Spectronaut 21.0.260602.94842
Computer Name: HALBARAD
User Domain Name: SPECTROMASSE
User Name: voyager
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 31-July-2026 23:06:38 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
   │  └─ Calibration Carry-Over:	False
   ├─ 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
   │  ├─ ISF Filter Rule:	Keep "Likely In-Source Fragmented" Peptides
   │  └─ Pvalue Estimator:	Kernel Density Estimator
   ├─ DIA Analysis\Pipeline Mode
   │  ├─ Export All XICs:	False
   │  ├─ Export report in Parquet format:	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
   │  │  ├─ Modification Enrichment:	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:	C:\Users\voyager\AppData\Roaming\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\Tolerances
   │  └─ Tolerances:	
   │     ├─ Calibration Tolerances:	
   │     │  ├─ MS1 Mass Tolerance Strategy:	Dynamic
   │     │  │  └─ Correction Factor:	1
   │     │  └─ MS2 Mass Tolerance Strategy:	Dynamic
   │     │     └─ Correction Factor:	1
   │     └─ Main Search Tolerances:	
   │        ├─ MS1 Mass Tolerance Strategy:	Relative
   │        │  └─ Tolerance (ppm):	15
   │        └─ MS2 Mass Tolerance Strategy:	Relative
   │           └─ Tolerance (ppm):	15
   ├─ 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:	None
   │  ├─ 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
   ├─ Pulsar Search\Identification
   │  ├─ directDIA Workflow:	directDIA+ (Deep)
   │  │  ├─ IM Sampling Reduction:	7
   │  │  └─ RT Sampling Reduction:	1
   │  ├─ PTM Localization Filter:	False
   │  ├─ Grouped Peptide FDR:	None
   │  └─ Semi-Specific Pipeline:	Smart Enumeration (SN20)
   ├─ 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::	Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin/P
   │  ├─ 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:	False
   │  │  ├─ Ion Loss Type:	False
   │  │  ├─ Ion Type:	False
   │  │  ├─ m/z :	True
   │  │  │  ├─ Max:	1700
   │  │  │  └─ Min:	100
   │  │  ├─ 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:	True
   │     │  ├─ Max Charge:	5
   │     │  └─ Min Charge:	1
   │     └─ Proteotypicity:	False
   ├─ Pulsar Search\Speed-Up
   │  ├─ MS2 Index:	Automatic
   │  └─ dia-PASEF Pre-Processing:	Automatic
   └─ 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\Public datasets\ProteoBench\Module_quant_DIA_diaPASEF\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 1
   ├─ HTRMS Version: 21.0.260602.94842
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 24-February-2026 09:47:25 UTC +01:00 
   │     ├─ Date Modified: 31-July-2026 20:57:51 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\Public datasets\ProteoBench\Module_quant_DIA_diaPASEF\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 2
   ├─ HTRMS Version: 21.0.260602.94842
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 24-February-2026 09:47:25 UTC +01:00 
   │     ├─ Date Modified: 31-July-2026 20:57:51 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\Public datasets\ProteoBench\Module_quant_DIA_diaPASEF\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 3
   ├─ HTRMS Version: 21.0.260602.94842
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 24-February-2026 09:47:25 UTC +01:00 
   │     ├─ Date Modified: 31-July-2026 20:57:51 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\Public datasets\ProteoBench\Module_quant_DIA_diaPASEF\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 4
   ├─ HTRMS Version: 21.0.260602.94842
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 24-February-2026 09:47:25 UTC +01:00 
   │     ├─ Date Modified: 31-July-2026 20:57:51 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\Public datasets\ProteoBench\Module_quant_DIA_diaPASEF\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 5
   ├─ HTRMS Version: 21.0.260602.94842
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 24-February-2026 09:47:25 UTC +01:00 
   │     ├─ Date Modified: 31-July-2026 20:57:51 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\Public datasets\ProteoBench\Module_quant_DIA_diaPASEF\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 6
   ├─ HTRMS Version: 21.0.260602.94842
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 24-February-2026 09:47:25 UTC +01:00 
   │     ├─ Date Modified: 31-July-2026 20:57:51 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:    [31/07/2026 15:16:26] -> Initializing Pipeline...
INFO:    [31/07/2026 15:16:26] -> Preprocessing Run #1 of 6...
INFO:    [31/07/2026 15:16:26] -> Searching DIA with Pulsar...
INFO:    [31/07/2026 15:16:28] -> Initialize Pipeline...
INFO:    [31/07/2026 15:16:28] -> Initialize Pipeline
INFO:    [31/07/2026 15:17:25] -> Initialize Pipeline...
INFO:    [31/07/2026 15:17:25] -> Creating Experiment Environment
INFO:    [31/07/2026 15:17:25] -> SuperRun 1/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d)
INFO:    [31/07/2026 15:17:25] -> Run 1/6: Organizing Data from Run
INFO:    [31/07/2026 15:17:25] -> Run 1/6: Creating Calibration Search Space...
INFO:    [31/07/2026 15:17:27] -> Run 1/6: Creating Search Space...
INFO:    [31/07/2026 15:17:27] -> Run 1/6: MS2 Index Generation
INFO:    [31/07/2026 15:17:28] -> MS2 Index Generation Time: 1.19s
INFO:    [31/07/2026 15:17:28] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [31/07/2026 15:17:45] -> Initializing...
INFO:    [31/07/2026 15:22:41] -> Finalizing Scan Map...
