Spectronaut 20.0.250606.92449
Computer Name: HALBARAD
User Domain Name: SPECTROMASSE
User Name: chaoui
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 09-July-2025 09:42:16 UTC +02:00 


[BEGIN-SETTINGS]
Settings Used: BGS Factory Settings
   ├─ DIA Analysis\Calibration
   │  ├─ MZ Extraction Strategy:	Maximum Intensity
   │  ├─ Allow source specific iRT Calibration:	True
   │  ├─ Precision iRT:	True
   │  │  ├─ Exclude De-amidated Peptides:	True
   │  │  └─ iRT <-> RT Regression Type:	Local (Non-Linear) Regression
   │  ├─ MS1 Mass Tolerance Strategy:	System Default
   │  └─ MS2 Mass Tolerance Strategy:	System Default
   ├─ DIA Analysis\Identification
   │  ├─ Precursor Qvalue Cutoff:	0.01
   │  ├─ Precursor Qvalue Cutoff (Experiment):	0.01
   │  ├─ Precursor PEP Cutoff:	0.2
   │  ├─ Protein Qvalue Cutoff (Experiment):	0.01
   │  ├─ Protein Qvalue Cutoff (Run):	0.05
   │  ├─ Protein PEP Cutoff:	0.75
   │  ├─ Single Hit Definition:	By Stripped Sequence
   │  ├─ Single Hit Protein Rule:	Stratified Single Hit Protein FDR
   │  ├─ Run-Level Protein Scoring:	All Observations
   │  ├─ Exclude Duplicate Assays:	True
   │  ├─ Exclude Predicted Fragment Scores:	False
   │  ├─ Generate Decoys:	True
   │  │  ├─ Decoy Generation Method:	Mutated
   │  │  │  └─ Preferred Fragment Source:	NN Predicted Fragments
   │  │  └─ Decoy Limit Strategy:	Dynamic
   │  │     └─ Library Size Fraction:	0.1
   │  └─ Pvalue Estimator:	Kernel Density Estimator
   ├─ DIA Analysis\Pipeline Mode
   │  ├─ Export All XICs:	False
   │  ├─ Generate SNE File:	True
   │  │  └─ Store Ion traces in SNE:	True
   │  ├─ Post Analysis Reports:	
   │  │  ├─ Binned CVs:	False
   │  │  ├─ Binned Identification:	False
   │  │  ├─ CV Density Line Chart:	False
   │  │  ├─ CVs Below X Bar Chart:	False
   │  │  ├─ Data Completeness Bar Chart:	False
   │  │  ├─ Run Identifications Bar Chart:	False
   │  │  ├─ Scoring Histograms:	False
   │  │  └─ TIC Overlay:	False
   │  ├─ PTM Report Schema:	
   │  ├─ Report Schema:	BGS Factory Report (Normal)
   │  └─ Reporting Unit:	Across Experiment
   ├─ DIA Analysis\Post Analysis
   │  ├─ Differential Abundance Testing:	Unpaired t-test
   │  │  ├─ Assume Equal Variance:	False
   │  │  ├─ Group-Wise Testing Correction:	False
   │  │  ├─ Log2 Ratio Candidate Filter:	0.58
   │  │  └─ Confidence Candidate Filter:	Qvalue
   │  │     └─ Confidence:	0.05
   │  ├─ Differential Abundance Grouping:	Major Group (Quantification Settings)
   │  │  └─ Smallest Quantitative Unit:	Major Group (Quantification Settings)
   │  │     └─ Use All MS-Level Quantities:	False
   │  ├─ Calculate Explained TIC:	None
   │  ├─ Calculate Sample Correlation Matrix:	False
   │  ├─ Gene Ontology:	\\GANDALF\chaoui\AppData\Spectronaut\geneOntology\Ontologies\bgs_default_go-basic.obo
   │  └─ Hierarchical Clustering:	True
   │     ├─ Distance Metric:	Manhattan Distance
   │     ├─ Linkage Strategy:	Ward's Method
   │     ├─ Order Runs by Clustering:	True
   │     └─ Z-score Transformation:	False
   ├─ DIA Analysis\Protein Inference
   │  └─ Protein Inference Workflow:	Automatic
   │     └─ Inference Algorithm:	IDPicker
   ├─ DIA Analysis\PTM Workflow
   │  ├─ Input Normalization Strategy:	None
   │  └─ PTM Localization:	False
   ├─ DIA Analysis\Quantification
   │  ├─ Precursor Filtering:	Identified (Qvalue)
   │  │  ├─ Imputation Strategy:	None
   │  │  └─ Multi Channel Qvalue Filter:	Group Qvalue
   │  ├─ Proteotypicity Filter:	None
   │  ├─ Protein LFQ Method:	Automatic
   │  ├─ Quantity MS Level:	MS2
   │  ├─ Quantity Type:	Area
   │  ├─ Cross-Run Normalization:	True
   │  │  ├─ Normalization Filter Type:	None
   │  │  ├─ Normalization Strategy:	Automatic
   │  │  └─ Row Selection:	Automatic
   │  ├─ Perform background noise removal:	True
   │  ├─ Quantification window:	Synchronized
   │  ├─ Interference Correction:	True
   │  │  ├─ Only Identified Peptides:	True
   │  │  ├─ Exclude All Multi-Channel Interferences:	True
   │  │  ├─ MS1 Min:	2
   │  │  └─ MS2 Min:	3
   │  ├─ Major Group Quantity:	Mean peptide quantity
   │  ├─ Minor (Peptide) Grouping:	by Stripped Sequence
   │  ├─ Major (Protein) Grouping:	by Protein Group Id
   │  ├─ Major Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Minor Group Quantity:	Mean precursor quantity
   │  ├─ Minor Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Use Log2 Quantity Filter:	True
   │  │  └─ Minimum Log2 Precursor Quantity:	0
   │  └─ Perform IM Peak Picking for Quantification:	True
   ├─ DIA Analysis\Workflow
   │  ├─ Method Evaluation:	False
   │  ├─ MS2 DeMultiplexing:	Automatic
