/2019 03:00 PM (7): Protein FDR Validator: -- Total execution of Protein FDR Validator (7) took 32.8 s -- 06/14/2019 03:00 PM (8): Feature Mapper: Alignment is turned off by user, alignment is not performed. 06/14/2019 03:00 PM (8): Feature Mapper: Using RT tolerance of 1.00 min and mass tolerance of 6.0 ppm for mapping 06/14/2019 03:00 PM (8): Feature Mapper: Mapping 1 Fraction(s) 06/14/2019 03:01 PM (8): Feature Mapper: Mapping Fraction 1 of 1 06/14/2019 03:06 PM (8): Feature Mapper: Mapping 1 Fraction(s) took 5 min 54 s 06/14/2019 03:06 PM (8): Feature Mapper: -- Performing cross file mapping took 5 min 55 s. -- 06/14/2019 03:06 PM (8): Feature Mapper: Storing Top Apex RT for Peptide Groups 06/14/2019 03:07 PM (8): Feature Mapper: Storing Top Apex RT for Peptide Groups took 15.2 s 06/14/2019 03:07 PM (8): Feature Mapper: -- Total execution of Feature Mapper (8) took 6 min 25 s -- 06/14/2019 03:07 PM (9): Precursor Ions Quantifier: Validating LCMS features 06/14/2019 03:07 PM (9): Precursor Ions Quantifier: Validating Consensus Features 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Validation of quantification results took 1 min 6 s 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Updating spectrum match areas 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Classify quan usage of PSMs 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Classifying Peptide Groups quan usage 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Classifying Peptide Groups quan usage for 2163 items took 7.9 s 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Calculating Peptide Group Abundances 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Classifying Protein Quan Usage 06/14/2019 03:08 PM (9): Precursor Ions Quantifier: Calculating Protein Abundances 06/14/2019 03:09 PM (9): Precursor Ions Quantifier: Start normalization of abundance values... 06/14/2019 03:09 PM (9): Precursor Ions Quantifier: Calculating normalization took 20.1 s 06/14/2019 03:09 PM (9): Precursor Ions Quantifier: Calculating Normalized Peptide Group Abundances 06/14/2019 03:09 PM (9): Precursor Ions Quantifier: Calculating Normalized Protein Abundances 06/14/2019 03:09 PM (9): Precursor Ions Quantifier: Calculating and applying normalization took 36.8 s 06/14/2019 03:10 PM (9): Precursor Ions Quantifier: Cannot calculate quan ratios, because no ratios are specified. 06/14/2019 03:10 PM (9): Precursor Ions Quantifier: Precursor Ion Quantification took 3 min 6 s. 06/14/2019 03:10 PM (9): Precursor Ions Quantifier: Preparing spectrum visualization took 3.2 s. 06/14/2019 03:10 PM (9): Precursor Ions Quantifier: -- Total execution of Precursor Ions Quantifier (9) took 3 min 10 s -- 06/14/2019 03:10 PM (10): Display Settings: Applying display filter and layout 06/14/2019 03:10 PM (10): Display Settings: -- Total execution of Display Settings (10) took 47.8 ms -- 06/14/2019 03:10 PM Job Execution: Finalizing file took 19 s. 06/14/2019 03:10 PM Job Execution: Finished E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn7_SERISO.pdResult 06/14/2019 03:10 PM Job Execution: ----- Total Job execution took: 29 min 1 s. ----- ================================================================================ Processing Step A: Workflow ================================================================================ Result name: 19EDG05-06_aDn2-4_SERISO-Tryp Result file: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn2-4_SERISO-Tryp-(2).msf Description: Ab_Quan_Tryp Workflow based on template: Ab_Quan_Tryp Creation date: 6/14/2019 1:54:47 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_aDn7iso-13d-Tryp.raw E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-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: BCR-donor-133573_2013_Sanger.fasta 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 2.0: 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: ------------------------------------------------------------------ 06/14/2019 01:54 PM Job Execution: Processing E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn2-4_SERISO-Tryp-(2).msf 06/14/2019 01:54 PM (1): Spectrum Selector: Profile spectra are not sent. 06/14/2019 01:54 PM (1): Spectrum Selector: Reading from file 1 of 2 F3: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (27076 spectra total) 06/14/2019 01:55 PM (2): MS Amanda 2.0: Starting MS Amanda search version 2.3.0.12368, Engine version 2.0.0.12368 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Loading database 06/14/2019 01:55 PM (2): MS Amanda 2.0: Loading database done 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Scored 14726 peptide hits and 14003 decoy peptide hits in 24.34 sec 06/14/2019 01:56 PM (2): MS Amanda 2.0: Stored 8044 PSMs for 6423 spectra 06/14/2019 01:57 PM (2): MS Amanda 2.0: Stored 8098 decoy PSMs for 6373 spectra 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:01 PM (2): MS Amanda 2.0: Scored 20140 peptide hits and 17208 decoy peptide hits in 144.15 sec 06/14/2019 02:01 PM (2): MS Amanda 2.0: Stored 9985 PSMs for 8690 spectra 06/14/2019 02:04 PM (2): MS Amanda 2.0: Stored 9703 decoy PSMs for 8328 spectra 06/14/2019 02:04 PM (1): Spectrum Selector: Sent 22334 spectra from file F3. 06/14/2019 02:04 PM (1): Spectrum Selector: Reading from file 2 of 2 F14: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (25381 spectra total) 06/14/2019 02:05 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:05 PM (2): MS Amanda 2.0: Searching 10334 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:05 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:05 PM (2): MS Amanda 2.0: Searching 10334 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:05 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:05 PM (2): MS Amanda 2.0: Searching 10334 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:05 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:05 PM (2): MS Amanda 2.0: Searching 10334 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:05 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:05 PM (2): MS Amanda 2.0: Searching 10334 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:05 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:05 PM (2): MS Amanda 2.0: Searching 10334 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:06 PM (2): MS Amanda 2.0: Scored 13976 peptide hits and 12450 decoy peptide hits in 31.97 sec 06/14/2019 02:06 PM (2): MS Amanda 2.0: Stored 7389 PSMs for 5880 spectra 06/14/2019 02:06 PM (2): MS Amanda 2.0: Stored 7347 decoy PSMs for 5729 spectra 06/14/2019 02:08 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:08 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:08 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:08 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:08 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:08 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:08 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:08 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:08 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:08 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:08 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:08 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:09 PM (2): MS Amanda 2.0: Scored 20973 peptide hits and 17902 decoy peptide hits in 52.54 sec 06/14/2019 02:09 PM (2): MS Amanda 2.0: Stored 10513 PSMs for 9009 spectra 06/14/2019 02:11 PM (2): MS Amanda 2.0: Stored 10316 decoy PSMs for 8607 spectra 06/14/2019 02:11 PM (1): Spectrum Selector: Sent 20756 spectra from file F14. 06/14/2019 02:11 PM (1): Spectrum Selector: Sent 43090 spectra from 2 files (processing time: 2 min 30 s). 