INFO:    [31/07/2026 15:27:49] -> Processed in 10.1m
INFO:    [31/07/2026 15:27:56] -> Done
INFO:    [31/07/2026 15:28:13] -> Run 1/6: Process Raw File...
INFO:    [31/07/2026 15:28:16] -> Run 1/6: Preparing Partitions...
INFO:    [31/07/2026 15:28:16] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [31/07/2026 15:28:17] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [31/07/2026 15:28:34] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [31/07/2026 15:28:56] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2772 [21.8s]
INFO:    [31/07/2026 15:29:12] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [31/07/2026 15:29:13] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [31/07/2026 15:33:08] -> Extracting 316182 MS1 XICs
INFO:    [31/07/2026 15:42:11] -> Run 1/6: Score Post-Processing
INFO:    [31/07/2026 15:45:07] -> Run 1/6: Cleaning Up Run...
INFO:    [31/07/2026 15:45:11] -> SuperRun 2/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d)
INFO:    [31/07/2026 15:45:11] -> Run 2/6: Organizing Data from Run
INFO:    [31/07/2026 15:45:11] -> Run 2/6: Creating Calibration Search Space...
INFO:    [31/07/2026 15:45:11] -> Run 2/6: Creating Search Space...
INFO:    [31/07/2026 15:45:11] -> Run 2/6: MS2 Index Generation
INFO:    [31/07/2026 15:45:12] -> MS2 Index Generation Time: 1.29s
INFO:    [31/07/2026 15:45:12] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [31/07/2026 15:45:39] -> Initializing...
INFO:    [31/07/2026 15:54:31] -> Finalizing Scan Map...
INFO:    [31/07/2026 15:58:50] -> Processed in 13.2m
INFO:    [31/07/2026 15:58:54] -> Done
INFO:    [31/07/2026 15:59:14] -> Run 2/6: Process Raw File...
INFO:    [31/07/2026 15:59:16] -> Run 2/6: Preparing Partitions...
INFO:    [31/07/2026 15:59:16] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [31/07/2026 15:59:17] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [31/07/2026 15:59:34] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [31/07/2026 15:59:54] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2863 [20.1s]
INFO:    [31/07/2026 16:00:12] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [31/07/2026 16:00:13] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [31/07/2026 16:04:26] -> Extracting 343192 MS1 XICs
INFO:    [31/07/2026 16:13:54] -> Run 2/6: Score Post-Processing
INFO:    [31/07/2026 16:15:42] -> Run 2/6: Cleaning Up Run...
INFO:    [31/07/2026 16:15:45] -> SuperRun 3/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d)
INFO:    [31/07/2026 16:15:45] -> Run 3/6: Organizing Data from Run
INFO:    [31/07/2026 16:15:45] -> Run 3/6: Creating Calibration Search Space...
INFO:    [31/07/2026 16:15:45] -> Run 3/6: Creating Search Space...
INFO:    [31/07/2026 16:15:45] -> Run 3/6: MS2 Index Generation
INFO:    [31/07/2026 16:15:46] -> MS2 Index Generation Time: 1.24s
INFO:    [31/07/2026 16:15:46] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [31/07/2026 16:16:06] -> Initializing...
INFO:    [31/07/2026 16:21:28] -> Finalizing Scan Map...
INFO:    [31/07/2026 16:26:01] -> Processed in 9.9m
INFO:    [31/07/2026 16:26:05] -> Done
INFO:    [31/07/2026 16:26:23] -> Run 3/6: Process Raw File...
INFO:    [31/07/2026 16:26:27] -> Run 3/6: Preparing Partitions...
INFO:    [31/07/2026 16:26:27] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [31/07/2026 16:26:28] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [31/07/2026 16:26:46] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [31/07/2026 16:27:06] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2717 [19.7s]
INFO:    [31/07/2026 16:27:32] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [31/07/2026 16:27:33] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [31/07/2026 16:32:26] -> Extracting 342318 MS1 XICs
INFO:    [31/07/2026 16:41:57] -> Run 3/6: Score Post-Processing
INFO:    [31/07/2026 16:44:07] -> Run 3/6: Cleaning Up Run...
INFO:    [31/07/2026 16:44:10] -> SuperRun 4/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d)
INFO:    [31/07/2026 16:44:10] -> Run 4/6: Organizing Data from Run
INFO:    [31/07/2026 16:44:10] -> Run 4/6: Creating Calibration Search Space...
INFO:    [31/07/2026 16:44:10] -> Run 4/6: Creating Search Space...
INFO:    [31/07/2026 16:44:10] -> Run 4/6: MS2 Index Generation
INFO:    [31/07/2026 16:44:12] -> MS2 Index Generation Time: 1.34s
INFO:    [31/07/2026 16:44:12] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [31/07/2026 16:44:41] -> Initializing...
INFO:    [31/07/2026 16:51:40] -> Finalizing Scan Map...
INFO:    [31/07/2026 16:59:35] -> Processed in 14.9m
INFO:    [31/07/2026 16:59:41] -> Done
INFO:    [31/07/2026 17:00:00] -> Run 4/6: Process Raw File...
INFO:    [31/07/2026 17:00:04] -> Run 4/6: Preparing Partitions...
INFO:    [31/07/2026 17:00:04] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [31/07/2026 17:00:06] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [31/07/2026 17:00:22] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [31/07/2026 17:00:41] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2852 [18.7s]
INFO:    [31/07/2026 17:01:06] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [31/07/2026 17:01:08] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [31/07/2026 17:05:08] -> Extracting 357995 MS1 XICs
INFO:    [31/07/2026 17:15:42] -> Run 4/6: Score Post-Processing
INFO:    [31/07/2026 17:18:04] -> Run 4/6: Cleaning Up Run...
