Spectronaut 20.0.250606.92449
Computer Name: HALBARAD
User Domain Name: SPECTROMASSE
User Name: chaoui
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 07-July-2025 19:54:39 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:	1
   │     ├─ Fixed Modifications::	Carbamidomethyl (C)
   │     └─ Variable Modifications::	Acetyl (Protein N-term), Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin
   │  ├─ Digest Type:	Specific
   │  ├─ Decoy Generation Rule:	KR
   │  ├─ Max Peptide Length:	30
   │  ├─ Min Peptide Length:	6
   │  ├─ Missed Cleavages:	1
   │  └─ Toggle N-terminal M:	True
   ├─ Pulsar Search\Result Filters
   │  ├─ Fragment Ions:	
   │  │  ├─ Ion AA Length:	True
   │  │  │  └─ N:	3
   │  │  ├─ Ion Charge:	True
   │  │  │  └─ Max:	5
   │  │  ├─ Ion Loss Type:	False
   │  │  ├─ Ion Type:	False
   │  │  ├─ m/z :	True
   │  │  │  ├─ Max:	2000
   │  │  │  └─ Min:	150
   │  │  ├─ 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: 07-July-2025 19:53:06 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: 07-July-2025 19:53:06 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: 07-July-2025 19:53:06 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: 07-July-2025 19:53:06 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: 07-July-2025 19:53:06 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: 07-July-2025 19:53:06 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 12:11:20] -> Initializing Pipeline...
INFO:    [07/07/2025 12:11:20] -> Preprocessing Run #1 of 6...
INFO:    [07/07/2025 12:11:20] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 12:11:22] -> Initialize Pipeline...
INFO:    [07/07/2025 12:11:22] -> Initialize Pipeline
INFO:    [07/07/2025 12:13:12] -> Initialize Pipeline...
INFO:    [07/07/2025 12:13:12] -> Creating Experiment Environment
INFO:    [07/07/2025 12:13:12] -> SuperRun 1/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d)
INFO:    [07/07/2025 12:13:12] -> Run 1/6: Organizing Data from Run
INFO:    [07/07/2025 12:13:12] -> Run 1/6: Creating Calibration Search Space...
INFO:    [07/07/2025 12:13:18] -> Run 1/6: Creating Search Space...
INFO:    [07/07/2025 12:13:18] -> Size of search space [MB]: 0
INFO:    [07/07/2025 12:13:18] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 12:13:18] -> Run 1/6: MS2 Index Generation
INFO:    [07/07/2025 12:13:19] -> MS2 Index Generation Time: 1.12s
INFO:    [07/07/2025 12:13:19] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 12:13:36] -> Initializing...
INFO:    [07/07/2025 12:18:19] -> Finalizing HTRMS File...
INFO:    [07/07/2025 12:23:29] -> Processed in 9.9m
INFO:    [07/07/2025 12:23:32] -> Done
INFO:    [07/07/2025 12:23:32] -> Run 1/6: Process Raw File...
INFO:    [07/07/2025 12:24:12] -> Run 1/6: Preparing Partitions...
INFO:    [07/07/2025 12:24:12] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [07/07/2025 12:24:13] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [07/07/2025 12:24:29] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [07/07/2025 12:24:46] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3553 [16.9s]
INFO:    [07/07/2025 12:24:50] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [07/07/2025 12:24:51] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [07/07/2025 12:28:52] -> Extracting 322201 MS1 XICs
INFO:    [07/07/2025 12:33:56] -> Run 1/6: Cleaning Up Run...
INFO:    [07/07/2025 12:33:58] -> SuperRun 2/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d)
INFO:    [07/07/2025 12:33:58] -> Run 2/6: Organizing Data from Run
INFO:    [07/07/2025 12:33:58] -> Run 2/6: Creating Calibration Search Space...
INFO:    [07/07/2025 12:33:58] -> Run 2/6: Creating Search Space...
INFO:    [07/07/2025 12:33:58] -> Size of search space [MB]: 0
INFO:    [07/07/2025 12:33:58] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 12:33:58] -> Run 2/6: MS2 Index Generation
INFO:    [07/07/2025 12:33:59] -> MS2 Index Generation Time: 1.18s
INFO:    [07/07/2025 12:33:59] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 12:34:13] -> Initializing...
INFO:    [07/07/2025 12:39:05] -> Finalizing HTRMS File...
INFO:    [07/07/2025 12:44:13] -> Processed in 10m
INFO:    [07/07/2025 12:44:27] -> Done
INFO:    [07/07/2025 12:44:27] -> Run 2/6: Process Raw File...