06/14/2019 02:11 PM (1): Spectrum Selector: -- Total execution of Spectrum Selector (1) took 16 min 53 s -- 06/14/2019 02:11 PM (2): MS Amanda 2.0: Storing spectra took 2 min 16 s. 06/14/2019 02:11 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:11 PM (2): MS Amanda 2.0: Searching 2756 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:11 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:11 PM (2): MS Amanda 2.0: Searching 2756 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:11 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:11 PM (2): MS Amanda 2.0: Searching 2756 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:11 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:11 PM (2): MS Amanda 2.0: Searching 2756 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:11 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:11 PM (2): MS Amanda 2.0: Searching 2756 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:11 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:11 PM (2): MS Amanda 2.0: Searching 2756 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:12 PM (2): MS Amanda 2.0: Scored 3875 peptide hits and 2982 decoy peptide hits in 19.19 sec 06/14/2019 02:12 PM (2): MS Amanda 2.0: Stored 1791 PSMs for 1586 spectra 06/14/2019 02:12 PM (2): MS Amanda 2.0: Stored 1718 decoy PSMs for 1469 spectra 06/14/2019 02:12 PM (2): MS Amanda 2.0: Finalizing search results... 06/14/2019 02:13 PM (2): MS Amanda 2.0: -- Total search time was 12 min 34 s -- 06/14/2019 02:17 PM (3): Percolator: Creating input file for MS Amanda 2.0 (2) took 3 min 35 s. 06/14/2019 02:17 PM (3): Percolator: The input file contains 20159 PSMs, 13514 decoy PSMs and 32 features. 06/14/2019 02:17 PM (3): Percolator: Generated percolator input for concatenated mode 06/14/2019 02:17 PM (3): Percolator: Percolator version 3.02.1, Build Date Aug 14 2018 00:44:01 06/14/2019 02:17 PM (3): Percolator: Copyright (c) 2006-9 University of Washington. All rights reserved. 06/14/2019 02:17 PM (3): Percolator: Written by Lukas K├ñll (lukall@u.washington.edu) in the 06/14/2019 02:17 PM (3): Percolator: Department of Genome Sciences at the University of Washington. 06/14/2019 02:17 PM (3): Percolator: Issued command: 06/14/2019 02:17 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\Job65\Percol(3)\output.xml -Z -I auto -k C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job65\Percol(3)\input.xml 06/14/2019 02:17 PM (3): Percolator: Started Fri Jun 14 14:17:34 2019 06/14/2019 02:17 PM (3): Percolator: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 06/14/2019 02:17 PM (3): Percolator: Reading pin-xml input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job65\Percol(3)\input.xml 06/14/2019 02:17 PM (3): Percolator: enzyme=Trypsin 06/14/2019 02:17 PM (3): Percolator: Features: 06/14/2019 02:17 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] 06/14/2019 02:17 PM (3): Percolator: Concatenated search input detected, skipping both target-decoy competition and mix-max. 06/14/2019 02:17 PM (3): Percolator: Train/test set contains 20159 positives and 13514 negatives, size ratio=1.49171 and pi0=1 06/14/2019 02:17 PM (3): Percolator: Selecting Cpos by cross-validation. 06/14/2019 02:17 PM (3): Percolator: Selecting Cneg by cross-validation. 06/14/2019 02:17 PM (3): Percolator: Split 1: Selected feature 26 as initial direction. Could separate 3548 training set positives with q<0.01 in that direction. 06/14/2019 02:17 PM (3): Percolator: Split 2: Selected feature 26 as initial direction. Could separate 3495 training set positives with q<0.01 in that direction. 06/14/2019 02:17 PM (3): Percolator: Split 3: Selected feature 26 as initial direction. Could separate 3577 training set positives with q<0.01 in that direction. 06/14/2019 02:17 PM (3): Percolator: Found 5310 test set positives with q<0.01 in initial direction 06/14/2019 02:17 PM (3): Percolator: Reading in data and feature calculation took 18.905 cpu seconds or 19 seconds wall clock time. 06/14/2019 02:17 PM (3): Percolator: ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 06/14/2019 02:17 PM (3): Percolator: Iteration 1: Estimated 6521 PSMs with q<0.01 06/14/2019 02:17 PM (3): Percolator: Iteration 2: Estimated 6715 PSMs with q<0.01 06/14/2019 02:17 PM (3): Percolator: Iteration 3: Estimated 6752 PSMs with q<0.01 06/14/2019 02:17 PM (3): Percolator: Iteration 4: Estimated 6777 PSMs with q<0.01 06/14/2019 02:18 PM (3): Percolator: Iteration 5: Estimated 6779 PSMs with q<0.01 06/14/2019 02:18 PM (3): Percolator: Iteration 6: Estimated 6783 PSMs with q<0.01 06/14/2019 02:18 PM (3): Percolator: Iteration 7: Estimated 6773 PSMs with q<0.01 06/14/2019 02:18 PM (3): Percolator: Iteration 8: Estimated 6789 PSMs with q<0.01 06/14/2019 02:18 PM (3): Percolator: Iteration 9: Estimated 6795 PSMs with q<0.01 06/14/2019 02:18 PM (3): Percolator: Iteration 10: Estimated 6797 PSMs with q<0.01 06/14/2019 02:18 PM (3): Percolator: Learned normalized SVM weights for the 3 cross-validation splits: 06/14/2019 02:18 PM (3): Percolator: Split1 Split2 Split3 FeatureName 06/14/2019 02:18 PM (3): Percolator: -0.4595 -0.1259 0.1950 CharmeRTCombinedScore 06/14/2019 02:18 PM (3): Percolator: 0.2414 0.2651 0.3342 Delta Cn From Second PSM 06/14/2019 02:18 PM (3): Percolator: 4.6812 3.3197 3.1438 Binomial Score 06/14/2019 02:18 PM (3): Percolator: 0.0656 0.0843 0.1409 Isolation Interference [%] 06/14/2019 02:18 PM (3): Percolator: -0.4614 0.0859 -0.1586 MH+ [Da] 06/14/2019 02:18 PM (3): Percolator: -0.3699 0.6329 0.3768 Delta Mass [Da] 06/14/2019 02:18 PM (3): Percolator: 0.5705 -0.4482 -0.1557 Delta Mass [ppm] 06/14/2019 02:18 PM (3): Percolator: -0.5369 -0.2012 -0.1704 Absolute Delta Mass [Da] 06/14/2019 02:18 PM (3): Percolator: 0.0304 0.0414 -0.0455 Absolute Delta Mass [ppm] 06/14/2019 02:18 PM (3): Percolator: 1.1630 0.6082 0.7481 Peptide Length 06/14/2019 02:18 PM (3): Percolator: 0.0000 0.0000 0.0000 Is z=1 06/14/2019 02:18 PM (3): Percolator: -0.2769 -0.3157 -0.3112 Is z=2 06/14/2019 02:18 PM (3): Percolator: 0.3031 0.2676 0.2478 Is z=3 06/14/2019 02:18 PM (3): Percolator: -0.1266 0.1002 0.1511 Is z=4 06/14/2019 02:18 PM (3): Percolator: 0.1920 0.1884 0.1736 Is z=5 06/14/2019 02:18 PM (3): Percolator: 0.0206 0.0142 0.0153 Is z>5 06/14/2019 02:18 PM (3): Percolator: -0.7886 -0.5291 -0.6732 # Missed Cleavages 06/14/2019 02:18 PM (3): Percolator: 0.0000 0.0000 0.0000 Log Peptides Matched 06/14/2019 02:18 PM (3): Percolator: 0.0547 0.1185 -0.0256 Log Total Intensity 06/14/2019 02:18 PM (3): Percolator: 0.0208 0.0783 -0.1132 Fraction Matched Intensity [%] 06/14/2019 02:18 PM (3): Percolator: -0.7262 -0.3088 -0.4875 Fragment Coverage Series A, B, C [%] 06/14/2019 02:18 PM (3): Percolator: 0.1272 0.3775 0.3890 Fragment Coverage Series X, Y, Z [%] 06/14/2019 02:18 PM (3): Percolator: 0.1612 0.0215 0.0179 Log Matched Fragment Series Intensities A, B, C 06/14/2019 02:18 PM (3): Percolator: -0.9312 -0.8844 -0.5784 Log Matched Fragment Series Intensities X, Y, Z 06/14/2019 02:18 PM (3): Percolator: 0.0563 -0.3907 -0.1261 Longest Sequence Series A, B, C 06/14/2019 02:18 PM (3): Percolator: 1.4280 0.9562 0.9461 Longest Sequence Series X, Y, Z 06/14/2019 02:18 PM (3): Percolator: 0.1112 -0.4036 -0.0009 IQR Fragment Delta Mass [Da] 06/14/2019 02:18 PM (3): Percolator: -0.2604 0.0324 -0.4322 IQR Fragment Delta Mass [ppm] 06/14/2019 02:18 PM (3): Percolator: -0.0554 -0.3437 0.0041 Mean Fragment Delta Mass [Da] 06/14/2019 02:18 PM (3): Percolator: 0.0168 0.4047 0.0517 Mean Fragment Delta Mass [ppm] 06/14/2019 02:18 PM (3): Percolator: -2.5419 -1.5734 -1.3448 Mean Absolute Fragment Delta Mass [Da] 06/14/2019 02:18 PM (3): Percolator: 0.3487 0.2955 -0.0648 Mean Absolute Fragment Delta Mass [ppm] 06/14/2019 02:18 PM (3): Percolator: -3.7724 -2.6055 -2.8002 m0 06/14/2019 02:18 PM (3): Percolator: Found 6718 test set PSMs with q<0.01. 06/14/2019 02:18 PM (3): Percolator: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. 06/14/2019 02:18 PM (3): Percolator: Calculating q values. 06/14/2019 02:18 PM (3): Percolator: Final list yields 1117 target peptides with q<0.01. 06/14/2019 02:18 PM (3): Percolator: Calculating posterior error probabilities (PEPs). 