INFO:    [31/07/2026 17:18:08] -> SuperRun 5/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d)
INFO:    [31/07/2026 17:18:08] -> Run 5/6: Organizing Data from Run
INFO:    [31/07/2026 17:18:08] -> Run 5/6: Creating Calibration Search Space...
INFO:    [31/07/2026 17:18:08] -> Run 5/6: Creating Search Space...
INFO:    [31/07/2026 17:18:08] -> Run 5/6: MS2 Index Generation
INFO:    [31/07/2026 17:18:09] -> MS2 Index Generation Time: 1.21s
INFO:    [31/07/2026 17:18:09] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [31/07/2026 17:18:32] -> Initializing...
INFO:    [31/07/2026 17:23:33] -> Finalizing Scan Map...
INFO:    [31/07/2026 17:27:53] -> Processed in 9.3m
INFO:    [31/07/2026 17:27:59] -> Done
INFO:    [31/07/2026 17:28:16] -> Run 5/6: Process Raw File...
INFO:    [31/07/2026 17:28:21] -> Run 5/6: Preparing Partitions...
INFO:    [31/07/2026 17:28:21] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [31/07/2026 17:28:22] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [31/07/2026 17:28:39] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [31/07/2026 17:28:57] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3026 [18.2s]
INFO:    [31/07/2026 17:29:28] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [31/07/2026 17:29:30] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [31/07/2026 17:34:18] -> Extracting 336962 MS1 XICs
INFO:    [31/07/2026 17:43:11] -> Run 5/6: Score Post-Processing
INFO:    [31/07/2026 17:45:14] -> Run 5/6: Cleaning Up Run...
INFO:    [31/07/2026 17:45:14] -> SuperRun 6/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d)
INFO:    [31/07/2026 17:45:14] -> Run 6/6: Organizing Data from Run
INFO:    [31/07/2026 17:45:14] -> Run 6/6: Creating Calibration Search Space...
INFO:    [31/07/2026 17:45:14] -> Run 6/6: Creating Search Space...
INFO:    [31/07/2026 17:45:14] -> Run 6/6: MS2 Index Generation
INFO:    [31/07/2026 17:45:15] -> MS2 Index Generation Time: 1.23s
INFO:    [31/07/2026 17:45:15] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [31/07/2026 17:45:39] -> Initializing...
INFO:    [31/07/2026 17:51:02] -> Finalizing Scan Map...
INFO:    [31/07/2026 17:54:58] -> Processed in 9.3m
INFO:    [31/07/2026 17:55:06] -> Done
INFO:    [31/07/2026 17:55:25] -> Run 6/6: Process Raw File...
INFO:    [31/07/2026 17:55:29] -> Run 6/6: Preparing Partitions...
INFO:    [31/07/2026 17:55:29] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [31/07/2026 17:55:30] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [31/07/2026 17:55:47] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [31/07/2026 17:56:08] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2835 [21.7s]
INFO:    [31/07/2026 17:56:28] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [31/07/2026 17:56:30] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [31/07/2026 18:00:36] -> Extracting 333776 MS1 XICs
INFO:    [31/07/2026 18:09:59] -> Run 6/6: Score Post-Processing
INFO:    [31/07/2026 18:11:39] -> Run 6/6: Cleaning Up Run...
INFO:    [31/07/2026 18:11:57] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [31/07/2026 18:12:01] -> PSM FDR...
INFO:    [31/07/2026 18:12:01] -> PSM FDR: 492.26ms
INFO:    [31/07/2026 18:12:05] -> Converting to non-redundant data structure...
INFO:    [31/07/2026 18:12:29] -> Performing Peptide FDR...
INFO:    [31/07/2026 18:12:39] -> Performing Protein Inference...
INFO:    [31/07/2026 18:12:47] -> Performing Protein FDR...
INFO:    [31/07/2026 18:12:51] -> Calculating Result Values at Run and Experiment Level...
INFO:    [31/07/2026 18:13:03] -> Pulsar identified 360584 PSMs, 78540 stripped sequences, 88776 peptide precursors, 9781 protein groups.
INFO:    [31/07/2026 18:13:03] -> Annotating In-Source Fragmentation...
INFO:    [31/07/2026 18:13:04] -> iRT Calibration...
INFO:    [31/07/2026 18:13:09] -> Performing directDIA+ search fine tuning...
INFO:    [31/07/2026 18:54:59] -> Performing directDIA+ search...
INFO:    [31/07/2026 18:55:00] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
INFO:    [31/07/2026 19:21:44] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
INFO:    [31/07/2026 19:39:16] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
INFO:    [31/07/2026 19:54:03] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
INFO:    [31/07/2026 20:06:29] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
INFO:    [31/07/2026 20:21:09] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
INFO:    [31/07/2026 20:33:48] -> Total nr of Searched Peptides: 1 502 070 of 2 338 049
INFO:    [31/07/2026 20:33:52] -> Initializing Combined Protein Inference...
INFO:    [31/07/2026 20:47:43] -> Performing Protein Inference...
INFO:    [31/07/2026 20:47:52] -> Performing Protein FDR...
INFO:    [31/07/2026 20:47:53] -> Calculating Result Values at Run and Experiment Level...