INFO:    [07/07/2025 12:45:13] -> Run 2/6: Preparing Partitions...
INFO:    [07/07/2025 12:45:13] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [07/07/2025 12:45:14] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [07/07/2025 12:45:30] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [07/07/2025 12:45:47] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3073 [17s]
INFO:    [07/07/2025 12:45:51] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [07/07/2025 12:45:52] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [07/07/2025 12:49:47] -> Extracting 325556 MS1 XICs
INFO:    [07/07/2025 12:54:32] -> Run 2/6: Cleaning Up Run...
INFO:    [07/07/2025 12:54:33] -> SuperRun 3/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d)
INFO:    [07/07/2025 12:54:33] -> Run 3/6: Organizing Data from Run
INFO:    [07/07/2025 12:54:33] -> Run 3/6: Creating Calibration Search Space...
INFO:    [07/07/2025 12:54:33] -> Run 3/6: Creating Search Space...
INFO:    [07/07/2025 12:54:33] -> Size of search space [MB]: 0
INFO:    [07/07/2025 12:54:33] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 12:54:33] -> Run 3/6: MS2 Index Generation
INFO:    [07/07/2025 12:54:35] -> MS2 Index Generation Time: 1.22s
INFO:    [07/07/2025 12:54:35] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 12:54:43] -> Initializing...
INFO:    [07/07/2025 13:00:17] -> Finalizing HTRMS File...
INFO:    [07/07/2025 13:04:42] -> Processed in 10m
INFO:    [07/07/2025 13:04:44] -> Done
INFO:    [07/07/2025 13:04:44] -> Run 3/6: Process Raw File...
INFO:    [07/07/2025 13:05:24] -> Run 3/6: Preparing Partitions...
INFO:    [07/07/2025 13:05:24] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [07/07/2025 13:05:26] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [07/07/2025 13:05:41] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [07/07/2025 13:05:59] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3299 [17.7s]
INFO:    [07/07/2025 13:06:03] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [07/07/2025 13:06:04] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [07/07/2025 13:09:58] -> Extracting 325218 MS1 XICs
INFO:    [07/07/2025 13:16:13] -> Run 3/6: Cleaning Up Run...
INFO:    [07/07/2025 13:16:15] -> SuperRun 4/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d)
INFO:    [07/07/2025 13:16:15] -> Run 4/6: Organizing Data from Run
INFO:    [07/07/2025 13:16:15] -> Run 4/6: Creating Calibration Search Space...
INFO:    [07/07/2025 13:16:15] -> Run 4/6: Creating Search Space...
INFO:    [07/07/2025 13:16:15] -> Size of search space [MB]: 0
INFO:    [07/07/2025 13:16:15] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 13:16:15] -> Run 4/6: MS2 Index Generation
INFO:    [07/07/2025 13:16:17] -> MS2 Index Generation Time: 1.42s
INFO:    [07/07/2025 13:16:17] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 13:16:38] -> Initializing...
INFO:    [07/07/2025 13:21:11] -> Finalizing HTRMS File...
INFO:    [07/07/2025 13:25:24] -> Processed in 8.8m
INFO:    [07/07/2025 13:25:31] -> Done
INFO:    [07/07/2025 13:25:31] -> Run 4/6: Process Raw File...
INFO:    [07/07/2025 13:26:12] -> Run 4/6: Preparing Partitions...
INFO:    [07/07/2025 13:26:12] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [07/07/2025 13:26:13] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [07/07/2025 13:26:28] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [07/07/2025 13:26:44] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3474 [15.6s]
INFO:    [07/07/2025 13:26:48] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [07/07/2025 13:26:50] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [07/07/2025 13:30:39] -> Extracting 339694 MS1 XICs
INFO:    [07/07/2025 13:36:07] -> Run 4/6: Cleaning Up Run...
INFO:    [07/07/2025 13:36:10] -> SuperRun 5/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d)
INFO:    [07/07/2025 13:36:10] -> Run 5/6: Organizing Data from Run
INFO:    [07/07/2025 13:36:10] -> Run 5/6: Creating Calibration Search Space...
INFO:    [07/07/2025 13:36:10] -> Run 5/6: Creating Search Space...