06/14/2019 02:18 PM (3): Percolator: Processing took 33.35 cpu seconds or 33 seconds wall clock time. 06/14/2019 02:18 PM (3): Percolator: PSMId score q-value posterior_error_prob peptide proteinIds 06/14/2019 02:18 PM (3): Percolator: 6727/66 high confident target/decoy peptides were found for MS Amanda 2.0 (2). 06/14/2019 02:18 PM (3): Percolator: 592/298 medium confident target/decoy peptides were found for MS Amanda 2.0 (2). 06/14/2019 02:18 PM (3): Percolator: -- Total execution of Percolator (64Bit) for MS Amanda 2.0 (2) took 4 min 41 s -- 06/14/2019 02:18 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 06/14/2019 02:18 PM (5): IMP-ptmRS: More nodes and documentations can be found here http://ms.imp.ac.at/?goto=pd-nodes. 06/14/2019 02:18 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. 06/14/2019 02:18 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. 06/14/2019 02:18 PM (5): IMP-ptmRS: -- Total execution of IMP-ptmRS (5) took 542.9 ms -- 06/14/2019 02:18 PM (4): IMP-apQuant: 8 Processors found 06/14/2019 02:18 PM (4): IMP-apQuant: Start IMP-apQuant Version 3.1.1.16751 06/14/2019 02:18 PM (4): IMP-apQuant: Reading TargetPeptideSpectrumMatch 06/14/2019 02:19 PM (4): IMP-apQuant: Done 06/14/2019 02:19 PM (4): IMP-apQuant: creating file in E:\Work\data_MS_plus_raw\19EDG05\raw 06/14/2019 02:19 PM (4): IMP-apQuant: Collecting Modifications 06/14/2019 02:19 PM (4): IMP-apQuant: Filtering Items 06/14/2019 02:19 PM (4): IMP-apQuant: Calculating Alignment 06/14/2019 02:19 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw 06/14/2019 02:19 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw 06/14/2019 02:19 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (3126 items) 06/14/2019 02:19 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (3014 items) 06/14/2019 02:19 PM (4): IMP-apQuant: Worker 2 Finished Processing 38 items 06/14/2019 02:19 PM (4): IMP-apQuant: Worker 1 Finished Processing 42 items 06/14/2019 02:19 PM (4): IMP-apQuant: Worker 0 Finished Processing 37 items 06/14/2019 02:19 PM (4): IMP-apQuant: Collecting Traces 06/14/2019 02:19 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw 06/14/2019 02:19 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw 06/14/2019 02:20 PM (4): IMP-apQuant: Creating items 06/14/2019 02:20 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (3858 items) 06/14/2019 02:20 PM (4): IMP-apQuant: Creating items 06/14/2019 02:20 PM (4): IMP-apQuant: Creating items 06/14/2019 02:20 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (3855 items) 06/14/2019 02:21 PM (4): IMP-apQuant: Worker 1 Finished Processing 509 items 06/14/2019 02:21 PM (4): IMP-apQuant: Worker 0 Finished Processing 538 items 06/14/2019 02:21 PM (4): IMP-apQuant: Worker 2 Finished Processing 600 items 06/14/2019 02:21 PM (4): IMP-apQuant: Creating items 06/14/2019 02:22 PM (4): IMP-apQuant: Finished writing 06/14/2019 02:22 PM (4): IMP-apQuant: Collecting Decoy Traces 1647 06/14/2019 02:22 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw 06/14/2019 02:22 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw 06/14/2019 02:22 PM (4): IMP-apQuant: Extraction is waiting, 1001 items in the queue 06/14/2019 02:22 PM (4): IMP-apQuant: Extraction is waiting, 1001 items in the queue 06/14/2019 02:22 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw (3579 items) 06/14/2019 02:22 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw (3599 items) 06/14/2019 02:24 PM (4): IMP-apQuant: Worker 0 Finished Processing 500 items 06/14/2019 02:24 PM (4): IMP-apQuant: Worker 1 Finished Processing 547 items 06/14/2019 02:25 PM (4): IMP-apQuant: Worker 2 Finished Processing 600 items 06/14/2019 02:26 PM (4): IMP-apQuant: Finished writing 06/14/2019 02:26 PM (4): IMP-apQuant: Calculating Areas 06/14/2019 02:26 PM (4): IMP-apQuant: It took me 00:07:03.0529339 seconds to finish the task 06/14/2019 02:26 PM (4): IMP-apQuant: Calculating Scores 06/14/2019 02:26 PM (4): IMP-apQuant: Calculating Scores 06/14/2019 02:27 PM (4): IMP-apQuant: Reading features from table 06/14/2019 02:27 PM (4): IMP-apQuant: Creating Percolator input 06/14/2019 02:27 PM (4): IMP-apQuant: Starting Percolator 06/14/2019 02:27 PM (4): IMP-apQuant: Percolator version 3.01, Build Date Nov 16 2016 08:44:38 06/14/2019 02:27 PM (4): IMP-apQuant: Copyright (c) 2006-9 University of Washington. All rights reserved. 06/14/2019 02:27 PM (4): IMP-apQuant: Written by Lukas K├ñll (lukall@u.washington.edu) in the 06/14/2019 02:27 PM (4): IMP-apQuant: Department of Genome Sciences at the University of Washington. 06/14/2019 02:27 PM (4): IMP-apQuant: Issued command: 06/14/2019 02:27 PM (4): IMP-apQuant: C:\Program Files\Thermo\Proteome Discoverer 2.3\Tools\apQuant\percolator.exe C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job65\IMPapQ(4)\percoInput.txt -m C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job65\IMPapQ(4)\percoOutput_Target.txt -M C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job65\IMPapQ(4)\percoOutput_Decoy.txt -U -Y 06/14/2019 02:27 PM (4): IMP-apQuant: Started Fri Jun 14 14:27:37 2019 06/14/2019 02:27 PM (4): IMP-apQuant: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 06/14/2019 02:27 PM (4): IMP-apQuant: Reading tab-delimited input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job65\IMPapQ(4)\percoInput.txt 06/14/2019 02:27 PM (4): IMP-apQuant: Features: 06/14/2019 02:27 PM (4): IMP-apQuant: DeltaT1 DeltaT2 DeltaM1 DeltaM2 RMSD F1 F2 F3 F4 distF N/S Score 06/14/2019 02:27 PM (4): IMP-apQuant: Found 6588 PSMs 06/14/2019 02:27 PM (4): IMP-apQuant: Concatenated search input detected, skipping both target-decoy competition and mix-max. 06/14/2019 02:27 PM (4): IMP-apQuant: Train/test set contains 3294 positives and 3294 negatives, size ratio=1 and pi0=1 06/14/2019 02:27 PM (4): IMP-apQuant: Selecting Cpos by cross-validation. 06/14/2019 02:27 PM (4): IMP-apQuant: Selecting Cneg by cross-validation. 06/14/2019 02:27 PM (4): IMP-apQuant: Split 1: Exception caught: Error in the input data: cannot find an initial direction with positive training examples. Consider raising the training FDR threshold (-F flag). 06/14/2019 02:27 PM (4): IMP-apQuant: Terminating. 06/14/2019 02:27 PM (4): IMP-apQuant: 06/14/2019 02:27 PM (4): IMP-apQuant: Finished Percolator 06/14/2019 02:27 PM (4): IMP-apQuant: Percolator could not process the dataset. Falling back to other method. See the verbose output for more information 06/14/2019 02:27 PM (4): IMP-apQuant: Calculating Scores 06/14/2019 02:28 PM (4): IMP-apQuant: IMP-apQuant finished in 0:9:25 06/14/2019 02:28 PM (4): IMP-apQuant: -- Total execution of IMP-apQuant (4) took 9 min 25 s -- 06/14/2019 02:28 PM (6): Minora Feature Detector: Start detecting lcmspeaks... 06/14/2019 02:28 PM (6): Minora Feature Detector: Running 2 jobs with 2 jobs in parallel. 06/14/2019 02:28 PM (6): Minora Feature Detector: Start F14 with 'FTMS + p NSI Full ms [350.0000-1850.0000]' 06/14/2019 02:28 PM (6): Minora Feature Detector: Start F3 with 'FTMS + p NSI Full ms [350.0000-1850.0000]' 06/14/2019 02:35 PM (6): Minora Feature Detector: Detecting LcmsPeaks took 7 min 9 s 06/14/2019 02:35 PM (6): Minora Feature Detector: Start processing F3: '190328_EDG_Fus_19EDG05_aDn7iso-13d-Tryp.raw'. 06/14/2019 02:35 PM (6): Minora Feature Detector: Start processing F14: '190328_EDG_Fus_19EDG05_aDn7ser-13d-Tryp.raw'. 06/14/2019 02:35 PM (6): Minora Feature Detector: Importing peaks for F3 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])... 06/14/2019 02:35 PM (6): Minora Feature Detector: Importing peaks for F14 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])... 06/14/2019 02:35 PM (6): Minora Feature Detector: F3: Found 186494 chromatographic peaks. 06/14/2019 02:35 PM (6): Minora Feature Detector: F14: Found 234305 chromatographic peaks. 06/14/2019 02:35 PM (6): Minora Feature Detector: F3: Importing auto traces... 06/14/2019 02:35 PM (6): Minora Feature Detector: F3: Imported 125889 auto traces. 06/14/2019 02:35 PM (6): Minora Feature Detector: F14: Importing auto traces... 