INFO:    [31/07/2026 20:48:05] -> Pulsar identified 360588 PSMs, 78544 stripped sequences, 88780 peptide precursors, 9804 protein groups.
INFO:    [31/07/2026 20:48:05] -> Calculating Summary...
INFO:    [31/07/2026 20:48:11] -> Identifying Calibration Peptides...
INFO:    [31/07/2026 20:48:12] -> Performing directDIA+ Post Processing...
INFO:    [31/07/2026 20:51:40] -> Combining Protein-Group FDR Results...
INFO:    [31/07/2026 20:51:41] -> Combined Protein-Group Identifications at 1% Qvalue: 13 013
INFO:    [31/07/2026 20:51:41] -> Writing experiment store..
INFO:    [31/07/2026 20:52:06] -> Assigning iRT Source...
INFO:    [31/07/2026 20:52:06] -> Calculating iRT...
INFO:    [31/07/2026 20:52:07] -> Cleaning Up Experiment...
INFO:    [31/07/2026 20:52:07] -> Summarizing Identifications
INFO:    [31/07/2026 20:53:41] -> Predicting Ion Mobility
INFO:    [31/07/2026 20:56:01] -> Calculating Median iRT
INFO:    [31/07/2026 20:56:04] -> Building BGS Protein Grouping...
INFO:    [31/07/2026 20:56:05] -> Digesting Fasta...
INFO:    [31/07/2026 20:56:05] -> Annotating Proteins...
INFO:    [31/07/2026 20:56:06] -> Grouping Proteins...
INFO:    [31/07/2026 20:56:10] -> Calculating Run Summary Statistics...
INFO:    [31/07/2026 20:56:22] -> Building Consensus Fragment Spectra...
INFO:    [31/07/2026 20:56:46] -> Selecting best fragment ions
INFO:    [31/07/2026 20:56:46] -> Condensing Global Results...
INFO:    [31/07/2026 20:58:05] -> Protein Groups: 12316 (12440), Protein Id: 12500 (12643), Modified Peptides: 126969, Precursors: 147125, Peptides: 125799, Fragments: 877604
INFO:    [31/07/2026 20:58:59] -> Initializing Experiment...
INFO:    [31/07/2026 20:58:59] -> Loading Spectral Libraries...
INFO:    [31/07/2026 21:33:23] -> Initialize Scoring...
INFO:    [31/07/2026 21:33:23] -> Generating Scan Map...
INFO:    [31/07/2026 21:33:23] -> Initializing Workpackages...
INFO:    [31/07/2026 21:33:23] -> Performing Basic Calibration...
INFO:    [31/07/2026 21:33:24] -> Calibration successful
INFO:    [31/07/2026 21:33:24] -> Identifying Calibration Peptides...
INFO:    [31/07/2026 21:33:24] -> Calibration successful
INFO:    [31/07/2026 21:33:24] -> Correcting Gradient Fine Structure...
INFO:    [31/07/2026 21:33:29] -> Initializing Pipeline...
INFO:    [31/07/2026 21:33:29] -> Preprocessing Run #1 of 6...
INFO:    [31/07/2026 21:33:29] -> Initialize Scoring...
INFO:    [31/07/2026 21:33:29] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:34:34] -> Machine Learning...
INFO:    [31/07/2026 21:34:35] -> Pipeline executed in 1.1m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:34:35] -> Calibration successful
INFO:    [31/07/2026 21:34:40] -> Initializing Pipeline...
INFO:    [31/07/2026 21:34:40] -> Preprocessing Run #1 of 6...
INFO:    [31/07/2026 21:34:40] -> Initialize Scoring...
INFO:    [31/07/2026 21:34:40] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:35:48] -> Machine Learning...
INFO:    [31/07/2026 21:35:56] -> Pipeline executed in 1.27m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:36:04] -> Calibration successful
INFO:    [31/07/2026 21:36:04] -> Initialize Scoring...
INFO:    [31/07/2026 21:36:04] -> Preprocessing Run #2 of 6...
INFO:    [31/07/2026 21:36:04] -> Searching DIA with Pulsar...
INFO:    [31/07/2026 21:36:04] -> Initializing Experiment...
INFO:    [31/07/2026 21:36:04] -> Loading Spectral Libraries...
INFO:    [31/07/2026 21:36:04] -> Initialize Scoring...
INFO:    [31/07/2026 21:36:04] -> Generating Scan Map...
INFO:    [31/07/2026 21:36:04] -> Initializing Workpackages...
INFO:    [31/07/2026 21:36:04] -> Performing Basic Calibration...
INFO:    [31/07/2026 21:36:05] -> Calibration successful
INFO:    [31/07/2026 21:36:05] -> Identifying Calibration Peptides...
INFO:    [31/07/2026 21:36:05] -> Calibration successful
INFO:    [31/07/2026 21:36:05] -> Correcting Gradient Fine Structure...
INFO:    [31/07/2026 21:36:09] -> Initializing Pipeline...
INFO:    [31/07/2026 21:36:09] -> Preprocessing Run #2 of 6...
INFO:    [31/07/2026 21:36:09] -> Initialize Scoring...
INFO:    [31/07/2026 21:36:09] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:36:59] -> Machine Learning...
INFO:    [31/07/2026 21:37:00] -> Pipeline executed in 50.88s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:37:01] -> Calibration successful
INFO:    [31/07/2026 21:37:05] -> Initializing Pipeline...
INFO:    [31/07/2026 21:37:05] -> Preprocessing Run #2 of 6...
INFO:    [31/07/2026 21:37:05] -> Initialize Scoring...