   │  ├─ Multi-Channel Workflow Definition:	From Library Annotation
   │  │  └─ Fallback Option:	Labeled
   │  ├─ Profiling Strategy:	None
   │  ├─ Run Limit for directDIA Library:	-1
   │  ├─ Hybrid (DDA + DIA) Library:	False
   │  └─ Unify Peptide Peaks Strategy:	None
   ├─ DIA Analysis\XIC Extraction
   │  ├─ XIC IM Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ XIC RT Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ MS1 Mass Tolerance Strategy:	Dynamic
   │  │  └─ Correction Factor:	1
   │  └─ MS2 Mass Tolerance Strategy:	Dynamic
   │     └─ Correction Factor:	1
   ├─ Pulsar Search\Identification
   │  ├─ PSM FDR:	0.01
   │  ├─ Peptide FDR:	0.01
   │  ├─ Protein Group FDR:	0.01
   │  ├─ directDIA Workflow:	directDIA+ (Deep)
   │  └─ PTM Localization Filter:	False
   ├─ Pulsar Search\iRT Calibration
   │  ├─ Calibrate from Empirical RT:	False
   │  ├─ Auto-assign iRT source:	True
   │  ├─ iRT Reference Strategy:	Deep Learning Assisted iRT Regression
   │  ├─ Use Source Specific iRT:	Auto
   │  └─ Minimum Rsquare:	0.8
   ├─ Pulsar Search\Labeling
   │  └─ Channels:	
   │     ├─ Channel 1:	False
   │     ├─ Channel 2:	False
   │     ├─ Channel 3:	False
   │     ├─ Channel 4:	False
   │     └─ Channel 5:	False
   ├─ Pulsar Search\Modifications
   │  └─ Search Mode:	Closed Search
   │     ├─ Max Variable Modifications:	5
   │     ├─ Fixed Modifications::	Carbamidomethyl (C)
   │     └─ Variable Modifications::	Acetyl (Protein N-term), Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin/P
   │  ├─ Digest Type:	Specific
   │  ├─ Decoy Generation Rule:	KR
   │  ├─ Max Peptide Length:	52
   │  ├─ Min Peptide Length:	7
   │  ├─ Missed Cleavages:	2
   │  └─ Toggle N-terminal M:	True
   ├─ Pulsar Search\Result Filters
   │  ├─ Fragment Ions:	
   │  │  ├─ Ion AA Length:	True
   │  │  │  └─ N:	3
   │  │  ├─ Ion Charge:	False
   │  │  ├─ Ion Loss Type:	False
   │  │  ├─ Ion Type:	False
   │  │  ├─ m/z :	True
   │  │  │  ├─ Max:	3000
   │  │  │  └─ Min:	200
   │  │  ├─ Overlapping between Channels:	False
   │  │  └─ Relative Intensity:	True
   │  │     └─ Min:	1
   │  └─ Precursors:	
   │     ├─ Amino Acids:	False
   │     ├─ Best N Fragments per Peptide:	True
   │     │  ├─ Max:	6
   │     │  └─ Min:	3
   │     ├─ Best N Peptides per Protein Group:	False
   │     ├─ Channel Count:	False
   │     ├─ FASTA Matched:	False
   │     ├─ Missed Cleavage:	False
   │     ├─ Modifications:	None
   │     ├─ Peptide Charge:	False
   │     └─ Proteotypicity:	False
   ├─ Pulsar Search\Speed-Up
   │  ├─ MS2 Index:	Automatic
   │  └─ diaPASEF Pre-Processing:	Automatic
   ├─ Pulsar Search\Tolerances
   │  └─ Tolerance Parameters:	
   │     ├─ Thermo IonTrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     ├─ Thermo Orbitrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     └─ TOF:	
   │        ├─ Calibration Search:	Dynamic
   │        │  ├─ MS1 Correction Factor:	1
   │        │  └─ MS2 Correction Factor:	1
   │        └─ Main Search:	Dynamic
   │           ├─ MS1 Correction Factor:	1
   │           └─ MS2 Correction Factor:	1
   └─ Pulsar Search\Workflow
      ├─ Fragment Ion Selection Strategy:	Intensity Based
      ├─ In-Silico Generate Missing Channels:	False
      └─ Use DNN Predicted Ion Mobility:	Auto
[END-SETTINGS]

[BEGIN-SETUP]
Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 1
   ├─ HTRMS Version: 20.0.250606.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 09-July-2025 09:41:35 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 2
   ├─ HTRMS Version: 20.0.250606.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 09-July-2025 09:41:35 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 3
   ├─ HTRMS Version: 20.0.250606.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 09-July-2025 09:41:35 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 1
   ├─ HTRMS Version: 20.0.250606.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 09-July-2025 09:41:35 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 2
   ├─ HTRMS Version: 20.0.250606.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 09-July-2025 09:41:35 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 3
   ├─ HTRMS Version: 20.0.250606.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 09-July-2025 09:41:35 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

[END-SETUP]

[BEGIN-LOG]
INFO:    [07/07/2025 20:08:51] -> Initializing Pipeline...
INFO:    [07/07/2025 20:08:51] -> Preprocessing Run #1 of 6...
INFO:    [07/07/2025 20:08:51] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 20:08:53] -> Initialize Pipeline...