06/14/2019 02:36 PM (6): Minora Feature Detector: F14: Imported 150740 auto traces. 06/14/2019 02:36 PM (6): Minora Feature Detector: Importing peak to spectrum links... 06/14/2019 02:37 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 16 s 06/14/2019 02:37 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 31 s 06/14/2019 02:39 PM (6): Minora Feature Detector: Found 4068 features (F3: 1909, F14: 2159) 06/14/2019 02:39 PM (6): Minora Feature Detector: Writing data took 3.9 s. 06/14/2019 02:39 PM (6): Minora Feature Detector: Creating features for PSMs took 12.5 s. 06/14/2019 02:40 PM (6): Minora Feature Detector: F3: Unidentified feature detection took 31.8 s 06/14/2019 02:40 PM (6): Minora Feature Detector: F14: Unidentified feature detection took 39.5 s 06/14/2019 02:40 PM (6): Minora Feature Detector: Found 85216 unidentified features (F3 : 37107, F14 : 48109). 06/14/2019 02:40 PM (6): Minora Feature Detector: -- Total execution of Minora Feature Detector (6) took 12 min 15 s -- 06/14/2019 02:40 PM Job Execution: Finished E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\19EDG05-06_aDn2-4_SERISO-Tryp-(2).msf 06/14/2019 02:40 PM Job Execution: ----- Total Job execution took: 45 min 36 s. ----- ================================================================================ Processing Step B: Workflow ================================================================================ Result name: 190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo Result file: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo-(2).msf Description: Ab_Quan_Chymo Workflow based on template: Ab_Quan_Chymo Creation date: 6/14/2019 1:54:52 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_aDn7iso-13d-Chymo.raw E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.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: BCR-donor-133573_2013_Sanger.fasta 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: Chymotrypsin (Full) - Missed Cleavages: 3 - 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 2.0: 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: ------------------------------------------------------------------ 06/14/2019 01:54 PM Job Execution: Processing E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo-(2).msf 06/14/2019 01:54 PM (1): Spectrum Selector: Profile spectra are not sent. 06/14/2019 01:55 PM (1): Spectrum Selector: Reading from file 1 of 2 F1: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw (27890 spectra total) 06/14/2019 01:55 PM (2): MS Amanda 2.0: Starting MS Amanda search version 2.3.0.12368, Engine version 2.0.0.12368 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Loading database 06/14/2019 01:55 PM (2): MS Amanda 2.0: Loading database done 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 01:57 PM (2): MS Amanda 2.0: Scored 16339 peptide hits and 15537 decoy peptide hits in 81.03 sec 06/14/2019 01:57 PM (2): MS Amanda 2.0: Stored 9095 PSMs for 7073 spectra 06/14/2019 01:57 PM (2): MS Amanda 2.0: Stored 9083 decoy PSMs for 6917 spectra 06/14/2019 02:01 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:01 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:01 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:01 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:01 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:01 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:01 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:01 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:01 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:01 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:02 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:02 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:04 PM (2): MS Amanda 2.0: Scored 20228 peptide hits and 17914 decoy peptide hits in 137.41 sec 06/14/2019 02:04 PM (2): MS Amanda 2.0: Stored 10538 PSMs for 8729 spectra 06/14/2019 02:04 PM (2): MS Amanda 2.0: Stored 10314 decoy PSMs for 8464 spectra 06/14/2019 02:05 PM (1): Spectrum Selector: Sent 23301 spectra from file F1. 06/14/2019 02:05 PM (1): Spectrum Selector: Reading from file 2 of 2 F11: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw (25302 spectra total) 06/14/2019 02:06 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:06 PM (2): MS Amanda 2.0: Searching 10301 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:06 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:06 PM (2): MS Amanda 2.0: Searching 10301 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:06 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:06 PM (2): MS Amanda 2.0: Searching 10301 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:06 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:06 PM (2): MS Amanda 2.0: Searching 10301 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:06 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:06 PM (2): MS Amanda 2.0: Searching 10301 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:06 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:06 PM (2): MS Amanda 2.0: Searching 10301 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Scored 13879 peptide hits and 12834 decoy peptide hits in 58.44 sec 06/14/2019 02:07 PM (2): MS Amanda 2.0: Stored 7764 PSMs for 5786 spectra 06/14/2019 02:08 PM (2): MS Amanda 2.0: Stored 7722 decoy PSMs for 5714 spectra 06/14/2019 02:09 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:09 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:09 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:09 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:09 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:09 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:09 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:11 PM (2): MS Amanda 2.0: Scored 21301 peptide hits and 18691 decoy peptide hits in 102.09 sec 06/14/2019 02:11 PM (2): MS Amanda 2.0: Stored 11429 PSMs for 9048 spectra 06/14/2019 02:11 PM (2): MS Amanda 2.0: Stored 11335 decoy PSMs for 8707 spectra 06/14/2019 02:12 PM (1): Spectrum Selector: Sent 20701 spectra from file F11. 06/14/2019 02:12 PM (1): Spectrum Selector: Sent 44002 spectra from 2 files (processing time: 3 min 7 s). 06/14/2019 02:12 PM (1): Spectrum Selector: -- Total execution of Spectrum Selector (1) took 17 min 37 s -- 06/14/2019 02:12 PM (2): MS Amanda 2.0: Storing spectra took 4 min 0 s. 06/14/2019 02:12 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:12 PM (2): MS Amanda 2.0: Searching 3701 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:12 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:12 PM (2): MS Amanda 2.0: Searching 3701 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:12 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:12 PM (2): MS Amanda 2.0: Searching 3701 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:12 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:12 PM (2): MS Amanda 2.0: Searching 3701 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:12 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:12 PM (2): MS Amanda 2.0: Searching 3701 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:12 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:12 PM (2): MS Amanda 2.0: Searching 3701 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:13 PM (2): MS Amanda 2.0: Scored 4939 peptide hits and 4647 decoy peptide hits in 42.08 sec 06/14/2019 02:13 PM (2): MS Amanda 2.0: Stored 2662 PSMs for 2183 spectra 06/14/2019 02:13 PM (2): MS Amanda 2.0: Stored 2682 decoy PSMs for 2165 spectra 06/14/2019 02:13 PM (2): MS Amanda 2.0: Finalizing search results... 06/14/2019 02:14 PM (2): MS Amanda 2.0: -- Total search time was 11 min 28 s -- 06/14/2019 02:19 PM (3): Percolator: Creating input file for MS Amanda 2.0 (2) took 4 min 5 s. 06/14/2019 02:19 PM (3): Percolator: The input file contains 19962 PSMs, 14962 decoy PSMs and 32 features. 