INFO:    [31/07/2026 21:37:05] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:38:13] -> Machine Learning...
INFO:    [31/07/2026 21:38:21] -> Pipeline executed in 1.26m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:38:30] -> Calibration successful
INFO:    [31/07/2026 21:38:30] -> Initialize Scoring...
INFO:    [31/07/2026 21:38:30] -> Preprocessing Run #3 of 6...
INFO:    [31/07/2026 21:38:30] -> Searching DIA with Pulsar...
INFO:    [31/07/2026 21:38:30] -> Initializing Experiment...
INFO:    [31/07/2026 21:38:30] -> Loading Spectral Libraries...
INFO:    [31/07/2026 21:38:30] -> Initialize Scoring...
INFO:    [31/07/2026 21:38:30] -> Generating Scan Map...
INFO:    [31/07/2026 21:38:30] -> Initializing Workpackages...
INFO:    [31/07/2026 21:38:30] -> Performing Basic Calibration...
INFO:    [31/07/2026 21:38:30] -> Calibration successful
INFO:    [31/07/2026 21:38:30] -> Identifying Calibration Peptides...
INFO:    [31/07/2026 21:38:30] -> Calibration successful
INFO:    [31/07/2026 21:38:30] -> Correcting Gradient Fine Structure...
INFO:    [31/07/2026 21:38:35] -> Initializing Pipeline...
INFO:    [31/07/2026 21:38:35] -> Preprocessing Run #3 of 6...
INFO:    [31/07/2026 21:38:35] -> Initialize Scoring...
INFO:    [31/07/2026 21:38:35] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:39:25] -> Machine Learning...
INFO:    [31/07/2026 21:39:27] -> Pipeline executed in 52.12s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:39:27] -> Calibration successful
INFO:    [31/07/2026 21:39:31] -> Initializing Pipeline...
INFO:    [31/07/2026 21:39:31] -> Preprocessing Run #3 of 6...
INFO:    [31/07/2026 21:39:31] -> Initialize Scoring...
INFO:    [31/07/2026 21:39:32] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:40:37] -> Machine Learning...
INFO:    [31/07/2026 21:40:45] -> Pipeline executed in 1.22m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:40:53] -> Calibration successful
INFO:    [31/07/2026 21:40:53] -> Initialize Scoring...
INFO:    [31/07/2026 21:40:53] -> Preprocessing Run #4 of 6...
INFO:    [31/07/2026 21:40:53] -> Searching DIA with Pulsar...
INFO:    [31/07/2026 21:40:53] -> Initializing Experiment...
INFO:    [31/07/2026 21:40:53] -> Loading Spectral Libraries...
INFO:    [31/07/2026 21:40:53] -> Initialize Scoring...
INFO:    [31/07/2026 21:40:53] -> Generating Scan Map...
INFO:    [31/07/2026 21:40:53] -> Initializing Workpackages...
INFO:    [31/07/2026 21:40:53] -> Performing Basic Calibration...
INFO:    [31/07/2026 21:40:54] -> Calibration successful
INFO:    [31/07/2026 21:40:54] -> Identifying Calibration Peptides...
INFO:    [31/07/2026 21:40:54] -> Calibration successful
INFO:    [31/07/2026 21:40:54] -> Correcting Gradient Fine Structure...
INFO:    [31/07/2026 21:40:58] -> Initializing Pipeline...
INFO:    [31/07/2026 21:40:58] -> Preprocessing Run #4 of 6...
INFO:    [31/07/2026 21:40:58] -> Initialize Scoring...
INFO:    [31/07/2026 21:40:58] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:41:49] -> Machine Learning...
INFO:    [31/07/2026 21:41:50] -> Pipeline executed in 52.17s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:41:50] -> Calibration successful
INFO:    [31/07/2026 21:41:55] -> Initializing Pipeline...
INFO:    [31/07/2026 21:41:55] -> Preprocessing Run #4 of 6...
INFO:    [31/07/2026 21:41:55] -> Initialize Scoring...
INFO:    [31/07/2026 21:41:55] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:43:04] -> Machine Learning...
INFO:    [31/07/2026 21:43:13] -> Pipeline executed in 1.31m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:43:21] -> Calibration successful
INFO:    [31/07/2026 21:43:21] -> Initialize Scoring...
INFO:    [31/07/2026 21:43:21] -> Preprocessing Run #5 of 6...
INFO:    [31/07/2026 21:43:21] -> Searching DIA with Pulsar...
INFO:    [31/07/2026 21:43:21] -> Initializing Experiment...
INFO:    [31/07/2026 21:43:21] -> Loading Spectral Libraries...
INFO:    [31/07/2026 21:43:21] -> Initialize Scoring...
INFO:    [31/07/2026 21:43:21] -> Generating Scan Map...
INFO:    [31/07/2026 21:43:22] -> Initializing Workpackages...
INFO:    [31/07/2026 21:43:22] -> Performing Basic Calibration...
INFO:    [31/07/2026 21:43:22] -> Calibration successful
INFO:    [31/07/2026 21:43:22] -> Identifying Calibration Peptides...
INFO:    [31/07/2026 21:43:22] -> Calibration successful
INFO:    [31/07/2026 21:43:22] -> Correcting Gradient Fine Structure...
INFO:    [31/07/2026 21:43:26] -> Initializing Pipeline...
INFO:    [31/07/2026 21:43:26] -> Preprocessing Run #5 of 6...
INFO:    [31/07/2026 21:43:26] -> Initialize Scoring...