INFO:    [07/07/2025 20:08:53] -> Initialize Pipeline
INFO:    [07/07/2025 20:09:43] -> Initialize Pipeline...
INFO:    [07/07/2025 20:09:43] -> Creating Experiment Environment
INFO:    [07/07/2025 20:09:43] -> SuperRun 1/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d)
INFO:    [07/07/2025 20:09:43] -> Run 1/6: Organizing Data from Run
INFO:    [07/07/2025 20:09:43] -> Run 1/6: Creating Calibration Search Space...
INFO:    [07/07/2025 20:09:45] -> Collecting Search Space Parameters...
INFO:    [07/07/2025 20:09:50] -> Creating the Search Space...
INFO:    [07/07/2025 20:09:58] -> Run 1/6: Creating Search Space...
INFO:    [07/07/2025 20:09:58] -> Collecting Search Space Parameters...
INFO:    [07/07/2025 20:10:23] -> Creating the Search Space...
INFO:    [07/07/2025 20:10:30] -> Size of search space [MB]: 0
INFO:    [07/07/2025 20:10:30] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 20:10:30] -> Run 1/6: MS2 Index Generation
INFO:    [07/07/2025 20:11:47] -> MS2 Index Generation Time: 1.28m
INFO:    [07/07/2025 20:11:47] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 20:12:00] -> Initializing...
INFO:    [07/07/2025 20:16:45] -> Finalizing HTRMS File...
INFO:    [07/07/2025 20:21:10] -> Processed in 9.2m
INFO:    [07/07/2025 20:21:13] -> Done
INFO:    [07/07/2025 20:21:13] -> Run 1/6: Process Raw File...
INFO:    [07/07/2025 20:21:53] -> Run 1/6: Preparing Partitions...
INFO:    [07/07/2025 20:21:53] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [07/07/2025 20:21:54] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [07/07/2025 20:22:10] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [07/07/2025 20:22:31] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3118 [20.4s]
INFO:    [07/07/2025 20:22:35] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [07/07/2025 20:22:36] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [07/07/2025 20:28:07] -> Extracting 300945 MS1 XICs
INFO:    [07/07/2025 20:32:04] -> Run 1/6: Cleaning Up Run...
INFO:    [07/07/2025 20:32:06] -> SuperRun 2/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d)
INFO:    [07/07/2025 20:32:06] -> Run 2/6: Organizing Data from Run
INFO:    [07/07/2025 20:32:06] -> Run 2/6: Creating Calibration Search Space...
INFO:    [07/07/2025 20:32:07] -> Run 2/6: Creating Search Space...
INFO:    [07/07/2025 20:32:07] -> Size of search space [MB]: 0
INFO:    [07/07/2025 20:32:07] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 20:32:07] -> Run 2/6: MS2 Index Generation
INFO:    [07/07/2025 20:32:08] -> MS2 Index Generation Time: 1.11s
INFO:    [07/07/2025 20:32:08] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 20:32:15] -> Initializing...
INFO:    [07/07/2025 20:36:55] -> Finalizing HTRMS File...
INFO:    [07/07/2025 20:41:22] -> Processed in 9.1m
INFO:    [07/07/2025 20:41:25] -> Done
INFO:    [07/07/2025 20:41:25] -> Run 2/6: Process Raw File...
INFO:    [07/07/2025 20:41:59] -> Run 2/6: Preparing Partitions...
INFO:    [07/07/2025 20:41:59] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [07/07/2025 20:42:00] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [07/07/2025 20:42:32] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [07/07/2025 20:43:27] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2857 [55.1s]
INFO:    [07/07/2025 20:43:31] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [07/07/2025 20:43:32] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [07/07/2025 20:49:02] -> Extracting 347058 MS1 XICs
INFO:    [07/07/2025 20:53:57] -> Run 2/6: Cleaning Up Run...
INFO:    [07/07/2025 20:54:00] -> SuperRun 3/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d)
INFO:    [07/07/2025 20:54:00] -> Run 3/6: Organizing Data from Run
INFO:    [07/07/2025 20:54:00] -> Run 3/6: Creating Calibration Search Space...
INFO:    [07/07/2025 20:54:00] -> Run 3/6: Creating Search Space...
INFO:    [07/07/2025 20:54:00] -> Size of search space [MB]: 0
INFO:    [07/07/2025 20:54:00] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 20:54:00] -> Run 3/6: MS2 Index Generation
INFO:    [07/07/2025 20:54:01] -> MS2 Index Generation Time: 1.35s
INFO:    [07/07/2025 20:54:01] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 20:54:15] -> Initializing...
INFO:    [07/07/2025 20:59:20] -> Finalizing HTRMS File...
INFO:    [07/07/2025 21:04:09] -> Processed in 9.9m
INFO:    [07/07/2025 21:04:12] -> Done
INFO:    [07/07/2025 21:04:12] -> Run 3/6: Process Raw File...
INFO:    [07/07/2025 21:04:50] -> Run 3/6: Preparing Partitions...
INFO:    [07/07/2025 21:04:50] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [07/07/2025 21:04:52] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [07/07/2025 21:05:07] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [07/07/2025 21:05:30] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3065 [23.1s]
INFO:    [07/07/2025 21:05:34] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [07/07/2025 21:05:36] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [07/07/2025 21:10:44] -> Extracting 326284 MS1 XICs
INFO:    [07/07/2025 21:15:34] -> Run 3/6: Cleaning Up Run...
INFO:    [07/07/2025 21:15:37] -> SuperRun 4/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d)
INFO:    [07/07/2025 21:15:37] -> Run 4/6: Organizing Data from Run
INFO:    [07/07/2025 21:15:37] -> Run 4/6: Creating Calibration Search Space...