INFO:    [07/07/2025 13:36:10] -> Size of search space [MB]: 0
INFO:    [07/07/2025 13:36:10] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 13:36:10] -> Run 5/6: MS2 Index Generation
INFO:    [07/07/2025 13:36:11] -> MS2 Index Generation Time: 1.23s
INFO:    [07/07/2025 13:36:11] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 13:36:30] -> Initializing...
INFO:    [07/07/2025 13:41:02] -> Finalizing HTRMS File...
INFO:    [07/07/2025 13:44:56] -> Processed in 8.4m
INFO:    [07/07/2025 13:44:59] -> Done
INFO:    [07/07/2025 13:44:59] -> Run 5/6: Process Raw File...
INFO:    [07/07/2025 13:45:34] -> Run 5/6: Preparing Partitions...
INFO:    [07/07/2025 13:45:34] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [07/07/2025 13:45:35] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [07/07/2025 13:45:50] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [07/07/2025 13:46:05] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3366 [15.3s]
INFO:    [07/07/2025 13:46:10] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [07/07/2025 13:46:11] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [07/07/2025 13:50:45] -> Extracting 320422 MS1 XICs
INFO:    [07/07/2025 13:55:22] -> Run 5/6: Cleaning Up Run...
INFO:    [07/07/2025 13:55:24] -> SuperRun 6/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d)
INFO:    [07/07/2025 13:55:24] -> Run 6/6: Organizing Data from Run
INFO:    [07/07/2025 13:55:24] -> Run 6/6: Creating Calibration Search Space...
INFO:    [07/07/2025 13:55:24] -> Run 6/6: Creating Search Space...
INFO:    [07/07/2025 13:55:24] -> Size of search space [MB]: 0
INFO:    [07/07/2025 13:55:24] -> Number of IMPGs in search space: 0
INFO:    [07/07/2025 13:55:24] -> Run 6/6: MS2 Index Generation
INFO:    [07/07/2025 13:55:26] -> MS2 Index Generation Time: 1.42s
INFO:    [07/07/2025 13:55:26] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [07/07/2025 13:55:40] -> Initializing...
INFO:    [07/07/2025 14:00:16] -> Finalizing HTRMS File...
INFO:    [07/07/2025 14:04:20] -> Processed in 8.7m
INFO:    [07/07/2025 14:04:27] -> Done
INFO:    [07/07/2025 14:04:27] -> Run 6/6: Process Raw File...
INFO:    [07/07/2025 14:05:04] -> Run 6/6: Preparing Partitions...
INFO:    [07/07/2025 14:05:04] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [07/07/2025 14:05:05] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [07/07/2025 14:05:35] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [07/07/2025 14:06:09] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3280 [33.3s]
INFO:    [07/07/2025 14:06:13] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [07/07/2025 14:06:14] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [07/07/2025 14:10:00] -> Extracting 318350 MS1 XICs
INFO:    [07/07/2025 14:14:26] -> Run 6/6: Cleaning Up Run...
INFO:    [07/07/2025 14:14:42] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [07/07/2025 14:14:48] -> Score Post-Processing
INFO:    [07/07/2025 14:18:06] -> Score Post-Processing: 3.31m
INFO:    [07/07/2025 14:18:06] -> PSM FDR...
INFO:    [07/07/2025 14:18:40] -> PSM FDR: 33.84s
INFO:    [07/07/2025 14:18:40] -> Converting to non-redundant data structure...
INFO:    [07/07/2025 14:18:59] -> Performing Peptide FDR...
INFO:    [07/07/2025 14:19:04] -> Performing Protein Inference...
INFO:    [07/07/2025 14:19:07] -> Performing Protein FDR...
INFO:    [07/07/2025 14:19:07] -> Calculating Result Values at Run and Experiment Level...
INFO:    [07/07/2025 14:19:20] -> Pulsar identified 352613 PSMs, 74765 stripped sequences, 84857 peptide precursors, 9532 protein groups.
INFO:    [07/07/2025 14:19:20] -> Calculating Summary...
INFO:    [07/07/2025 14:19:25] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 14:19:26] -> iRT Calibration...
INFO:    [07/07/2025 14:19:30] -> Performing directDIA+ search...
INFO:    [07/07/2025 14:23:13] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
INFO:    [07/07/2025 14:30:55] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
INFO:    [07/07/2025 14:38:42] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
INFO:    [07/07/2025 14:46:20] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
INFO:    [07/07/2025 14:53:52] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
INFO:    [07/07/2025 15:01:56] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
INFO:    [07/07/2025 15:08:52] -> Total nr of Searched Peptides: 2 038 707 of 2 038 707
INFO:    [07/07/2025 15:08:54] -> Performing directDIA+ Post Processing...