INFO:    [31/07/2026 21:43:26] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:44:21] -> Machine Learning...
INFO:    [31/07/2026 21:44:24] -> Pipeline executed in 57.94s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:44:25] -> Calibration successful
INFO:    [31/07/2026 21:44:29] -> Initializing Pipeline...
INFO:    [31/07/2026 21:44:29] -> Preprocessing Run #5 of 6...
INFO:    [31/07/2026 21:44:29] -> Initialize Scoring...
INFO:    [31/07/2026 21:44:29] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:45:35] -> Machine Learning...
INFO:    [31/07/2026 21:45:42] -> Pipeline executed in 1.22m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:45:51] -> Calibration successful
INFO:    [31/07/2026 21:45:51] -> Initialize Scoring...
INFO:    [31/07/2026 21:45:51] -> Preprocessing Run #6 of 6...
INFO:    [31/07/2026 21:45:51] -> Searching DIA with Pulsar...
INFO:    [31/07/2026 21:45:51] -> Initializing Experiment...
INFO:    [31/07/2026 21:45:51] -> Loading Spectral Libraries...
INFO:    [31/07/2026 21:45:51] -> Initialize Scoring...
INFO:    [31/07/2026 21:45:51] -> Generating Scan Map...
INFO:    [31/07/2026 21:45:51] -> Initializing Workpackages...
INFO:    [31/07/2026 21:45:51] -> Performing Basic Calibration...
INFO:    [31/07/2026 21:45:52] -> Calibration successful
INFO:    [31/07/2026 21:45:52] -> Identifying Calibration Peptides...
INFO:    [31/07/2026 21:45:52] -> Calibration successful
INFO:    [31/07/2026 21:45:52] -> Correcting Gradient Fine Structure...
INFO:    [31/07/2026 21:45:56] -> Initializing Pipeline...
INFO:    [31/07/2026 21:45:56] -> Preprocessing Run #6 of 6...
INFO:    [31/07/2026 21:45:56] -> Initialize Scoring...
INFO:    [31/07/2026 21:45:56] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:46:51] -> Machine Learning...
INFO:    [31/07/2026 21:46:52] -> Pipeline executed in 56.35s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:46:53] -> Calibration successful
INFO:    [31/07/2026 21:46:57] -> Initializing Pipeline...
INFO:    [31/07/2026 21:46:57] -> Preprocessing Run #6 of 6...
INFO:    [31/07/2026 21:46:57] -> Initialize Scoring...
INFO:    [31/07/2026 21:46:57] -> Extracting Ion Currents...
INFO:    [31/07/2026 21:48:29] -> Machine Learning...
INFO:    [31/07/2026 21:48:38] -> Pipeline executed in 1.68m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [31/07/2026 21:48:50] -> Calibration successful
INFO:    [31/07/2026 21:48:50] -> Initialize Scoring...
INFO:    [31/07/2026 21:48:51] -> Initializing QC...
INFO:    [31/07/2026 21:48:51] -> Determining Calibration Parameter...
INFO:    [31/07/2026 21:48:52] -> Assigning ML Features...
INFO:    [31/07/2026 21:48:54] -> Generating Decoys...
INFO:    [31/07/2026 22:02:27] -> Extracting Ion Currents...
INFO:    [31/07/2026 22:05:49] -> Releasing Raw Files...
INFO:    [31/07/2026 22:05:49] -> Machine Learning...
INFO:    [31/07/2026 22:10:00] -> Initializing HTRMS...
INFO:    [31/07/2026 22:10:00] -> Releasing Run Resources...
INFO:    [31/07/2026 22:10:02] -> Reducing Score Cache...
INFO:    [31/07/2026 22:10:15] -> Calculating Qvalues...
INFO:    [31/07/2026 22:10:22] -> Unique precursors: 141 292 of 147 125 | modified peptides: 122 798 of 126 969 | peptides: 121 649 of 125 799 |  protein groups: 12 126 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d]
INFO:    [31/07/2026 22:10:22] -> Calibration successful
INFO:    [31/07/2026 22:10:22] -> Annotating In-Source Fragmentation...
INFO:    [31/07/2026 22:10:24] -> Collapsing Search Tree...
INFO:    [31/07/2026 22:10:24] -> Processed in 21.57m
INFO:    [31/07/2026 22:10:25] -> Initializing QC...
INFO:    [31/07/2026 22:10:25] -> Determining Calibration Parameter...
INFO:    [31/07/2026 22:10:26] -> Assigning ML Features...
INFO:    [31/07/2026 22:10:26] -> Generating Decoys...
INFO:    [31/07/2026 22:10:27] -> Extracting Ion Currents...
INFO:    [31/07/2026 22:14:52] -> Releasing Raw Files...
INFO:    [31/07/2026 22:14:53] -> Machine Learning...
INFO:    [31/07/2026 22:19:23] -> Initializing HTRMS...
INFO:    [31/07/2026 22:19:23] -> Releasing Run Resources...
INFO:    [31/07/2026 22:19:24] -> Reducing Score Cache...
INFO:    [31/07/2026 22:19:29] -> Calculating Qvalues...
INFO:    [31/07/2026 22:19:36] -> Unique precursors: 140 257 of 147 125 | modified peptides: 122 022 of 126 969 | peptides: 120 877 of 125 799 |  protein groups: 12 053 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d]
INFO:    [31/07/2026 22:19:36] -> Calibration successful
INFO:    [31/07/2026 22:19:37] -> Annotating In-Source Fragmentation...