INFO:    [07/07/2025 21:15:37] -> Run 4/6: Creating Search Space...
INFO:    [07/07/2025 21:15:37] -> Size of search space [MB]: 0
INFO:    [07/07/2025 21:15:37] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 21:15:37] -> Run 4/6: MS2 Index Generation
INFO:    [07/07/2025 21:15:39] -> MS2 Index Generation Time: 1.24s
INFO:    [07/07/2025 21:15:39] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 21:15:47] -> Initializing...
INFO:    [07/07/2025 21:20:38] -> Finalizing HTRMS File...
INFO:    [07/07/2025 21:24:40] -> Processed in 8.9m
INFO:    [07/07/2025 21:24:49] -> Done
INFO:    [07/07/2025 21:24:49] -> Run 4/6: Process Raw File...
INFO:    [07/07/2025 21:25:27] -> Run 4/6: Preparing Partitions...
INFO:    [07/07/2025 21:25:27] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [07/07/2025 21:25:28] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [07/07/2025 21:25:44] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [07/07/2025 21:26:01] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3232 [18s]
INFO:    [07/07/2025 21:26:06] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [07/07/2025 21:26:07] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [07/07/2025 21:31:18] -> Extracting 340614 MS1 XICs
INFO:    [07/07/2025 21:36:35] -> Run 4/6: Cleaning Up Run...
INFO:    [07/07/2025 21:36:39] -> SuperRun 5/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d)
INFO:    [07/07/2025 21:36:39] -> Run 5/6: Organizing Data from Run
INFO:    [07/07/2025 21:36:39] -> Run 5/6: Creating Calibration Search Space...
INFO:    [07/07/2025 21:36:39] -> Run 5/6: Creating Search Space...
INFO:    [07/07/2025 21:36:39] -> Size of search space [MB]: 0
INFO:    [07/07/2025 21:36:39] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 21:36:39] -> Run 5/6: MS2 Index Generation
INFO:    [07/07/2025 21:36:40] -> MS2 Index Generation Time: 1.09s
INFO:    [07/07/2025 21:36:40] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 21:36:46] -> Initializing...
INFO:    [07/07/2025 21:41:17] -> Finalizing HTRMS File...
INFO:    [07/07/2025 21:45:17] -> Processed in 8.5m
INFO:    [07/07/2025 21:45:20] -> Done
INFO:    [07/07/2025 21:45:20] -> Run 5/6: Process Raw File...
INFO:    [07/07/2025 21:46:00] -> Run 5/6: Preparing Partitions...
INFO:    [07/07/2025 21:46:00] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [07/07/2025 21:46:01] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [07/07/2025 21:46:17] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [07/07/2025 21:46:39] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3228 [22s]
INFO:    [07/07/2025 21:46:43] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [07/07/2025 21:46:44] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [07/07/2025 21:52:22] -> Extracting 321436 MS1 XICs
INFO:    [07/07/2025 21:57:04] -> Run 5/6: Cleaning Up Run...
INFO:    [07/07/2025 21:57:04] -> SuperRun 6/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d)
INFO:    [07/07/2025 21:57:04] -> Run 6/6: Organizing Data from Run
INFO:    [07/07/2025 21:57:04] -> Run 6/6: Creating Calibration Search Space...
INFO:    [07/07/2025 21:57:04] -> Run 6/6: Creating Search Space...
INFO:    [07/07/2025 21:57:04] -> Size of search space [MB]: 0
INFO:    [07/07/2025 21:57:04] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 21:57:04] -> Run 6/6: MS2 Index Generation
INFO:    [07/07/2025 21:57:06] -> MS2 Index Generation Time: 1.43s
INFO:    [07/07/2025 21:57:06] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 21:57:13] -> Initializing...
INFO:    [07/07/2025 22:01:41] -> Finalizing HTRMS File...
INFO:    [07/07/2025 22:06:00] -> Processed in 8.8m
INFO:    [07/07/2025 22:06:04] -> Done
INFO:    [07/07/2025 22:06:04] -> Run 6/6: Process Raw File...
INFO:    [07/07/2025 22:06:45] -> Run 6/6: Preparing Partitions...
INFO:    [07/07/2025 22:06:45] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [07/07/2025 22:06:46] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [07/07/2025 22:07:16] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [07/07/2025 22:07:43] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3105 [26.8s]
INFO:    [07/07/2025 22:07:47] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [07/07/2025 22:07:48] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [07/07/2025 22:12:41] -> Extracting 319270 MS1 XICs
INFO:    [07/07/2025 22:17:37] -> Run 6/6: Cleaning Up Run...
INFO:    [07/07/2025 22:17:49] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [07/07/2025 22:17:50] -> Score Post-Processing
INFO:    [07/07/2025 22:21:16] -> Score Post-Processing: 3.43m
INFO:    [07/07/2025 22:21:16] -> PSM FDR...
INFO:    [07/07/2025 22:21:51] -> PSM FDR: 35.41s
INFO:    [07/07/2025 22:21:51] -> Converting to non-redundant data structure...
INFO:    [07/07/2025 22:22:10] -> Performing Peptide FDR...
INFO:    [07/07/2025 22:22:16] -> Performing Protein Inference...
INFO:    [07/07/2025 22:22:20] -> Performing Protein FDR...
INFO:    [07/07/2025 22:22:21] -> Calculating Result Values at Run and Experiment Level...
INFO:    [07/07/2025 22:22:38] -> Pulsar identified 355924 PSMs, 76104 stripped sequences, 86085 peptide precursors, 9532 protein groups.
INFO:    [07/07/2025 22:22:38] -> Calculating Summary...
INFO:    [07/07/2025 22:22:46] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 22:22:48] -> iRT Calibration...