INFO:    [07/07/2025 15:09:05] -> Writing experiment store..
INFO:    [07/07/2025 15:09:14] -> Assigning iRT Source...
INFO:    [07/07/2025 15:09:14] -> Calculating iRT...
INFO:    [07/07/2025 15:09:14] -> Cleaning Up Experiment...
INFO:    [07/07/2025 15:09:14] -> Summarizing Identifications
INFO:    [07/07/2025 15:11:02] -> Identifiying Significant Precursors...
INFO:    [07/07/2025 15:11:27] -> Predicting Ion Mobility
INFO:    [07/07/2025 15:11:41] -> Calculating Median iRT
INFO:    [07/07/2025 15:11:44] -> Building BGS Protein Grouping...
INFO:    [07/07/2025 15:11:45] -> Digesting Fasta...
INFO:    [07/07/2025 15:11:45] -> Annotating Proteins...
INFO:    [07/07/2025 15:11:46] -> Grouping Proteins...
INFO:    [07/07/2025 15:11:49] -> Calculating Run Summary Statistics...
INFO:    [07/07/2025 15:12:30] -> Building Consensus Fragment Spectra...
INFO:    [07/07/2025 15:13:48] -> Selecting best fragment ions
INFO:    [07/07/2025 15:17:55] -> Initializing Experiment...
INFO:    [07/07/2025 15:17:55] -> Loading Spectral Libraries...
INFO:    [07/07/2025 15:18:48] -> Initialize Scoring...
INFO:    [07/07/2025 15:18:48] -> Generating Scan Map...
INFO:    [07/07/2025 15:18:49] -> Initializing Workpackages...
INFO:    [07/07/2025 15:18:49] -> Performing Basic Calibration...
INFO:    [07/07/2025 15:18:51] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 15:18:51] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 15:18:57] -> Initializing Pipeline...
INFO:    [07/07/2025 15:18:57] -> Preprocessing Run #1 of 6...
INFO:    [07/07/2025 15:18:57] -> Initialize Scoring...
INFO:    [07/07/2025 15:18:57] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:19:53] -> Machine Learning...
INFO:    [07/07/2025 15:19:55] -> Pipeline executed in 57.49s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:20:04] -> Initializing Pipeline...
INFO:    [07/07/2025 15:20:04] -> Preprocessing Run #1 of 6...
INFO:    [07/07/2025 15:20:04] -> Initialize Scoring...
INFO:    [07/07/2025 15:20:04] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:21:19] -> Machine Learning...
INFO:    [07/07/2025 15:21:26] -> Pipeline executed in 1.38m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:21:40] -> Initialize Scoring...
INFO:    [07/07/2025 15:21:40] -> Preprocessing Run #2 of 6...
INFO:    [07/07/2025 15:21:40] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 15:21:40] -> Initializing Experiment...
INFO:    [07/07/2025 15:21:40] -> Loading Spectral Libraries...
INFO:    [07/07/2025 15:21:40] -> Initialize Scoring...
INFO:    [07/07/2025 15:21:40] -> Generating Scan Map...
INFO:    [07/07/2025 15:21:40] -> Initializing Workpackages...
INFO:    [07/07/2025 15:21:40] -> Performing Basic Calibration...
INFO:    [07/07/2025 15:21:42] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 15:21:42] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 15:21:47] -> Initializing Pipeline...
INFO:    [07/07/2025 15:21:47] -> Preprocessing Run #2 of 6...
INFO:    [07/07/2025 15:21:47] -> Initialize Scoring...
INFO:    [07/07/2025 15:21:47] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:22:45] -> Machine Learning...
INFO:    [07/07/2025 15:22:46] -> Pipeline executed in 58.37s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:22:54] -> Initializing Pipeline...
INFO:    [07/07/2025 15:22:54] -> Preprocessing Run #2 of 6...
INFO:    [07/07/2025 15:22:54] -> Initialize Scoring...
INFO:    [07/07/2025 15:22:55] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:24:09] -> Machine Learning...
INFO:    [07/07/2025 15:24:15] -> Pipeline executed in 1.35m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:24:28] -> Initialize Scoring...
INFO:    [07/07/2025 15:24:28] -> Preprocessing Run #3 of 6...
INFO:    [07/07/2025 15:24:28] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 15:24:28] -> Initializing Experiment...
INFO:    [07/07/2025 15:24:28] -> Loading Spectral Libraries...
