Spectronaut 21.0.260602.94842
Computer Name: HALBARAD
User Domain Name: SPECTROMASSE
User Name: voyager
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 01-August-2026 12:30:10 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:	Dynamic
   │        │  └─ Correction Factor:	1
   │        └─ MS2 Mass Tolerance Strategy:	Dynamic
   │           └─ Correction Factor:	1
   ├─ 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:	5
   │     ├─ Fixed Modifications::	Carbamidomethyl (C)
   │     └─ Variable Modifications::	Acetyl (Protein N-term), Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin/P
   │  ├─ Digest Type:	Specific
   │  ├─ Decoy Generation Rule:	KR
   │  ├─ Max Peptide Length:	52
   │  ├─ Min Peptide Length:	7
   │  ├─ Missed Cleavages:	2
   │  └─ Toggle N-terminal M:	True
   ├─ Pulsar Search\Result Filters
   │  ├─ Fragment Ions:	
   │  │  ├─ Ion AA Length:	True
   │  │  │  └─ N:	3
   │  │  ├─ Ion Charge:	False
   │  │  ├─ Ion Loss Type:	False
   │  │  ├─ Ion Type:	False
   │  │  ├─ m/z :	True
   │  │  │  ├─ Max:	3000
   │  │  │  └─ Min:	200
   │  │  ├─ Overlapping between Channels:	False
   │  │  └─ Relative Intensity:	True
   │  │     └─ Min:	1
   │  └─ Precursors:	
   │     ├─ Amino Acids:	False
   │     ├─ Best N Fragments per Peptide:	True
   │     │  ├─ Max:	6
   │     │  └─ Min:	3
   │     ├─ Best N Peptides per Protein Group:	False
   │     ├─ Channel Count:	False
   │     ├─ FASTA Matched:	False
   │     ├─ Missed Cleavage:	False
   │     ├─ Modifications:	None
   │     ├─ Peptide Charge:	False
   │     └─ Proteotypicity:	False
   ├─ Pulsar Search\Speed-Up
   │  ├─ MS2 Index:	Automatic
   │  └─ 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: 01-August-2026 10:20:40 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: 01-August-2026 10:20:40 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: 01-August-2026 10:20:40 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: 01-August-2026 10:20:40 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: 01-August-2026 10:20:40 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: 01-August-2026 10:20:40 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:    [01/08/2026 04:02:36] -> Initializing Pipeline...
INFO:    [01/08/2026 04:02:36] -> Preprocessing Run #1 of 6...
INFO:    [01/08/2026 04:02:37] -> Searching DIA with Pulsar...
INFO:    [01/08/2026 04:02:39] -> Initialize Pipeline...
INFO:    [01/08/2026 04:02:39] -> Initialize Pipeline
INFO:    [01/08/2026 04:03:19] -> Initialize Pipeline...
INFO:    [01/08/2026 04:03:19] -> Creating Experiment Environment
INFO:    [01/08/2026 04:03:19] -> SuperRun 1/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d)
INFO:    [01/08/2026 04:03:19] -> Run 1/6: Organizing Data from Run
INFO:    [01/08/2026 04:03:19] -> Run 1/6: Creating Calibration Search Space...
INFO:    [01/08/2026 04:03:21] -> Run 1/6: Creating Search Space...
INFO:    [01/08/2026 04:03:21] -> Run 1/6: MS2 Index Generation
INFO:    [01/08/2026 04:03:22] -> MS2 Index Generation Time: 1.23s
INFO:    [01/08/2026 04:03:22] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [01/08/2026 04:03:38] -> Initializing...
INFO:    [01/08/2026 04:12:39] -> Finalizing Scan Map...
INFO:    [01/08/2026 04:17:35] -> Processed in 14m
INFO:    [01/08/2026 04:17:44] -> Done
INFO:    [01/08/2026 04:18:04] -> Run 1/6: Process Raw File...
INFO:    [01/08/2026 04:18:08] -> Run 1/6: Preparing Partitions...
INFO:    [01/08/2026 04:18:08] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [01/08/2026 04:18:10] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [01/08/2026 04:18:26] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [01/08/2026 04:18:49] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3141 [23s]
INFO:    [01/08/2026 04:19:27] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [01/08/2026 04:19:28] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [01/08/2026 04:26:04] -> Extracting 315601 MS1 XICs
INFO:    [01/08/2026 04:34:16] -> Run 1/6: Score Post-Processing
INFO:    [01/08/2026 04:37:03] -> Run 1/6: Cleaning Up Run...
INFO:    [01/08/2026 04:37:07] -> SuperRun 2/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d)
INFO:    [01/08/2026 04:37:07] -> Run 2/6: Organizing Data from Run
INFO:    [01/08/2026 04:37:07] -> Run 2/6: Creating Calibration Search Space...
INFO:    [01/08/2026 04:37:07] -> Run 2/6: Creating Search Space...