INFO:    [07/07/2025 22:22:51] -> Performing directDIA+ search...
INFO:    [07/07/2025 22:26:40] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
INFO:    [07/07/2025 22:34:36] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
INFO:    [07/07/2025 22:42:58] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
INFO:    [07/07/2025 22:51:06] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
INFO:    [07/07/2025 22:59:37] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
INFO:    [07/07/2025 23:07:40] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
INFO:    [07/07/2025 23:15:51] -> Total nr of Searched Peptides: 2 172 375 of 2 172 375
INFO:    [07/07/2025 23:15:51] -> Performing directDIA+ Post Processing...
INFO:    [07/07/2025 23:16:04] -> Writing experiment store..
INFO:    [07/07/2025 23:16:15] -> Assigning iRT Source...
INFO:    [07/07/2025 23:16:15] -> Calculating iRT...
INFO:    [07/07/2025 23:16:15] -> Cleaning Up Experiment...
INFO:    [07/07/2025 23:16:15] -> Summarizing Identifications
INFO:    [07/07/2025 23:18:07] -> Identifiying Significant Precursors...
INFO:    [07/07/2025 23:18:33] -> Predicting Ion Mobility
INFO:    [07/07/2025 23:18:49] -> Calculating Median iRT
INFO:    [07/07/2025 23:18:51] -> Building BGS Protein Grouping...
INFO:    [07/07/2025 23:18:52] -> Digesting Fasta...
INFO:    [07/07/2025 23:18:53] -> Annotating Proteins...
INFO:    [07/07/2025 23:18:54] -> Grouping Proteins...
INFO:    [07/07/2025 23:18:58] -> Calculating Run Summary Statistics...
INFO:    [07/07/2025 23:19:38] -> Building Consensus Fragment Spectra...
INFO:    [07/07/2025 23:20:48] -> Selecting best fragment ions
INFO:    [07/07/2025 23:24:32] -> Initializing Experiment...
INFO:    [07/07/2025 23:24:32] -> Loading Spectral Libraries...
INFO:    [07/07/2025 23:25:30] -> Initialize Scoring...
INFO:    [07/07/2025 23:25:30] -> Generating Scan Map...
INFO:    [07/07/2025 23:25:31] -> Initializing Workpackages...
INFO:    [07/07/2025 23:25:31] -> Performing Basic Calibration...
INFO:    [07/07/2025 23:25:33] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 23:25:33] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 23:25:40] -> Initializing Pipeline...
INFO:    [07/07/2025 23:25:40] -> Preprocessing Run #1 of 6...
INFO:    [07/07/2025 23:25:40] -> Initialize Scoring...
INFO:    [07/07/2025 23:25:40] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:26:39] -> Machine Learning...
INFO:    [07/07/2025 23:26:40] -> Pipeline executed in 1m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:26:49] -> Initializing Pipeline...
INFO:    [07/07/2025 23:26:49] -> Preprocessing Run #1 of 6...
INFO:    [07/07/2025 23:26:49] -> Initialize Scoring...
INFO:    [07/07/2025 23:26:49] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:28:10] -> Machine Learning...
INFO:    [07/07/2025 23:28:17] -> Pipeline executed in 1.47m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:28:32] -> Initialize Scoring...
INFO:    [07/07/2025 23:28:32] -> Preprocessing Run #2 of 6...
INFO:    [07/07/2025 23:28:32] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 23:28:32] -> Initializing Experiment...
INFO:    [07/07/2025 23:28:32] -> Loading Spectral Libraries...
INFO:    [07/07/2025 23:28:32] -> Initialize Scoring...
INFO:    [07/07/2025 23:28:32] -> Generating Scan Map...
INFO:    [07/07/2025 23:28:32] -> Initializing Workpackages...
INFO:    [07/07/2025 23:28:32] -> Performing Basic Calibration...
INFO:    [07/07/2025 23:28:34] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 23:28:34] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 23:28:40] -> Initializing Pipeline...
INFO:    [07/07/2025 23:28:40] -> Preprocessing Run #2 of 6...
INFO:    [07/07/2025 23:28:40] -> Initialize Scoring...
INFO:    [07/07/2025 23:28:40] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:29:32] -> Machine Learning...
INFO:    [07/07/2025 23:29:33] -> Pipeline executed in 53.52s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:29:41] -> Initializing Pipeline...
INFO:    [07/07/2025 23:29:41] -> Preprocessing Run #2 of 6...
INFO:    [07/07/2025 23:29:41] -> Initialize Scoring...
INFO:    [07/07/2025 23:29:41] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:31:03] -> Machine Learning...
INFO:    [07/07/2025 23:31:11] -> Pipeline executed in 1.49m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:31:27] -> Initialize Scoring...
INFO:    [07/07/2025 23:31:27] -> Preprocessing Run #3 of 6...
INFO:    [07/07/2025 23:31:27] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 23:31:27] -> Initializing Experiment...
INFO:    [07/07/2025 23:31:27] -> Loading Spectral Libraries...
INFO:    [07/07/2025 23:31:27] -> Initialize Scoring...
INFO:    [07/07/2025 23:31:27] -> Generating Scan Map...
INFO:    [07/07/2025 23:31:27] -> Initializing Workpackages...
INFO:    [07/07/2025 23:31:27] -> Performing Basic Calibration...
INFO:    [07/07/2025 23:31:29] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 23:31:29] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 23:31:36] -> Initializing Pipeline...
INFO:    [07/07/2025 23:31:36] -> Preprocessing Run #3 of 6...
INFO:    [07/07/2025 23:31:36] -> Initialize Scoring...
INFO:    [07/07/2025 23:31:36] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:33:02] -> Machine Learning...