INFO:    [07/07/2025 15:24:28] -> Initialize Scoring...
INFO:    [07/07/2025 15:24:28] -> Generating Scan Map...
INFO:    [07/07/2025 15:24:29] -> Initializing Workpackages...
INFO:    [07/07/2025 15:24:29] -> Performing Basic Calibration...
INFO:    [07/07/2025 15:24:31] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 15:24:31] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 15:24:36] -> Initializing Pipeline...
INFO:    [07/07/2025 15:24:36] -> Preprocessing Run #3 of 6...
INFO:    [07/07/2025 15:24:36] -> Initialize Scoring...
INFO:    [07/07/2025 15:24:36] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:25:30] -> Machine Learning...
INFO:    [07/07/2025 15:25:31] -> Pipeline executed in 55.13s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:25:39] -> Initializing Pipeline...
INFO:    [07/07/2025 15:25:39] -> Preprocessing Run #3 of 6...
INFO:    [07/07/2025 15:25:39] -> Initialize Scoring...
INFO:    [07/07/2025 15:25:39] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:26:55] -> Machine Learning...
INFO:    [07/07/2025 15:27:02] -> Pipeline executed in 1.38m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:27:16] -> Initialize Scoring...
INFO:    [07/07/2025 15:27:16] -> Preprocessing Run #4 of 6...
INFO:    [07/07/2025 15:27:16] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 15:27:16] -> Initializing Experiment...
INFO:    [07/07/2025 15:27:16] -> Loading Spectral Libraries...
INFO:    [07/07/2025 15:27:16] -> Initialize Scoring...
INFO:    [07/07/2025 15:27:16] -> Generating Scan Map...
INFO:    [07/07/2025 15:27:16] -> Initializing Workpackages...
INFO:    [07/07/2025 15:27:16] -> Performing Basic Calibration...
INFO:    [07/07/2025 15:27:18] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 15:27:18] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 15:27:24] -> Initializing Pipeline...
INFO:    [07/07/2025 15:27:24] -> Preprocessing Run #4 of 6...
INFO:    [07/07/2025 15:27:24] -> Initialize Scoring...
INFO:    [07/07/2025 15:27:24] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:28:15] -> Machine Learning...
INFO:    [07/07/2025 15:28:16] -> Pipeline executed in 52.49s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:28:24] -> Initializing Pipeline...
INFO:    [07/07/2025 15:28:24] -> Preprocessing Run #4 of 6...
INFO:    [07/07/2025 15:28:24] -> Initialize Scoring...
INFO:    [07/07/2025 15:28:24] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:30:24] -> Machine Learning...
INFO:    [07/07/2025 15:30:32] -> Pipeline executed in 2.13m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:30:45] -> Initialize Scoring...
INFO:    [07/07/2025 15:30:45] -> Preprocessing Run #5 of 6...
INFO:    [07/07/2025 15:30:45] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 15:30:45] -> Initializing Experiment...
INFO:    [07/07/2025 15:30:45] -> Loading Spectral Libraries...
INFO:    [07/07/2025 15:30:45] -> Initialize Scoring...
INFO:    [07/07/2025 15:30:45] -> Generating Scan Map...
INFO:    [07/07/2025 15:30:45] -> Initializing Workpackages...
INFO:    [07/07/2025 15:30:45] -> Performing Basic Calibration...
INFO:    [07/07/2025 15:30:47] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 15:30:47] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 15:30:52] -> Initializing Pipeline...
INFO:    [07/07/2025 15:30:52] -> Preprocessing Run #5 of 6...
INFO:    [07/07/2025 15:30:52] -> Initialize Scoring...
INFO:    [07/07/2025 15:30:53] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:31:47] -> Machine Learning...
INFO:    [07/07/2025 15:31:48] -> Pipeline executed in 55.75s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:31:56] -> Initializing Pipeline...
INFO:    [07/07/2025 15:31:56] -> Preprocessing Run #5 of 6...
INFO:    [07/07/2025 15:31:56] -> Initialize Scoring...
INFO:    [07/07/2025 15:31:56] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:33:11] -> Machine Learning...
INFO:    [07/07/2025 15:33:17] -> Pipeline executed in 1.36m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:33:31] -> Initialize Scoring...
INFO:    [07/07/2025 15:33:31] -> Preprocessing Run #6 of 6...
INFO:    [07/07/2025 15:33:31] -> Searching DIA with Pulsar...
INFO:    [07/07/2025 15:33:31] -> Initializing Experiment...