INFO:    [01/08/2026 04:37:07] -> Run 2/6: MS2 Index Generation
INFO:    [01/08/2026 04:37:08] -> MS2 Index Generation Time: 1.33s
INFO:    [01/08/2026 04:37:08] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [01/08/2026 04:37:35] -> Initializing...
INFO:    [01/08/2026 04:43:03] -> Finalizing Scan Map...
INFO:    [01/08/2026 04:47:32] -> Processed in 9.9m
INFO:    [01/08/2026 04:47:39] -> Done
INFO:    [01/08/2026 04:48:02] -> Run 2/6: Process Raw File...
INFO:    [01/08/2026 04:48:06] -> Run 2/6: Preparing Partitions...
INFO:    [01/08/2026 04:48:06] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [01/08/2026 04:48:08] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [01/08/2026 04:48:26] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [01/08/2026 04:48:48] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3030 [22.7s]
INFO:    [01/08/2026 04:49:13] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [01/08/2026 04:49:14] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [01/08/2026 04:56:14] -> Extracting 364620 MS1 XICs
INFO:    [01/08/2026 05:05:45] -> Run 2/6: Score Post-Processing
INFO:    [01/08/2026 05:08:04] -> Run 2/6: Cleaning Up Run...
INFO:    [01/08/2026 05:08:07] -> SuperRun 3/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d)
INFO:    [01/08/2026 05:08:07] -> Run 3/6: Organizing Data from Run
INFO:    [01/08/2026 05:08:07] -> Run 3/6: Creating Calibration Search Space...
INFO:    [01/08/2026 05:08:07] -> Run 3/6: Creating Search Space...
INFO:    [01/08/2026 05:08:07] -> Run 3/6: MS2 Index Generation
INFO:    [01/08/2026 05:08:09] -> MS2 Index Generation Time: 1.34s
INFO:    [01/08/2026 05:08:09] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [01/08/2026 05:08:27] -> Initializing...
INFO:    [01/08/2026 05:14:25] -> Finalizing Scan Map...
INFO:    [01/08/2026 05:18:55] -> Processed in 10.5m
INFO:    [01/08/2026 05:19:02] -> Done
INFO:    [01/08/2026 05:19:22] -> Run 3/6: Process Raw File...
INFO:    [01/08/2026 05:19:26] -> Run 3/6: Preparing Partitions...
INFO:    [01/08/2026 05:19:27] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [01/08/2026 05:19:28] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [01/08/2026 05:19:45] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [01/08/2026 05:20:09] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2762 [24.2s]
INFO:    [01/08/2026 05:20:29] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [01/08/2026 05:20:31] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [01/08/2026 05:26:18] -> Extracting 341490 MS1 XICs
INFO:    [01/08/2026 05:35:23] -> Run 3/6: Score Post-Processing
INFO:    [01/08/2026 05:38:06] -> Run 3/6: Cleaning Up Run...
INFO:    [01/08/2026 05:38:10] -> SuperRun 4/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d)
INFO:    [01/08/2026 05:38:10] -> Run 4/6: Organizing Data from Run
INFO:    [01/08/2026 05:38:10] -> Run 4/6: Creating Calibration Search Space...
INFO:    [01/08/2026 05:38:10] -> Run 4/6: Creating Search Space...
INFO:    [01/08/2026 05:38:10] -> Run 4/6: MS2 Index Generation
INFO:    [01/08/2026 05:38:12] -> MS2 Index Generation Time: 1.35s
INFO:    [01/08/2026 05:38:12] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [01/08/2026 05:38:31] -> Initializing...
INFO:    [01/08/2026 05:43:24] -> Finalizing Scan Map...
INFO:    [01/08/2026 05:50:04] -> Processed in 11.6m
INFO:    [01/08/2026 05:50:11] -> Done
INFO:    [01/08/2026 05:50:33] -> Run 4/6: Process Raw File...
INFO:    [01/08/2026 05:50:38] -> Run 4/6: Preparing Partitions...
INFO:    [01/08/2026 05:50:38] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [01/08/2026 05:50:39] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [01/08/2026 05:51:13] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [01/08/2026 05:52:04] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2964 [50.6s]
INFO:    [01/08/2026 05:52:34] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [01/08/2026 05:52:35] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [01/08/2026 06:02:08] -> Extracting 334028 MS1 XICs
INFO:    [01/08/2026 06:10:38] -> Run 4/6: Score Post-Processing
INFO:    [01/08/2026 06:13:21] -> Run 4/6: Cleaning Up Run...
INFO:    [01/08/2026 06:13:21] -> SuperRun 5/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d)
INFO:    [01/08/2026 06:13:21] -> Run 5/6: Organizing Data from Run
INFO:    [01/08/2026 06:13:21] -> Run 5/6: Creating Calibration Search Space...