INFO:    [07/07/2025 23:33:03] -> Pipeline executed in 1.46m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:33:11] -> Initializing Pipeline...
INFO:    [07/07/2025 23:33:11] -> Preprocessing Run #3 of 6...
INFO:    [07/07/2025 23:33:11] -> Initialize Scoring...
INFO:    [07/07/2025 23:33:11] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:34:28] -> Machine Learning...
INFO:    [07/07/2025 23:34:35] -> Pipeline executed in 1.4m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:34:52] -> Initialize Scoring...
INFO:    [07/07/2025 23:34:52] -> Preprocessing Run #4 of 6...
INFO:    [07/07/2025 23:34:52] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 23:34:52] -> Initializing Experiment...
INFO:    [07/07/2025 23:34:52] -> Loading Spectral Libraries...
INFO:    [07/07/2025 23:34:52] -> Initialize Scoring...
INFO:    [07/07/2025 23:34:52] -> Generating Scan Map...
INFO:    [07/07/2025 23:34:52] -> Initializing Workpackages...
INFO:    [07/07/2025 23:34:52] -> Performing Basic Calibration...
INFO:    [07/07/2025 23:34:54] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 23:34:54] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 23:35:00] -> Initializing Pipeline...
INFO:    [07/07/2025 23:35:00] -> Preprocessing Run #4 of 6...
INFO:    [07/07/2025 23:35:00] -> Initialize Scoring...
INFO:    [07/07/2025 23:35:00] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:35:53] -> Machine Learning...
INFO:    [07/07/2025 23:35:54] -> Pipeline executed in 54.43s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:36:02] -> Initializing Pipeline...
INFO:    [07/07/2025 23:36:02] -> Preprocessing Run #4 of 6...
INFO:    [07/07/2025 23:36:02] -> Initialize Scoring...
INFO:    [07/07/2025 23:36:02] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:37:19] -> Machine Learning...
INFO:    [07/07/2025 23:37:25] -> Pipeline executed in 1.39m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:37:39] -> Initialize Scoring...
INFO:    [07/07/2025 23:37:39] -> Preprocessing Run #5 of 6...
INFO:    [07/07/2025 23:37:39] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 23:37:39] -> Initializing Experiment...
INFO:    [07/07/2025 23:37:39] -> Loading Spectral Libraries...
INFO:    [07/07/2025 23:37:39] -> Initialize Scoring...
INFO:    [07/07/2025 23:37:39] -> Generating Scan Map...
INFO:    [07/07/2025 23:37:39] -> Initializing Workpackages...
INFO:    [07/07/2025 23:37:39] -> Performing Basic Calibration...
INFO:    [07/07/2025 23:37:42] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 23:37:42] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 23:37:47] -> Initializing Pipeline...
INFO:    [07/07/2025 23:37:47] -> Preprocessing Run #5 of 6...
INFO:    [07/07/2025 23:37:47] -> Initialize Scoring...
INFO:    [07/07/2025 23:37:47] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:38:42] -> Machine Learning...
INFO:    [07/07/2025 23:38:43] -> Pipeline executed in 55.77s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:38:51] -> Initializing Pipeline...
INFO:    [07/07/2025 23:38:51] -> Preprocessing Run #5 of 6...
INFO:    [07/07/2025 23:38:51] -> Initialize Scoring...
INFO:    [07/07/2025 23:38:51] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:40:08] -> Machine Learning...
INFO:    [07/07/2025 23:40:14] -> Pipeline executed in 1.39m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:40:28] -> Initialize Scoring...
INFO:    [07/07/2025 23:40:28] -> Preprocessing Run #6 of 6...
INFO:    [07/07/2025 23:40:28] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 23:40:28] -> Initializing Experiment...
INFO:    [07/07/2025 23:40:28] -> Loading Spectral Libraries...
INFO:    [07/07/2025 23:40:28] -> Initialize Scoring...
INFO:    [07/07/2025 23:40:28] -> Generating Scan Map...
INFO:    [07/07/2025 23:40:28] -> Initializing Workpackages...
INFO:    [07/07/2025 23:40:28] -> Performing Basic Calibration...
INFO:    [07/07/2025 23:40:31] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 23:40:31] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 23:40:36] -> Initializing Pipeline...
INFO:    [07/07/2025 23:40:36] -> Preprocessing Run #6 of 6...
INFO:    [07/07/2025 23:40:36] -> Initialize Scoring...
INFO:    [07/07/2025 23:40:36] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:41:31] -> Machine Learning...
INFO:    [07/07/2025 23:41:32] -> Pipeline executed in 56.02s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:41:41] -> Initializing Pipeline...
INFO:    [07/07/2025 23:41:41] -> Preprocessing Run #6 of 6...
INFO:    [07/07/2025 23:41:41] -> Initialize Scoring...
INFO:    [07/07/2025 23:41:41] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:42:56] -> Machine Learning...
INFO:    [07/07/2025 23:43:03] -> Pipeline executed in 1.37m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 23:43:15] -> Initialize Scoring...
INFO:    [07/07/2025 23:43:15] -> Initializing QC...
INFO:    [07/07/2025 23:43:16] -> Determining Calibration Parameter...
INFO:    [07/07/2025 23:43:16] -> Assigning ML Features...
INFO:    [07/07/2025 23:43:17] -> Generating Decoys...
INFO:    [07/07/2025 23:43:29] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:45:15] -> Releasing Raw Files...
INFO:    [07/07/2025 23:45:15] -> Machine Learning...
INFO:    [07/07/2025 23:47:57] -> Initializing HTRMS...
INFO:    [07/07/2025 23:47:57] -> Releasing Run Resources...