INFO:    [07/07/2025 15:33:31] -> Loading Spectral Libraries...
INFO:    [07/07/2025 15:33:31] -> Initialize Scoring...
INFO:    [07/07/2025 15:33:31] -> Generating Scan Map...
INFO:    [07/07/2025 15:33:31] -> Initializing Workpackages...
INFO:    [07/07/2025 15:33:31] -> Performing Basic Calibration...
INFO:    [07/07/2025 15:33:33] -> Identifying Calibration Peptides...
INFO:    [07/07/2025 15:33:33] -> Correcting Gradient Fine Structure...
INFO:    [07/07/2025 15:33:38] -> Initializing Pipeline...
INFO:    [07/07/2025 15:33:38] -> Preprocessing Run #6 of 6...
INFO:    [07/07/2025 15:33:38] -> Initialize Scoring...
INFO:    [07/07/2025 15:33:38] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:34:29] -> Machine Learning...
INFO:    [07/07/2025 15:34:30] -> Pipeline executed in 51.75s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:34:37] -> Initializing Pipeline...
INFO:    [07/07/2025 15:34:37] -> Preprocessing Run #6 of 6...
INFO:    [07/07/2025 15:34:37] -> Initialize Scoring...
INFO:    [07/07/2025 15:34:37] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:35:51] -> Machine Learning...
INFO:    [07/07/2025 15:35:57] -> Pipeline executed in 1.33m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 15:36:10] -> Initialize Scoring...
INFO:    [07/07/2025 15:36:10] -> Initializing QC...
INFO:    [07/07/2025 15:36:11] -> Determining Calibration Parameter...
INFO:    [07/07/2025 15:36:11] -> Assigning ML Features...
INFO:    [07/07/2025 15:36:12] -> Generating Decoys...
INFO:    [07/07/2025 15:36:23] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:38:10] -> Releasing Raw Files...
INFO:    [07/07/2025 15:38:11] -> Machine Learning...
INFO:    [07/07/2025 15:40:43] -> Initializing HTRMS...
INFO:    [07/07/2025 15:40:43] -> Releasing Run Resources...
INFO:    [07/07/2025 15:40:43] -> Reducing Score Cache...
INFO:    [07/07/2025 15:40:47] -> Calculating Qvalues...
INFO:    [07/07/2025 15:40:52] -> Unique precursors: 129 944 of 137 255 | modified peptides: 114 182 of 119 836 | peptides: 112 996 of 118 612 |  protein groups: 11 793 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d]
INFO:    [07/07/2025 15:40:53] -> Collapsing Search Tree...
INFO:    [07/07/2025 15:40:53] -> Processed in 4.71m
INFO:    [07/07/2025 15:40:53] -> Initializing QC...
INFO:    [07/07/2025 15:40:53] -> Determining Calibration Parameter...
INFO:    [07/07/2025 15:40:53] -> Assigning ML Features...
INFO:    [07/07/2025 15:40:53] -> Generating Decoys...
INFO:    [07/07/2025 15:40:54] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:42:30] -> Releasing Raw Files...
INFO:    [07/07/2025 15:42:31] -> Machine Learning...
INFO:    [07/07/2025 15:45:25] -> Initializing HTRMS...
INFO:    [07/07/2025 15:45:25] -> Releasing Run Resources...
INFO:    [07/07/2025 15:45:26] -> Reducing Score Cache...
INFO:    [07/07/2025 15:45:30] -> Calculating Qvalues...
INFO:    [07/07/2025 15:45:37] -> Unique precursors: 129 795 of 137 255 | modified peptides: 114 041 of 119 836 | peptides: 112 858 of 118 612 |  protein groups: 11 779 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d]
INFO:    [07/07/2025 15:45:37] -> Collapsing Search Tree...
INFO:    [07/07/2025 15:45:37] -> Processed in 4.73m
INFO:    [07/07/2025 15:45:37] -> Initializing QC...
INFO:    [07/07/2025 15:45:37] -> Determining Calibration Parameter...
INFO:    [07/07/2025 15:45:37] -> Assigning ML Features...
INFO:    [07/07/2025 15:45:37] -> Generating Decoys...
INFO:    [07/07/2025 15:45:38] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:48:07] -> Releasing Raw Files...
INFO:    [07/07/2025 15:48:07] -> Machine Learning...
INFO:    [07/07/2025 15:50:29] -> Initializing HTRMS...
INFO:    [07/07/2025 15:50:29] -> Releasing Run Resources...