INFO:    [31/07/2026 22:19:39] -> Collapsing Search Tree...
INFO:    [31/07/2026 22:19:40] -> Processed in 9.25m
INFO:    [31/07/2026 22:19:40] -> Initializing QC...
INFO:    [31/07/2026 22:19:40] -> Determining Calibration Parameter...
INFO:    [31/07/2026 22:19:41] -> Assigning ML Features...
INFO:    [31/07/2026 22:19:42] -> Generating Decoys...
INFO:    [31/07/2026 22:19:44] -> Extracting Ion Currents...
INFO:    [31/07/2026 22:23:36] -> Releasing Raw Files...
INFO:    [31/07/2026 22:23:36] -> Machine Learning...
INFO:    [31/07/2026 22:27:38] -> Initializing HTRMS...
INFO:    [31/07/2026 22:27:38] -> Releasing Run Resources...
INFO:    [31/07/2026 22:27:40] -> Reducing Score Cache...
INFO:    [31/07/2026 22:27:52] -> Calculating Qvalues...
INFO:    [31/07/2026 22:28:00] -> Unique precursors: 141 291 of 147 125 | modified peptides: 122 793 of 126 969 | peptides: 121 649 of 125 799 |  protein groups: 12 111 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d]
INFO:    [31/07/2026 22:28:00] -> Calibration successful
INFO:    [31/07/2026 22:28:01] -> Annotating In-Source Fragmentation...
INFO:    [31/07/2026 22:28:02] -> Collapsing Search Tree...
INFO:    [31/07/2026 22:28:03] -> Processed in 8.38m
INFO:    [31/07/2026 22:28:03] -> Initializing QC...
INFO:    [31/07/2026 22:28:03] -> Determining Calibration Parameter...
INFO:    [31/07/2026 22:28:04] -> Assigning ML Features...
INFO:    [31/07/2026 22:28:04] -> Generating Decoys...
INFO:    [31/07/2026 22:28:05] -> Extracting Ion Currents...
INFO:    [31/07/2026 22:33:19] -> Releasing Raw Files...
INFO:    [31/07/2026 22:33:19] -> Machine Learning...
INFO:    [31/07/2026 22:38:33] -> Initializing HTRMS...
INFO:    [31/07/2026 22:38:33] -> Releasing Run Resources...
INFO:    [31/07/2026 22:38:34] -> Reducing Score Cache...
INFO:    [31/07/2026 22:38:43] -> Calculating Qvalues...
INFO:    [31/07/2026 22:38:58] -> Unique precursors: 141 439 of 147 125 | modified peptides: 122 913 of 126 969 | peptides: 121 753 of 125 799 |  protein groups: 12 182 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d]
INFO:    [31/07/2026 22:38:58] -> Calibration successful
INFO:    [31/07/2026 22:38:58] -> Annotating In-Source Fragmentation...
INFO:    [31/07/2026 22:39:00] -> Collapsing Search Tree...
INFO:    [31/07/2026 22:39:01] -> Processed in 10.96m
INFO:    [31/07/2026 22:39:01] -> Initializing QC...
INFO:    [31/07/2026 22:39:01] -> Determining Calibration Parameter...
INFO:    [31/07/2026 22:39:02] -> Assigning ML Features...
INFO:    [31/07/2026 22:39:02] -> Generating Decoys...
INFO:    [31/07/2026 22:39:04] -> Extracting Ion Currents...
INFO:    [31/07/2026 22:42:58] -> Releasing Raw Files...
INFO:    [31/07/2026 22:42:58] -> Machine Learning...
INFO:    [31/07/2026 22:47:09] -> Initializing HTRMS...
INFO:    [31/07/2026 22:47:10] -> Releasing Run Resources...
INFO:    [31/07/2026 22:47:12] -> Reducing Score Cache...
INFO:    [31/07/2026 22:47:32] -> Calculating Qvalues...
INFO:    [31/07/2026 22:47:41] -> Unique precursors: 141 652 of 147 125 | modified peptides: 123 135 of 126 969 | peptides: 121 977 of 125 799 |  protein groups: 12 162 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d]
INFO:    [31/07/2026 22:47:41] -> Calibration successful
INFO:    [31/07/2026 22:47:41] -> Annotating In-Source Fragmentation...
INFO:    [31/07/2026 22:47:43] -> Collapsing Search Tree...
INFO:    [31/07/2026 22:47:43] -> Processed in 8.7m
INFO:    [31/07/2026 22:47:44] -> Initializing QC...
INFO:    [31/07/2026 22:47:44] -> Determining Calibration Parameter...
INFO:    [31/07/2026 22:47:44] -> Assigning ML Features...
INFO:    [31/07/2026 22:47:45] -> Generating Decoys...
INFO:    [31/07/2026 22:47:47] -> Extracting Ion Currents...
INFO:    [31/07/2026 22:53:10] -> Releasing Raw Files...
INFO:    [31/07/2026 22:53:10] -> Machine Learning...
INFO:    [31/07/2026 22:57:33] -> Initializing HTRMS...
INFO:    [31/07/2026 22:57:33] -> Releasing Run Resources...
INFO:    [31/07/2026 22:57:33] -> Reducing Score Cache...
INFO:    [31/07/2026 22:57:38] -> Calculating Qvalues...
INFO:    [31/07/2026 22:57:42] -> Unique precursors: 141 104 of 147 125 | modified peptides: 122 639 of 126 969 | peptides: 121 488 of 125 799 |  protein groups: 12 151 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d]
INFO:    [31/07/2026 22:57:42] -> Calibration successful
INFO:    [31/07/2026 22:57:42] -> Annotating In-Source Fragmentation...