INFO:    [07/07/2025 23:47:58] -> Reducing Score Cache...
INFO:    [07/07/2025 23:48:02] -> Calculating Qvalues...
INFO:    [07/07/2025 23:48:09] -> Unique precursors: 134 521 of 142 227 | modified peptides: 118 717 of 124 589 | peptides: 117 496 of 123 324 |  protein groups: 11 685 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d]
INFO:    [07/07/2025 23:48:09] -> Collapsing Search Tree...
INFO:    [07/07/2025 23:48:09] -> Processed in 4.89m
INFO:    [07/07/2025 23:48:09] -> Initializing QC...
INFO:    [07/07/2025 23:48:09] -> Determining Calibration Parameter...
INFO:    [07/07/2025 23:48:10] -> Assigning ML Features...
INFO:    [07/07/2025 23:48:10] -> Generating Decoys...
INFO:    [07/07/2025 23:48:11] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:50:30] -> Releasing Raw Files...
INFO:    [07/07/2025 23:50:30] -> Machine Learning...
INFO:    [07/07/2025 23:52:57] -> Initializing HTRMS...
INFO:    [07/07/2025 23:52:57] -> Releasing Run Resources...
INFO:    [07/07/2025 23:52:58] -> Reducing Score Cache...
INFO:    [07/07/2025 23:53:01] -> Calculating Qvalues...
INFO:    [07/07/2025 23:53:10] -> Unique precursors: 134 786 of 142 227 | modified peptides: 118 879 of 124 589 | peptides: 117 658 of 123 324 |  protein groups: 11 665 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d]
INFO:    [07/07/2025 23:53:10] -> Collapsing Search Tree...
INFO:    [07/07/2025 23:53:10] -> Processed in 5.01m
INFO:    [07/07/2025 23:53:11] -> Initializing QC...
INFO:    [07/07/2025 23:53:11] -> Determining Calibration Parameter...
INFO:    [07/07/2025 23:53:11] -> Assigning ML Features...
INFO:    [07/07/2025 23:53:11] -> Generating Decoys...
INFO:    [07/07/2025 23:53:12] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:54:48] -> Releasing Raw Files...
INFO:    [07/07/2025 23:54:48] -> Machine Learning...
INFO:    [07/07/2025 23:57:14] -> Initializing HTRMS...
INFO:    [07/07/2025 23:57:14] -> Releasing Run Resources...
INFO:    [07/07/2025 23:57:14] -> Reducing Score Cache...
INFO:    [07/07/2025 23:57:18] -> Calculating Qvalues...
INFO:    [07/07/2025 23:57:26] -> Unique precursors: 135 092 of 142 227 | modified peptides: 119 142 of 124 589 | peptides: 117 931 of 123 324 |  protein groups: 11 672 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d]
INFO:    [07/07/2025 23:57:26] -> Collapsing Search Tree...
INFO:    [07/07/2025 23:57:26] -> Processed in 4.26m
INFO:    [07/07/2025 23:57:26] -> Initializing QC...
INFO:    [07/07/2025 23:57:27] -> Determining Calibration Parameter...
INFO:    [07/07/2025 23:57:27] -> Assigning ML Features...
INFO:    [07/07/2025 23:57:27] -> Generating Decoys...
INFO:    [07/07/2025 23:57:28] -> Extracting Ion Currents...
INFO:    [07/07/2025 23:59:06] -> Releasing Raw Files...
INFO:    [07/07/2025 23:59:06] -> Machine Learning...
INFO:    [08/07/2025 00:01:31] -> Initializing HTRMS...
INFO:    [08/07/2025 00:01:31] -> Releasing Run Resources...
INFO:    [08/07/2025 00:01:31] -> Reducing Score Cache...
INFO:    [08/07/2025 00:01:35] -> Calculating Qvalues...
INFO:    [08/07/2025 00:01:42] -> Unique precursors: 135 572 of 142 227 | modified peptides: 119 508 of 124 589 | peptides: 118 276 of 123 324 |  protein groups: 11 725 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d]
INFO:    [08/07/2025 00:01:42] -> Collapsing Search Tree...
INFO:    [08/07/2025 00:01:42] -> Processed in 4.26m
INFO:    [08/07/2025 00:01:42] -> Initializing QC...
INFO:    [08/07/2025 00:01:42] -> Determining Calibration Parameter...
INFO:    [08/07/2025 00:01:43] -> Assigning ML Features...
INFO:    [08/07/2025 00:01:43] -> Generating Decoys...
INFO:    [08/07/2025 00:01:44] -> Extracting Ion Currents...
INFO:    [08/07/2025 00:03:21] -> Releasing Raw Files...
INFO:    [08/07/2025 00:03:21] -> Machine Learning...
INFO:    [08/07/2025 00:05:53] -> Initializing HTRMS...
INFO:    [08/07/2025 00:05:53] -> Releasing Run Resources...
INFO:    [08/07/2025 00:05:53] -> Reducing Score Cache...
INFO:    [08/07/2025 00:05:57] -> Calculating Qvalues...
INFO:    [08/07/2025 00:06:09] -> Unique precursors: 135 883 of 142 227 | modified peptides: 119 769 of 124 589 | peptides: 118 540 of 123 324 |  protein groups: 11 746 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d]
INFO:    [08/07/2025 00:06:09] -> Collapsing Search Tree...
INFO:    [08/07/2025 00:06:10] -> Processed in 4.46m
INFO:    [08/07/2025 00:06:17] -> Initializing QC...
INFO:    [08/07/2025 00:06:18] -> Determining Calibration Parameter...
INFO:    [08/07/2025 00:06:18] -> Assigning ML Features...
INFO:    [08/07/2025 00:06:18] -> Generating Decoys...