06/14/2019 02:19 PM (3): Percolator: Generated percolator input for concatenated mode 06/14/2019 02:19 PM (3): Percolator: Percolator version 3.02.1, Build Date Aug 14 2018 00:44:01 06/14/2019 02:19 PM (3): Percolator: Copyright (c) 2006-9 University of Washington. All rights reserved. 06/14/2019 02:19 PM (3): Percolator: Written by Lukas K├ñll (lukall@u.washington.edu) in the 06/14/2019 02:19 PM (3): Percolator: Department of Genome Sciences at the University of Washington. 06/14/2019 02:19 PM (3): Percolator: Issued command: 06/14/2019 02:19 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\Job66\Percol(3)\output.xml -Z -I auto -k C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job66\Percol(3)\input.xml 06/14/2019 02:19 PM (3): Percolator: Started Fri Jun 14 14:19:05 2019 06/14/2019 02:19 PM (3): Percolator: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 06/14/2019 02:19 PM (3): Percolator: Reading pin-xml input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job66\Percol(3)\input.xml 06/14/2019 02:19 PM (3): Percolator: enzyme=Trypsin 06/14/2019 02:19 PM (3): Percolator: Features: 06/14/2019 02:19 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] 06/14/2019 02:19 PM (3): Percolator: Concatenated search input detected, skipping both target-decoy competition and mix-max. 06/14/2019 02:19 PM (3): Percolator: Train/test set contains 19962 positives and 14962 negatives, size ratio=1.33418 and pi0=1 06/14/2019 02:19 PM (3): Percolator: Selecting Cpos by cross-validation. 06/14/2019 02:19 PM (3): Percolator: Selecting Cneg by cross-validation. 06/14/2019 02:19 PM (3): Percolator: Split 1: Selected feature 3 as initial direction. Could separate 1658 training set positives with q<0.01 in that direction. 06/14/2019 02:19 PM (3): Percolator: Split 2: Selected feature 3 as initial direction. Could separate 1767 training set positives with q<0.01 in that direction. 06/14/2019 02:19 PM (3): Percolator: Split 3: Selected feature 3 as initial direction. Could separate 1649 training set positives with q<0.01 in that direction. 06/14/2019 02:19 PM (3): Percolator: Found 2454 test set positives with q<0.01 in initial direction 06/14/2019 02:19 PM (3): Percolator: Reading in data and feature calculation took 18.522 cpu seconds or 18 seconds wall clock time. 06/14/2019 02:19 PM (3): Percolator: ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 1: Estimated 3601 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 2: Estimated 3891 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 3: Estimated 4002 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 4: Estimated 4014 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 5: Estimated 4076 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 6: Estimated 4112 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 7: Estimated 4109 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 8: Estimated 4107 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 9: Estimated 4109 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Iteration 10: Estimated 4108 PSMs with q<0.01 06/14/2019 02:19 PM (3): Percolator: Learned normalized SVM weights for the 3 cross-validation splits: 06/14/2019 02:19 PM (3): Percolator: Split1 Split2 Split3 FeatureName 06/14/2019 02:19 PM (3): Percolator: 0.6905 0.5099 0.7604 CharmeRTCombinedScore 06/14/2019 02:19 PM (3): Percolator: 0.1642 0.1957 0.2376 Delta Cn From Second PSM 06/14/2019 02:19 PM (3): Percolator: 3.3286 2.9599 3.3101 Binomial Score 06/14/2019 02:19 PM (3): Percolator: 0.3590 0.5558 0.3241 Isolation Interference [%] 06/14/2019 02:19 PM (3): Percolator: 1.3837 0.6597 1.1201 MH+ [Da] 06/14/2019 02:19 PM (3): Percolator: 0.6508 -0.2616 0.1751 Delta Mass [Da] 06/14/2019 02:19 PM (3): Percolator: -1.2593 0.3275 -1.4579 Delta Mass [ppm] 06/14/2019 02:19 PM (3): Percolator: -1.9543 -0.8252 -3.1900 Absolute Delta Mass [Da] 06/14/2019 02:19 PM (3): Percolator: -1.4537 -0.9180 -0.1091 Absolute Delta Mass [ppm] 06/14/2019 02:19 PM (3): Percolator: -1.3236 -0.5091 -0.9554 Peptide Length 06/14/2019 02:19 PM (3): Percolator: 0.0000 0.0000 0.0000 Is z=1 06/14/2019 02:19 PM (3): Percolator: -0.2419 -0.2361 -0.2331 Is z=2 06/14/2019 02:19 PM (3): Percolator: 0.2347 0.2036 0.2258 Is z=3 06/14/2019 02:19 PM (3): Percolator: 0.0363 0.0986 0.0353 Is z=4 06/14/2019 02:19 PM (3): Percolator: 0.0123 0.0678 0.0132 Is z=5 06/14/2019 02:19 PM (3): Percolator: 0.0298 0.0187 0.0354 Is z>5 06/14/2019 02:19 PM (3): Percolator: -0.1422 -0.2605 -0.3747 # Missed Cleavages 06/14/2019 02:19 PM (3): Percolator: 0.0000 0.0000 0.0000 Log Peptides Matched 06/14/2019 02:19 PM (3): Percolator: -0.0106 -0.1431 -0.0578 Log Total Intensity 06/14/2019 02:19 PM (3): Percolator: 0.5315 0.2794 0.4196 Fraction Matched Intensity [%] 06/14/2019 02:19 PM (3): Percolator: -0.9607 -0.6219 -1.0029 Fragment Coverage Series A, B, C [%] 06/14/2019 02:19 PM (3): Percolator: -1.1390 -0.9353 -1.0913 Fragment Coverage Series X, Y, Z [%] 06/14/2019 02:19 PM (3): Percolator: -0.4452 -0.3329 -0.2709 Log Matched Fragment Series Intensities A, B, C 06/14/2019 02:19 PM (3): Percolator: -0.9982 -0.7343 -1.1193 Log Matched Fragment Series Intensities X, Y, Z 06/14/2019 02:19 PM (3): Percolator: 0.1898 -0.0676 0.1068 Longest Sequence Series A, B, C 06/14/2019 02:19 PM (3): Percolator: 0.5198 0.6483 0.6285 Longest Sequence Series X, Y, Z 06/14/2019 02:19 PM (3): Percolator: -0.9421 -0.8871 -1.0498 IQR Fragment Delta Mass [Da] 06/14/2019 02:19 PM (3): Percolator: 0.3150 0.4606 0.4425 IQR Fragment Delta Mass [ppm] 06/14/2019 02:19 PM (3): Percolator: -0.5067 -0.4541 -0.0553 Mean Fragment Delta Mass [Da] 06/14/2019 02:19 PM (3): Percolator: 0.1238 0.1053 -0.2575 Mean Fragment Delta Mass [ppm] 06/14/2019 02:19 PM (3): Percolator: -1.1780 -1.2632 -0.9961 Mean Absolute Fragment Delta Mass [Da] 06/14/2019 02:19 PM (3): Percolator: 0.3423 0.2103 0.1503 Mean Absolute Fragment Delta Mass [ppm] 06/14/2019 02:19 PM (3): Percolator: -6.7890 -5.1111 -6.6156 m0 06/14/2019 02:19 PM (3): Percolator: Found 3876 test set PSMs with q<0.01. 06/14/2019 02:20 PM (3): Percolator: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. 06/14/2019 02:20 PM (3): Percolator: Calculating q values. 06/14/2019 02:20 PM (3): Percolator: Final list yields 701 target peptides with q<0.01. 06/14/2019 02:20 PM (3): Percolator: Calculating posterior error probabilities (PEPs). 06/14/2019 02:20 PM (3): Percolator: Processing took 68.95 cpu seconds or 69 seconds wall clock time. 06/14/2019 02:20 PM (3): Percolator: PSMId score q-value posterior_error_prob peptide proteinIds 06/14/2019 02:21 PM (3): Percolator: 3879/37 high confident target/decoy peptides were found for MS Amanda 2.0 (2). 06/14/2019 02:21 PM (3): Percolator: 825/197 medium confident target/decoy peptides were found for MS Amanda 2.0 (2). 06/14/2019 02:21 PM (3): Percolator: -- Total execution of Percolator (64Bit) for MS Amanda 2.0 (2) took 6 min 22 s -- 06/14/2019 02:21 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 06/14/2019 02:21 PM (5): IMP-ptmRS: More nodes and documentations can be found here http://ms.imp.ac.at/?goto=pd-nodes. 