INFO:    [07/07/2025 15:50:29] -> Reducing Score Cache...
INFO:    [07/07/2025 15:50:33] -> Calculating Qvalues...
INFO:    [07/07/2025 15:50:40] -> Unique precursors: 130 238 of 137 255 | modified peptides: 114 366 of 119 836 | peptides: 113 193 of 118 612 |  protein groups: 11 781 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d]
INFO:    [07/07/2025 15:50:40] -> Collapsing Search Tree...
INFO:    [07/07/2025 15:50:40] -> Processed in 5.05m
INFO:    [07/07/2025 15:50:41] -> Initializing QC...
INFO:    [07/07/2025 15:50:41] -> Determining Calibration Parameter...
INFO:    [07/07/2025 15:50:41] -> Assigning ML Features...
INFO:    [07/07/2025 15:50:41] -> Generating Decoys...
INFO:    [07/07/2025 15:50:42] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:52:13] -> Releasing Raw Files...
INFO:    [07/07/2025 15:52:13] -> Machine Learning...
INFO:    [07/07/2025 15:54:28] -> Initializing HTRMS...
INFO:    [07/07/2025 15:54:28] -> Releasing Run Resources...
INFO:    [07/07/2025 15:54:28] -> Reducing Score Cache...
INFO:    [07/07/2025 15:54:32] -> Calculating Qvalues...
INFO:    [07/07/2025 15:54:41] -> Unique precursors: 129 967 of 137 255 | modified peptides: 114 150 of 119 836 | peptides: 112 964 of 118 612 |  protein groups: 11 807 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d]
INFO:    [07/07/2025 15:54:41] -> Collapsing Search Tree...
INFO:    [07/07/2025 15:54:41] -> Processed in 4.01m
INFO:    [07/07/2025 15:54:43] -> Initializing QC...
INFO:    [07/07/2025 15:54:43] -> Determining Calibration Parameter...
INFO:    [07/07/2025 15:54:43] -> Assigning ML Features...
INFO:    [07/07/2025 15:54:43] -> Generating Decoys...
INFO:    [07/07/2025 15:54:44] -> Extracting Ion Currents...
INFO:    [07/07/2025 15:56:18] -> Releasing Raw Files...
INFO:    [07/07/2025 15:56:18] -> Machine Learning...
INFO:    [07/07/2025 15:58:37] -> Initializing HTRMS...
INFO:    [07/07/2025 15:58:37] -> Releasing Run Resources...
INFO:    [07/07/2025 15:58:38] -> Reducing Score Cache...
INFO:    [07/07/2025 15:58:42] -> Calculating Qvalues...
INFO:    [07/07/2025 15:58:50] -> Unique precursors: 130 722 of 137 255 | modified peptides: 114 792 of 119 836 | peptides: 113 603 of 118 612 |  protein groups: 11 843 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d]
INFO:    [07/07/2025 15:58:50] -> Collapsing Search Tree...
INFO:    [07/07/2025 15:58:50] -> Processed in 4.12m
INFO:    [07/07/2025 15:58:50] -> Initializing QC...
INFO:    [07/07/2025 15:58:51] -> Determining Calibration Parameter...
INFO:    [07/07/2025 15:58:51] -> Assigning ML Features...
INFO:    [07/07/2025 15:58:51] -> Generating Decoys...
INFO:    [07/07/2025 15:58:52] -> Extracting Ion Currents...
INFO:    [07/07/2025 16:00:26] -> Releasing Raw Files...
INFO:    [07/07/2025 16:00:26] -> Machine Learning...
INFO:    [07/07/2025 16:03:30] -> Initializing HTRMS...
INFO:    [07/07/2025 16:03:30] -> Releasing Run Resources...
INFO:    [07/07/2025 16:03:31] -> Reducing Score Cache...
INFO:    [07/07/2025 16:03:34] -> Calculating Qvalues...
INFO:    [07/07/2025 16:03:38] -> Unique precursors: 129 248 of 137 255 | modified peptides: 113 445 of 119 836 | peptides: 112 271 of 118 612 |  protein groups: 11 821 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d]
INFO:    [07/07/2025 16:03:38] -> Collapsing Search Tree...
INFO:    [07/07/2025 16:03:38] -> Processed in 4.79m
INFO:    [07/07/2025 16:03:38] -> Normalizing Cscores...
INFO:    [07/07/2025 16:03:39] -> Calculating Global CVs
INFO:    [07/07/2025 16:03:40] -> Calculating Profile Qvalues...