INFO:    [31/07/2026 22:57:43] -> Collapsing Search Tree...
INFO:    [31/07/2026 22:57:43] -> Processed in 10m
INFO:    [31/07/2026 22:57:43] -> Normalizing Cscores...
INFO:    [31/07/2026 22:57:44] -> Calculating Global CVs
INFO:    [31/07/2026 22:57:46] -> Calculating Profile Qvalues...
INFO:    [31/07/2026 22:57:49] -> Initializing Protein Groups...
INFO:    [31/07/2026 22:58:20] -> Correcting Interferences...
INFO:    [31/07/2026 22:58:53] -> Calculating Global CVs
INFO:    [31/07/2026 22:58:55] -> Calculating Precursor Quantities...
INFO:    [31/07/2026 22:58:56] -> Normalizing Quantification...
INFO:    [31/07/2026 22:59:03] -> Performing Local Normalization...
INFO:    [31/07/2026 22:59:10] -> Calculating Global CVs
INFO:    [31/07/2026 22:59:13] -> Calculating Condition CVs
INFO:    [31/07/2026 22:59:24] -> Excluding Library Duplicates...
INFO:    [31/07/2026 22:59:27] -> Calculating Global CVs
INFO:    [31/07/2026 22:59:30] -> Building Protein Groups...
INFO:    [31/07/2026 23:00:28] -> Calculating Run-Wise Protein Group FDR...
INFO:    [31/07/2026 23:00:45] -> Annotating Protein Single Hits...
INFO:    [31/07/2026 23:00:51] -> Calculating Global CVs
INFO:    [31/07/2026 23:00:54] -> Updating Identification Counts...
INFO:    [31/07/2026 23:01:03] -> Subtracting background noise...
INFO:    [31/07/2026 23:01:21] -> Resetting existing imputation...
INFO:    [31/07/2026 23:01:22] -> Calculating Protein Quantities...
INFO:    [31/07/2026 23:01:28] -> Calculating Protein Quantities...
INFO:    [31/07/2026 23:01:28] -> Calculating MaxLFQ Protein Quantities...
INFO:    [31/07/2026 23:01:58] -> Collapsing PTM-Locations...
INFO:    [31/07/2026 23:01:58] -> PTM Stoichiometry calculation...
INFO:    [31/07/2026 23:01:59] -> Creating Protein Map...
INFO:    [31/07/2026 23:01:59] -> Compiling Run Summary Information...
INFO:    [31/07/2026 23:02:01] -> Running Post Analysis Processes...
INFO:    [31/07/2026 23:03:39] -> Saving Qc Data...
INFO:    [31/07/2026 23:03:49] -> Generating Output
INFO:    [31/07/2026 23:03:49] -> Generating Experiment Report
INFO:    [31/07/2026 23:06:29] -> 20260831_Quant_diaPASEF_DIA_forRobbe_Report_BGS Factory Report (Normal).tsv
INFO:    [31/07/2026 23:06:29] -> Generating RT Recalibration Report
INFO:    [31/07/2026 23:06:29] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d_1_iRTCalibration.tsv
INFO:    [31/07/2026 23:06:29] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d_2_iRTCalibration.tsv
INFO:    [31/07/2026 23:06:29] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d_3_iRTCalibration.tsv
INFO:    [31/07/2026 23:06:29] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d_4_iRTCalibration.tsv
INFO:    [31/07/2026 23:06:29] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d_5_iRTCalibration.tsv
INFO:    [31/07/2026 23:06:29] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d_6_iRTCalibration.tsv
INFO:    [31/07/2026 23:06:29] -> Generating Run Meta Report
INFO:    [31/07/2026 23:06:31] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d_1_RunOverview.tsv
INFO:    [31/07/2026 23:06:31] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d_2_RunOverview.tsv
INFO:    [31/07/2026 23:06:31] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d_3_RunOverview.tsv
INFO:    [31/07/2026 23:06:31] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d_4_RunOverview.tsv
INFO:    [31/07/2026 23:06:31] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d_5_RunOverview.tsv
INFO:    [31/07/2026 23:06:31] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d_6_RunOverview.tsv
INFO:    [31/07/2026 23:06:31] -> Generating Post Analysis Reports
INFO:    [31/07/2026 23:06:33] -> 20260831_Quant_diaPASEF_DIA_forRobbe_AnalyisOverview.txt
INFO:    [31/07/2026 23:06:33] -> ProteinFDR-Histogram.pdf
INFO:    [31/07/2026 23:06:33] -> Heatmap.png
INFO:    [31/07/2026 23:06:33] -> Generating Normalization Report
INFO:    [31/07/2026 23:06:38] -> 20260831_Quant_diaPASEF_DIA_forRobbe_Normalization.pdf
INFO:    [31/07/2026 23:06:38] -> Generating Condition Setup Report
INFO:    [31/07/2026 23:06:38] -> 20260831_Quant_diaPASEF_DIA_forRobbe_ConditionSetup.tsv
INFO:    [31/07/2026 23:06:38] -> Generating Memory Consumption Report
INFO:    [31/07/2026 23:06:38] -> 20260831_Quant_diaPASEF_DIA_forRobbe_MemoryConsumption.tsv
INFO:    [31/07/2026 23:06:38] -> Generating Experiment Settings Report
[END-LOG]