INFO:    [08/07/2025 00:06:19] -> Extracting Ion Currents...
INFO:    [08/07/2025 00:08:16] -> Releasing Raw Files...
INFO:    [08/07/2025 00:08:16] -> Machine Learning...
INFO:    [08/07/2025 00:10:49] -> Initializing HTRMS...
INFO:    [08/07/2025 00:10:49] -> Releasing Run Resources...
INFO:    [08/07/2025 00:10:50] -> Reducing Score Cache...
INFO:    [08/07/2025 00:10:54] -> Calculating Qvalues...
INFO:    [08/07/2025 00:10:57] -> Unique precursors: 134 983 of 142 227 | modified peptides: 119 011 of 124 589 | peptides: 117 792 of 123 324 |  protein groups: 11 729 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d]
INFO:    [08/07/2025 00:10:57] -> Collapsing Search Tree...
INFO:    [08/07/2025 00:10:57] -> Processed in 4.66m
INFO:    [08/07/2025 00:10:57] -> Normalizing Cscores...
INFO:    [08/07/2025 00:10:57] -> Calculating Global CVs
INFO:    [08/07/2025 00:10:59] -> Calculating Profile Qvalues...
INFO:    [08/07/2025 00:11:01] -> Initializing Protein Groups...
INFO:    [08/07/2025 00:11:23] -> Correcting Interferences...
INFO:    [08/07/2025 00:11:51] -> Calculating Global CVs
INFO:    [08/07/2025 00:11:52] -> Calculating Precursor Quantities...
INFO:    [08/07/2025 00:11:52] -> Normalizing Quantification...
INFO:    [08/07/2025 00:11:54] -> Performing Local Normalization...
INFO:    [08/07/2025 00:11:57] -> Calculating Global CVs
INFO:    [08/07/2025 00:11:58] -> Calculating Condition CVs
INFO:    [08/07/2025 00:12:02] -> Excluding Library Duplicates...
INFO:    [08/07/2025 00:12:03] -> Calculating Global CVs
INFO:    [08/07/2025 00:12:04] -> Building Protein Groups...
INFO:    [08/07/2025 00:12:21] -> Calculating Run-Wise Protein Group FDR...
INFO:    [08/07/2025 00:12:29] -> Annotating Protein Single Hits...
INFO:    [08/07/2025 00:12:30] -> Calculating Global CVs
INFO:    [08/07/2025 00:12:32] -> Updating Identification Counts...
INFO:    [08/07/2025 00:12:37] -> Subtracting background noise...
INFO:    [08/07/2025 00:12:43] -> Resetting existing imputation...
INFO:    [08/07/2025 00:12:43] -> Calculating Protein Quantities...
INFO:    [08/07/2025 00:12:45] -> Calculating Protein Quantities...
INFO:    [08/07/2025 00:12:45] -> Calculating MaxLFQ Protein Quantities...
INFO:    [08/07/2025 00:12:55] -> Collapsing PTM-Locations...
INFO:    [08/07/2025 00:12:55] -> PTM Stoichiometry calculation...
INFO:    [08/07/2025 00:12:55] -> Creating Protein Map...
INFO:    [08/07/2025 00:12:55] -> Compiling Run Summary Information...
INFO:    [08/07/2025 00:12:56] -> Running Post Analysis Processes...
INFO:    [08/07/2025 00:13:38] -> Saving Qc Data...
INFO:    [08/07/2025 00:13:45] -> Writing Summary Information...
INFO:    [08/07/2025 00:13:45] -> Unique precursors: 127 370 of 142 227 | modified peptides: 112 919 of 124 589 | peptides: 111 739 of 123 324 |  protein groups: 10 900 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [08/07/2025 00:13:45] -> Unique precursors: 127 863 of 142 227 | modified peptides: 113 309 of 124 589 | peptides: 112 122 of 123 324 |  protein groups: 10 902 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [08/07/2025 00:13:45] -> Unique precursors: 128 001 of 142 227 | modified peptides: 113 457 of 124 589 | peptides: 112 277 of 123 324 |  protein groups: 10 907 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [08/07/2025 00:13:45] -> Unique precursors: 128 350 of 142 227 | modified peptides: 113 718 of 124 589 | peptides: 112 526 of 123 324 |  protein groups: 11 002 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [08/07/2025 00:13:45] -> Unique precursors: 128 503 of 142 227 | modified peptides: 113 848 of 124 589 | peptides: 112 659 of 123 324 |  protein groups: 11 002 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [08/07/2025 00:13:45] -> Unique precursors: 128 275 of 142 227 | modified peptides: 113 691 of 124 589 | peptides: 112 502 of 123 324 |  protein groups: 10 995 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [08/07/2025 00:13:45] -> Unique precursors: 131 527 of 142 227 | modified peptides: 116 329 of 124 589 | peptides: 115 123 of 123 324 |  protein groups: 11 029 (Qvalue <= 0.01) for whole experiment "SN20_ttSCP_proteobench_defaultParams"

INFO:    [08/07/2025 00:13:45] -> Saving SNE File...
INFO:    [08/07/2025 00:13:45] -> Automatic SNE storage disabled
INFO:    [08/07/2025 00:13:45] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [08/07/2025 00:13:45] -> Pipeline executed in 4.08h - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/07/2025 09:41:35] -> Initializing Pipeline...
INFO:    [09/07/2025 09:41:35] -> Calculating Qvalues...
INFO:    [09/07/2025 09:41:35] -> Saving...
INFO:    [09/07/2025 09:41:50] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [09/07/2025 09:41:51] -> Pipeline executed in 15.18s - Current Experiment had 0 Warnings and 0 Errors.
[END-LOG]