INFO:    [07/07/2025 16:03:43] -> Initializing Protein Groups...
INFO:    [07/07/2025 16:04:10] -> Correcting Interferences...
INFO:    [07/07/2025 16:04:39] -> Calculating Global CVs
INFO:    [07/07/2025 16:04:41] -> Calculating Precursor Quantities...
INFO:    [07/07/2025 16:04:41] -> Normalizing Quantification...
INFO:    [07/07/2025 16:04:42] -> Performing Local Normalization...
INFO:    [07/07/2025 16:04:45] -> Calculating Global CVs
INFO:    [07/07/2025 16:04:47] -> Calculating Condition CVs
INFO:    [07/07/2025 16:04:50] -> Excluding Library Duplicates...
INFO:    [07/07/2025 16:04:51] -> Calculating Global CVs
INFO:    [07/07/2025 16:04:52] -> Building Protein Groups...
INFO:    [07/07/2025 16:05:09] -> Calculating Run-Wise Protein Group FDR...
INFO:    [07/07/2025 16:05:16] -> Annotating Protein Single Hits...
INFO:    [07/07/2025 16:05:17] -> Calculating Global CVs
INFO:    [07/07/2025 16:05:19] -> Updating Identification Counts...
INFO:    [07/07/2025 16:05:21] -> Subtracting background noise...
INFO:    [07/07/2025 16:05:28] -> Resetting existing imputation...
INFO:    [07/07/2025 16:05:28] -> Calculating Protein Quantities...
INFO:    [07/07/2025 16:05:30] -> Calculating Protein Quantities...
INFO:    [07/07/2025 16:05:30] -> Calculating MaxLFQ Protein Quantities...
INFO:    [07/07/2025 16:05:40] -> Collapsing PTM-Locations...
INFO:    [07/07/2025 16:05:40] -> PTM Stoichiometry calculation...
INFO:    [07/07/2025 16:05:40] -> Creating Protein Map...
INFO:    [07/07/2025 16:05:40] -> Compiling Run Summary Information...
INFO:    [07/07/2025 16:05:40] -> Running Post Analysis Processes...
INFO:    [07/07/2025 16:06:22] -> Saving Qc Data...
INFO:    [07/07/2025 16:06:29] -> Writing Summary Information...
INFO:    [07/07/2025 16:06:29] -> Unique precursors: 122 250 of 137 255 | modified peptides: 107 853 of 119 836 | peptides: 106 706 of 118 612 |  protein groups: 11 047 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [07/07/2025 16:06:29] -> Unique precursors: 122 711 of 137 255 | modified peptides: 108 255 of 119 836 | peptides: 107 104 of 118 612 |  protein groups: 11 047 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [07/07/2025 16:06:29] -> Unique precursors: 122 816 of 137 255 | modified peptides: 108 294 of 119 836 | peptides: 107 152 of 118 612 |  protein groups: 11 030 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [07/07/2025 16:06:29] -> Unique precursors: 122 911 of 137 255 | modified peptides: 108 382 of 119 836 | peptides: 107 227 of 118 612 |  protein groups: 11 133 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [07/07/2025 16:06:29] -> Unique precursors: 123 255 of 137 255 | modified peptides: 108 677 of 119 836 | peptides: 107 527 of 118 612 |  protein groups: 11 140 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [07/07/2025 16:06:29] -> Unique precursors: 123 115 of 137 255 | modified peptides: 108 569 of 119 836 | peptides: 107 422 of 118 612 |  protein groups: 11 133 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [07/07/2025 16:06:29] -> Unique precursors: 126 005 of 137 255 | modified peptides: 110 905 of 119 836 | peptides: 109 740 of 118 612 |  protein groups: 11 180 (Qvalue <= 0.01) for whole experiment "SN20_ttSCP_Proteobench_diaPASEF_july2025"

INFO:    [07/07/2025 16:06:29] -> Saving SNE File...
INFO:    [07/07/2025 16:06:29] -> Automatic SNE storage disabled
INFO:    [07/07/2025 16:06:31] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 16:06:31] -> Pipeline executed in 3.92h - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 19:53:06] -> Initializing Pipeline...
INFO:    [07/07/2025 19:53:06] -> Calculating Qvalues...
INFO:    [07/07/2025 19:53:06] -> Saving...
INFO:    [07/07/2025 19:53:21] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 19:53:21] -> Pipeline executed in 14.4s - Current Experiment had 0 Warnings and 0 Errors.
[END-LOG]