06/14/2019 02:21 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 02:21 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 02:21 PM (5): IMP-ptmRS: -- Total execution of IMP-ptmRS (5) took 413.8 ms -- 06/14/2019 02:21 PM (4): IMP-apQuant: 8 Processors found 06/14/2019 02:21 PM (4): IMP-apQuant: Start IMP-apQuant Version 3.1.1.16751 06/14/2019 02:21 PM (4): IMP-apQuant: Reading TargetPeptideSpectrumMatch 06/14/2019 02:21 PM (4): IMP-apQuant: Done 06/14/2019 02:21 PM (4): IMP-apQuant: creating file in E:\Work\data_MS_plus_raw\19EDG05\raw 06/14/2019 02:21 PM (4): IMP-apQuant: Collecting Modifications 06/14/2019 02:21 PM (4): IMP-apQuant: Filtering Items 06/14/2019 02:21 PM (4): IMP-apQuant: Calculating Alignment 06/14/2019 02:21 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw 06/14/2019 02:21 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw 06/14/2019 02:22 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw (3089 items) 06/14/2019 02:22 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw (3138 items) 06/14/2019 02:22 PM (4): IMP-apQuant: Worker 1 Finished Processing 37 items 06/14/2019 02:22 PM (4): IMP-apQuant: Worker 0 Finished Processing 37 items 06/14/2019 02:22 PM (4): IMP-apQuant: Worker 2 Finished Processing 42 items 06/14/2019 02:22 PM (4): IMP-apQuant: Collecting Traces 06/14/2019 02:22 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw 06/14/2019 02:22 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw 06/14/2019 02:23 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw (3255 items) 06/14/2019 02:23 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw (3058 items) 06/14/2019 02:23 PM (4): IMP-apQuant: Creating items 06/14/2019 02:23 PM (4): IMP-apQuant: Worker 1 Finished Processing 300 items 06/14/2019 02:23 PM (4): IMP-apQuant: Worker 2 Finished Processing 300 items 06/14/2019 02:25 PM (4): IMP-apQuant: Worker 0 Finished Processing 386 items 06/14/2019 02:25 PM (4): IMP-apQuant: Creating items 06/14/2019 02:25 PM (4): IMP-apQuant: Finished writing 06/14/2019 02:25 PM (4): IMP-apQuant: Collecting Decoy Traces 986 06/14/2019 02:25 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw 06/14/2019 02:25 PM (4): IMP-apQuant: Started reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw 06/14/2019 02:26 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw (2854 items) 06/14/2019 02:28 PM (4): IMP-apQuant: Finished reading file 190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw (3048 items) 06/14/2019 02:28 PM (4): IMP-apQuant: Worker 2 Finished Processing 300 items 06/14/2019 02:28 PM (4): IMP-apQuant: Worker 0 Finished Processing 300 items 06/14/2019 02:29 PM (4): IMP-apQuant: Worker 1 Finished Processing 386 items 06/14/2019 02:29 PM (4): IMP-apQuant: Finished writing 06/14/2019 02:29 PM (4): IMP-apQuant: Calculating Areas 06/14/2019 02:29 PM (4): IMP-apQuant: It took me 00:07:49.8507705 seconds to finish the task 06/14/2019 02:29 PM (4): IMP-apQuant: Calculating Scores 06/14/2019 02:29 PM (4): IMP-apQuant: Calculating Scores 06/14/2019 02:29 PM (4): IMP-apQuant: Reading features from table 06/14/2019 02:29 PM (4): IMP-apQuant: Creating Percolator input 06/14/2019 02:29 PM (4): IMP-apQuant: Starting Percolator 06/14/2019 02:29 PM (4): IMP-apQuant: Percolator version 3.01, Build Date Nov 16 2016 08:44:38 06/14/2019 02:29 PM (4): IMP-apQuant: Copyright (c) 2006-9 University of Washington. All rights reserved. 06/14/2019 02:29 PM (4): IMP-apQuant: Written by Lukas K├ñll (lukall@u.washington.edu) in the 06/14/2019 02:29 PM (4): IMP-apQuant: Department of Genome Sciences at the University of Washington. 06/14/2019 02:29 PM (4): IMP-apQuant: Issued command: 06/14/2019 02:29 PM (4): IMP-apQuant: C:\Program Files\Thermo\Proteome Discoverer 2.3\Tools\apQuant\percolator.exe C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job66\IMPapQ(4)\percoInput.txt -m C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job66\IMPapQ(4)\percoOutput_Target.txt -M C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job66\IMPapQ(4)\percoOutput_Decoy.txt -U -Y 06/14/2019 02:29 PM (4): IMP-apQuant: Started Fri Jun 14 14:29:22 2019 06/14/2019 02:29 PM (4): IMP-apQuant: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 06/14/2019 02:29 PM (4): IMP-apQuant: Reading tab-delimited input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job66\IMPapQ(4)\percoInput.txt 06/14/2019 02:29 PM (4): IMP-apQuant: Features: 06/14/2019 02:29 PM (4): IMP-apQuant: DeltaT1 DeltaT2 DeltaM1 DeltaM2 RMSD F1 F2 F3 F4 distF N/S Score 06/14/2019 02:29 PM (4): IMP-apQuant: Found 3944 PSMs 06/14/2019 02:29 PM (4): IMP-apQuant: Concatenated search input detected, skipping both target-decoy competition and mix-max. 06/14/2019 02:29 PM (4): IMP-apQuant: Train/test set contains 1972 positives and 1972 negatives, size ratio=1 and pi0=1 06/14/2019 02:29 PM (4): IMP-apQuant: Selecting Cpos by cross-validation. 06/14/2019 02:29 PM (4): IMP-apQuant: Selecting Cneg by cross-validation. 06/14/2019 02:29 PM (4): IMP-apQuant: Split 1: Exception caught: Error in the input data: cannot find an initial direction with positive training examples. Consider raising the training FDR threshold (-F flag). 06/14/2019 02:29 PM (4): IMP-apQuant: Terminating. 06/14/2019 02:29 PM (4): IMP-apQuant: 06/14/2019 02:29 PM (4): IMP-apQuant: Finished Percolator 06/14/2019 02:29 PM (4): IMP-apQuant: Percolator could not process the dataset. Falling back to other method. See the verbose output for more information 06/14/2019 02:29 PM (4): IMP-apQuant: Calculating Scores 06/14/2019 02:29 PM (4): IMP-apQuant: IMP-apQuant finished in 0:8:5 06/14/2019 02:29 PM (4): IMP-apQuant: -- Total execution of IMP-apQuant (4) took 8 min 5 s -- 06/14/2019 02:29 PM (6): Minora Feature Detector: Start detecting lcmspeaks... 06/14/2019 02:29 PM (6): Minora Feature Detector: Running 2 jobs with 2 jobs in parallel. 06/14/2019 02:29 PM (6): Minora Feature Detector: Start F11 with 'FTMS + p NSI Full ms [350.0000-1850.0000]' 06/14/2019 02:29 PM (6): Minora Feature Detector: Start F1 with 'FTMS + p NSI Full ms [350.0000-1850.0000]' 06/14/2019 02:36 PM (6): Minora Feature Detector: Detecting LcmsPeaks took 7 min 13 s 06/14/2019 02:36 PM (6): Minora Feature Detector: Start processing F1: '190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo.raw'. 06/14/2019 02:36 PM (6): Minora Feature Detector: Start processing F11: '190328_EDG_Fus_19EDG05_aDn7ser-13d-Chymo.raw'. 06/14/2019 02:36 PM (6): Minora Feature Detector: Importing peaks for F1 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])... 06/14/2019 02:36 PM (6): Minora Feature Detector: Importing peaks for F11 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])... 06/14/2019 02:36 PM (6): Minora Feature Detector: F1: Found 235870 chromatographic peaks. 06/14/2019 02:36 PM (6): Minora Feature Detector: F11: Found 248962 chromatographic peaks. 06/14/2019 02:36 PM (6): Minora Feature Detector: F1: Importing auto traces... 06/14/2019 02:36 PM (6): Minora Feature Detector: F1: Imported 158580 auto traces. 06/14/2019 02:37 PM (6): Minora Feature Detector: F11: Importing auto traces... 06/14/2019 02:37 PM (6): Minora Feature Detector: F11: Imported 157696 auto traces. 06/14/2019 02:37 PM (6): Minora Feature Detector: Importing peak to spectrum links... 06/14/2019 02:38 PM (6): Minora Feature Detector: F1: Standard deviations: m/z 4.72; RT 0.10; Intensity 59.61; Fraction Missing Intensity 0.20; Shoulder Score 0.000; Peak Length Score 0.0332505905798622 took 48.3 s 06/14/2019 02:38 PM (6): Minora Feature Detector: F11: Standard deviations: m/z 5.37; RT 0.11; Intensity 68.07; Fraction Missing Intensity 0.20; Shoulder Score 0.000; Peak Length Score 0.0479395129262796 took 51.4 s 06/14/2019 02:40 PM (6): Minora Feature Detector: Found 2441 features (F11: 1011, F1: 1430) 06/14/2019 02:40 PM (6): Minora Feature Detector: Writing data took 6.5 s. 06/14/2019 02:40 PM (6): Minora Feature Detector: Creating features for PSMs took 23.1 s. 06/14/2019 02:41 PM (6): Minora Feature Detector: F1: Unidentified feature detection took 42.8 s 06/14/2019 02:41 PM (6): Minora Feature Detector: F11: Unidentified feature detection took 48.7 s 06/14/2019 02:41 PM (6): Minora Feature Detector: Found 101543 unidentified features (F1 : 48639, F11 : 52904). 06/14/2019 02:41 PM (6): Minora Feature Detector: -- Total execution of Minora Feature Detector (6) took 11 min 58 s -- 06/14/2019 02:41 PM Job Execution: Finished E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Chymo-(2).msf 06/14/2019 02:41 PM Job Execution: ----- Total Job execution took: 46 min 34 s. ----- ================================================================================ Processing Step C: Workflow ================================================================================ Result name: 190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C Result file: E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C-(1).msf Description: Ab_Quan_GluC Workflow based on template: Ab_Quan_GluC Creation date: 6/14/2019 1:54:53 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_aDn7iso-13d-Glu-C.raw E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-13d-Glu-C.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: BCR-donor-133573_2013_Sanger.fasta 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: GluC (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: ------------------------------------------------------------------ 06/14/2019 01:54 PM Job Execution: Processing E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C-(1).msf 06/14/2019 01:55 PM (1): Spectrum Selector: Profile spectra are not sent. 06/14/2019 01:55 PM (1): Spectrum Selector: Reading from file 1 of 2 F2: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C.raw (25099 spectra total) 06/14/2019 01:55 PM (2): MS Amanda 2.0: Starting MS Amanda search version 2.3.0.12368, Engine version 2.0.0.12368 06/14/2019 01:55 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:55 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 01:55 PM (2): MS Amanda 2.0: Loading database 06/14/2019 01:56 PM (2): MS Amanda 2.0: Loading database done 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:56 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 01:56 PM (2): MS Amanda 2.0: Scored 15729 peptide hits and 14727 decoy peptide hits in 27.94 sec 06/14/2019 01:57 PM (2): MS Amanda 2.0: Stored 8922 PSMs for 6218 spectra 06/14/2019 01:57 PM (2): MS Amanda 2.0: Stored 8839 decoy PSMs for 6087 spectra 06/14/2019 01:58 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:58 PM (2): MS Amanda 2.0: Searching 10000 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 01:58 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:58 PM (2): MS Amanda 2.0: Searching 10000 spectra in common_contaminants.fasta and decoy database. 06/14/2019 01:58 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:58 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 01:59 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 01:59 PM (2): MS Amanda 2.0: Searching 10000 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:00 PM (2): MS Amanda 2.0: Scored 16721 peptide hits and 15088 decoy peptide hits in 111.33 sec 06/14/2019 02:01 PM (2): MS Amanda 2.0: Stored 9014 PSMs for 7392 spectra 06/14/2019 02:01 PM (2): MS Amanda 2.0: Stored 8731 decoy PSMs for 7159 spectra 06/14/2019 02:02 PM (1): Spectrum Selector: Sent 20223 spectra from file F2. 06/14/2019 02:02 PM (1): Spectrum Selector: Reading from file 2 of 2 F13: E:\Work\data_MS_plus_raw\19EDG05\raw\190328_EDG_Fus_19EDG05_aDn7ser-13d-Glu-C.raw (24041 spectra total) 06/14/2019 02:04 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:04 PM (2): MS Amanda 2.0: Searching 10223 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:04 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:04 PM (2): MS Amanda 2.0: Searching 10223 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:04 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:04 PM (2): MS Amanda 2.0: Searching 10223 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:04 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:04 PM (2): MS Amanda 2.0: Searching 10223 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:04 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:04 PM (2): MS Amanda 2.0: Searching 10223 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:04 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:04 PM (2): MS Amanda 2.0: Searching 10223 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:05 PM (2): MS Amanda 2.0: Scored 13075 peptide hits and 12273 decoy peptide hits in 33.05 sec 06/14/2019 02:05 PM (2): MS Amanda 2.0: Stored 7851 PSMs for 5003 spectra 06/14/2019 02:05 PM (2): MS Amanda 2.0: Stored 7734 decoy PSMs for 4926 spectra 06/14/2019 02:07 PM (1): Spectrum Selector: Sent 18856 spectra from file F13. 06/14/2019 02:07 PM (1): Spectrum Selector: Sent 39079 spectra from 2 files (processing time: 2 min 42 s). 06/14/2019 02:07 PM (1): Spectrum Selector: -- Total execution of Spectrum Selector (1) took 12 min 19 s -- 06/14/2019 02:07 PM (2): MS Amanda 2.0: Storing spectra took 2 min 20 s. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:07 PM (2): MS Amanda 2.0: Searching 8856 spectra in BCR-donor-133573_2013_Sanger.fasta and decoy database. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:07 PM (2): MS Amanda 2.0: Searching 8856 spectra in common_contaminants.fasta and decoy database. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:07 PM (2): MS Amanda 2.0: Searching 8856 spectra in IMGT-Human-IGHV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:07 PM (2): MS Amanda 2.0: Searching 8856 spectra in IMGT-Human-IGKV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:07 PM (2): MS Amanda 2.0: Searching 8856 spectra in IMGT-Human-IGLV-genes_20190403_noSTOP.fasta and decoy database. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Identifying Peptides 06/14/2019 02:07 PM (2): MS Amanda 2.0: Searching 8856 spectra in uniprot-Human-canonical-noIGHV-IGKV-IGLV-UP000005640_20181213.fasta and decoy database. 06/14/2019 02:07 PM (2): MS Amanda 2.0: Scored 12632 peptide hits and 11380 decoy peptide hits in 29.54 sec 06/14/2019 02:07 PM (2): MS Amanda 2.0: Stored 7165 PSMs for 5629 spectra 06/14/2019 02:08 PM (2): MS Amanda 2.0: Stored 6920 decoy PSMs for 5420 spectra 06/14/2019 02:08 PM (2): MS Amanda 2.0: Finalizing search results... 06/14/2019 02:09 PM (2): MS Amanda 2.0: -- Total search time was 7 min 25 s -- 06/14/2019 02:12 PM (3): Percolator: Creating input file for MS Amanda 2.0 (2) took 2 min 43 s. 06/14/2019 02:12 PM (3): Percolator: The input file contains 14189 PSMs, 11934 decoy PSMs and 32 features. 06/14/2019 02:12 PM (3): Percolator: Generated percolator input for concatenated mode 06/14/2019 02:12 PM (3): Percolator: Percolator version 3.02.1, Build Date Aug 14 2018 00:44:01 06/14/2019 02:12 PM (3): Percolator: Copyright (c) 2006-9 University of Washington. All rights reserved. 06/14/2019 02:12 PM (3): Percolator: Written by Lukas K├ñll (lukall@u.washington.edu) in the 06/14/2019 02:12 PM (3): Percolator: Department of Genome Sciences at the University of Washington. 06/14/2019 02:12 PM (3): Percolator: Issued command: 06/14/2019 02:12 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\Job67\Percol(3)\output.xml -Z -I auto -k C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job67\Percol(3)\input.xml 06/14/2019 02:12 PM (3): Percolator: Started Fri Jun 14 14:12:22 2019 06/14/2019 02:12 PM (3): Percolator: Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 06/14/2019 02:12 PM (3): Percolator: Reading pin-xml input from datafile C:\ProgramData\Thermo\Proteome Discoverer 2.3\Scratch\Job67\Percol(3)\input.xml 06/14/2019 02:12 PM (3): Percolator: enzyme=Trypsin 06/14/2019 02:12 PM (3): Percolator: Features: 06/14/2019 02:12 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] 06/14/2019 02:12 PM (3): Percolator: Concatenated search input detected, skipping both target-decoy competition and mix-max. 06/14/2019 02:12 PM (3): Percolator: Train/test set contains 14189 positives and 11934 negatives, size ratio=1.18896 and pi0=1 06/14/2019 02:12 PM (3): Percolator: Selecting Cpos by cross-validation. 06/14/2019 02:12 PM (3): Percolator: Selecting Cneg by cross-validation. 06/14/2019 02:12 PM (3): Percolator: Split 1: Selected feature 3 as initial direction. Could separate 641 training set positives with q<0.01 in that direction. 06/14/2019 02:12 PM (3): Percolator: Split 2: Selected feature 3 as initial direction. Could separate 711 training set positives with q<0.01 in that direction. 06/14/2019 02:12 PM (3): Percolator: Split 3: Selected feature 3 as initial direction. Could separate 673 training set positives with q<0.01 in that direction. 06/14/2019 02:12 PM (3): Percolator: Found 976 test set positives with q<0.01 in initial direction 06/14/2019 02:12 PM (3): Percolator: Reading in data and feature calculation took 6.378 cpu seconds or 6 seconds wall clock time. 06/14/2019 02:12 PM (3): Percolator: ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 1: Estimated 1535 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 2: Estimated 1650 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 3: Estimated 1697 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 4: Estimated 1703 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 5: Estimated 1704 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 6: Estimated 1709 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 7: Estimated 1712 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 8: Estimated 1706 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 9: Estimated 1712 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Iteration 10: Estimated 1718 PSMs with q<0.01 06/14/2019 02:12 PM (3): Percolator: Learned normalized SVM weights for the 3 cross-validation splits: 06/14/2019 02:12 PM (3): Percolator: Split1 Split2 Split3 FeatureName 06/14/2019 02:12 PM (3): Percolator: 0.0937 0.3876 0.0755 CharmeRTCombinedScore 06/14/2019 02:12 PM (3): Percolator: -0.1023 1.3207 0.8126 Delta Cn From Second PSM 06/14/2019 02:12 PM (3): Percolator: 3.2963 4.8619 4.4114 Binomial Score 06/14/2019 02:12 PM (3): Percolator: 0.3428 0.6671 0.5508 Isolation Interference [%] 06/14/2019 02:12 PM (3): Percolator: -0.3336 -2.2754 -0.6527 MH+ [Da] 06/14/2019 02:12 PM (3): Percolator: 0.0051 -0.6479 -1.4877 Delta Mass [Da] 06/14/2019 02:12 PM (3): Percolator: -1.1533 -0.7293 -0.6713 Delta Mass [ppm] 06/14/2019 02:12 PM (3): Percolator: -0.7327 1.0887 -1.8727 Absolute Delta Mass [Da] 06/14/2019 02:12 PM (3): Percolator: -0.3615 -2.1008 -1.9622 Absolute Delta Mass [ppm] 06/14/2019 02:12 PM (3): Percolator: 0.6904 3.4818 0.6596 Peptide Length 06/14/2019 02:12 PM (3): Percolator: 0.0000 0.0000 0.0000 Is z=1 06/14/2019 02:12 PM (3): Percolator: -0.4374 -0.8915 -0.4699 Is z=2 06/14/2019 02:12 PM (3): Percolator: 0.3181 0.4838 0.3185 Is z=3 06/14/2019 02:12 PM (3): Percolator: 0.2395 0.8569 0.2634 Is z=4 06/14/2019 02:12 PM (3): Percolator: 0.1743 0.4329 0.2967 Is z=5 06/14/2019 02:12 PM (3): Percolator: 0.0329 0.0622 0.0545 Is z>5 06/14/2019 02:12 PM (3): Percolator: -0.2641 -0.5162 -0.2972 # Missed Cleavages 06/14/2019 02:12 PM (3): Percolator: 0.0000 0.0000 0.0000 Log Peptides Matched 06/14/2019 02:12 PM (3): Percolator: -0.7819 -0.8872 -1.1251 Log Total Intensity 06/14/2019 02:12 PM (3): Percolator: -0.0702 0.4076 -0.0264 Fraction Matched Intensity [%] 06/14/2019 02:12 PM (3): Percolator: -0.7499 0.4370 -1.0264 Fragment Coverage Series A, B, C [%] 06/14/2019 02:12 PM (3): Percolator: 0.0334 0.4602 -0.0323 Fragment Coverage Series X, Y, Z [%] 06/14/2019 02:12 PM (3): Percolator: -0.3408 -0.2109 0.0121 Log Matched Fragment Series Intensities A, B, C 06/14/2019 02:12 PM (3): Percolator: -1.1743 -1.6991 -0.9637 Log Matched Fragment Series Intensities X, Y, Z 06/14/2019 02:12 PM (3): Percolator: 0.6019 -0.4708 0.6424 Longest Sequence Series A, B, C 06/14/2019 02:12 PM (3): Percolator: 0.0126 0.4074 -0.0839 Longest Sequence Series X, Y, Z 06/14/2019 02:12 PM (3): Percolator: -0.6379 -0.4208 0.6917 IQR Fragment Delta Mass [Da] 06/14/2019 02:12 PM (3): Percolator: -0.2688 0.0430 -1.5117 IQR Fragment Delta Mass [ppm] 06/14/2019 02:12 PM (3): Percolator: -1.4486 0.7143 -2.0655 Mean Fragment Delta Mass [Da] 06/14/2019 02:12 PM (3): Percolator: 0.4504 -1.4968 -0.1420 Mean Fragment Delta Mass [ppm] 06/14/2019 02:12 PM (3): Percolator: -1.1074 -1.9259 -2.2314 Mean Absolute Fragment Delta Mass [Da] 06/14/2019 02:12 PM (3): Percolator: 0.6678 0.6828 1.0550 Mean Absolute Fragment Delta Mass [ppm] 06/14/2019 02:12 PM (3): Percolator: -5.3451 -10.0601 -10.2724 m0 06/14/2019 02:12 PM (3): Percolator: Found 1524 test set PSMs with q<0.01. 06/14/2019 02:12 PM (3): Percolator: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide. 06/14/2019 02:12 PM (3): Percolator: Calculating q values. 06/14/2019 02:12 PM (3): Percolator: Final list yields 262 target peptides with q<0.01. 06/14/2019 02:12 PM (3): Percolator: Calculating posterior error probabilities (PEPs). 06/14/2019 02:12 PM (3): Percolator: Processing took 20.99 cpu seconds or 21 seconds wall clock time. 06/14/2019 02:12 PM (3): Percolator: PSMId score q-value posterior_error_prob peptide proteinIds 06/14/2019 02:13 PM (3): Percolator: 1534/14 high confident target/decoy peptides were found for MS Amanda 2.0 (2). 06/14/2019 02:13 PM (3): Percolator: 292/76 medium confident target/decoy peptides were found for MS Amanda 2.0 (2). 06/14/2019 02:13 PM (3): Percolator: -- Total execution of Percolator (64Bit) for MS Amanda 2.0 (2) took 3 min 44 s -- 06/14/2019 02:13 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 06/14/2019 02:13 PM (5): IMP-ptmRS: More nodes and documentations can be found here http://ms.imp.ac.at/?goto=pd-nodes. 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 -- 06/14/2019 02:13 PM (6): Minora Feature Detector: Start detecting lcmspeaks... 06/14/2019 02:13 PM (6): Minora Feature Detector: Running 2 jobs with 2 jobs in parallel. 06/14/2019 02:13 PM (6): Minora Feature Detector: Start F2 with 'FTMS + p NSI Full ms [350.0000-1850.0000]' 06/14/2019 02:13 PM (6): Minora Feature Detector: Start F13 with 'FTMS + p NSI Full ms [350.0000-1850.0000]' 06/14/2019 02:21 PM (6): Minora Feature Detector: Detecting LcmsPeaks took 8 min 5 s 06/14/2019 02:21 PM (6): Minora Feature Detector: Start processing F2: '190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C.raw'. 06/14/2019 02:21 PM (6): Minora Feature Detector: Start processing F13: '190328_EDG_Fus_19EDG05_aDn7ser-13d-Glu-C.raw'. 06/14/2019 02:21 PM (6): Minora Feature Detector: Importing peaks for F2 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])... 06/14/2019 02:21 PM (6): Minora Feature Detector: Importing peaks for F13 (scan filter: FTMS + p NSI Full ms [350.0000-1850.0000])... 06/14/2019 02:21 PM (6): Minora Feature Detector: F13: Found 246623 chromatographic peaks. 06/14/2019 02:21 PM (6): Minora Feature Detector: F2: Found 293455 chromatographic peaks. 06/14/2019 02:21 PM (6): Minora Feature Detector: F13: Importing auto traces... 06/14/2019 02:22 PM (6): Minora Feature Detector: F13: Imported 151970 auto traces. 06/14/2019 02:24 PM (6): Minora Feature Detector: F2: Importing auto traces... 06/14/2019 02:24 PM (6): Minora Feature Detector: F2: Imported 180716 auto traces. 06/14/2019 02:24 PM (6): Minora Feature Detector: Importing peak to spectrum links... 06/14/2019 02:29 PM (6): Minora Feature Detector: F13: Standard deviations: m/z 6.70; RT 0.11; Intensity 81.79; Fraction Missing Intensity 0.22; Shoulder Score 0.000; Peak Length Score 0.0559088435253572 took 4 min 57 s 06/14/2019 02:30 PM (6): Minora Feature Detector: F2: Standard deviations: m/z 6.38; RT 0.11; Intensity 75.05; Fraction Missing Intensity 0.21; Shoulder Score 0.000; Peak Length Score 0.0693297264025383 took 5 min 19 s 06/14/2019 02:32 PM (6): Minora Feature Detector: Found 977 features (F13: 264, F2: 713) 06/14/2019 02:32 PM (6): Minora Feature Detector: Writing data took 4.9 s. 06/14/2019 02:32 PM (6): Minora Feature Detector: Creating features for PSMs took 18.5 s. 06/14/2019 02:37 PM (6): Minora Feature Detector: F13: Unidentified feature detection took 4 min 42 s 06/14/2019 02:37 PM (6): Minora Feature Detector: F2: Unidentified feature detection took 5 min 3 s 06/14/2019 02:37 PM (6): Minora Feature Detector: Found 114304 unidentified features (F13 : 50659, F2 : 63645). 06/14/2019 02:37 PM (6): Minora Feature Detector: -- Total execution of Minora Feature Detector (6) took 24 min 21 s -- 06/14/2019 02:37 PM Job Execution: Finished E:\Work\data_MS_plus_raw\19EDG06 - aD serum\19EDG06 - aD serum\190328_EDG_Fus_19EDG05_aDn7iso-13d-Glu-C-(1).msf 06/14/2019 02:37 PM Job Execution: ----- Total Job execution took: 42 min 55 s. -----