INFO:    [01/08/2026 06:13:21] -> Run 5/6: Creating Search Space...
INFO:    [01/08/2026 06:13:21] -> Run 5/6: MS2 Index Generation
INFO:    [01/08/2026 06:13:22] -> MS2 Index Generation Time: 1.27s
INFO:    [01/08/2026 06:13:22] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [01/08/2026 06:13:43] -> Initializing...
INFO:    [01/08/2026 06:22:31] -> Finalizing Scan Map...
INFO:    [01/08/2026 06:27:26] -> Processed in 13.7m
INFO:    [01/08/2026 06:27:32] -> Done
INFO:    [01/08/2026 06:27:52] -> Run 5/6: Process Raw File...
INFO:    [01/08/2026 06:27:57] -> Run 5/6: Preparing Partitions...
INFO:    [01/08/2026 06:27:57] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [01/08/2026 06:27:59] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [01/08/2026 06:28:15] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [01/08/2026 06:28:36] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3097 [21.3s]
INFO:    [01/08/2026 06:29:05] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [01/08/2026 06:29:06] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [01/08/2026 06:34:24] -> Extracting 335800 MS1 XICs
INFO:    [01/08/2026 06:43:28] -> Run 5/6: Score Post-Processing
INFO:    [01/08/2026 06:45:46] -> Run 5/6: Cleaning Up Run...
INFO:    [01/08/2026 06:45:46] -> SuperRun 6/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d)
INFO:    [01/08/2026 06:45:46] -> Run 6/6: Organizing Data from Run
INFO:    [01/08/2026 06:45:46] -> Run 6/6: Creating Calibration Search Space...
INFO:    [01/08/2026 06:45:46] -> Run 6/6: Creating Search Space...
INFO:    [01/08/2026 06:45:46] -> Run 6/6: MS2 Index Generation
INFO:    [01/08/2026 06:45:47] -> MS2 Index Generation Time: 1.31s
INFO:    [01/08/2026 06:45:47] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [01/08/2026 06:46:07] -> Initializing...
INFO:    [01/08/2026 06:50:50] -> Finalizing Scan Map...
INFO:    [01/08/2026 06:54:48] -> Processed in 8.7m
INFO:    [01/08/2026 06:54:54] -> Done
INFO:    [01/08/2026 06:55:15] -> Run 6/6: Process Raw File...
INFO:    [01/08/2026 06:55:18] -> Run 6/6: Preparing Partitions...
INFO:    [01/08/2026 06:55:18] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [01/08/2026 06:55:20] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [01/08/2026 06:55:38] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [01/08/2026 06:55:59] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3083 [21s]
INFO:    [01/08/2026 06:56:28] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [01/08/2026 06:56:30] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [01/08/2026 07:01:54] -> Extracting 332991 MS1 XICs
INFO:    [01/08/2026 07:10:34] -> Run 6/6: Score Post-Processing
INFO:    [01/08/2026 07:12:55] -> Run 6/6: Cleaning Up Run...
INFO:    [01/08/2026 07:13:06] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [01/08/2026 07:13:10] -> PSM FDR...
INFO:    [01/08/2026 07:13:11] -> PSM FDR: 490.16ms
INFO:    [01/08/2026 07:13:14] -> Converting to non-redundant data structure...
INFO:    [01/08/2026 07:13:40] -> Performing Peptide FDR...
INFO:    [01/08/2026 07:13:51] -> Performing Protein Inference...
INFO:    [01/08/2026 07:13:57] -> Performing Protein FDR...
INFO:    [01/08/2026 07:14:01] -> Calculating Result Values at Run and Experiment Level...
INFO:    [01/08/2026 07:14:16] -> Pulsar identified 363887 PSMs, 79439 stripped sequences, 89808 peptide precursors, 9817 protein groups.
INFO:    [01/08/2026 07:14:16] -> Annotating In-Source Fragmentation...
INFO:    [01/08/2026 07:14:20] -> iRT Calibration...
INFO:    [01/08/2026 07:14:33] -> Performing directDIA+ search fine tuning...
INFO:    [01/08/2026 08:11:47] -> Performing directDIA+ search...
INFO:    [01/08/2026 08:11:47] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
INFO:    [01/08/2026 08:33:32] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
INFO:    [01/08/2026 08:47:37] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
INFO:    [01/08/2026 09:03:18] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
INFO:    [01/08/2026 09:20:46] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
INFO:    [01/08/2026 09:36:31] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
INFO:    [01/08/2026 09:50:40] -> Total nr of Searched Peptides: 1 634 876 of 2 544 725
INFO:    [01/08/2026 09:50:40] -> Initializing Combined Protein Inference...
INFO:    [01/08/2026 10:08:17] -> Performing Protein Inference...
INFO:    [01/08/2026 10:08:23] -> Performing Protein FDR...
INFO:    [01/08/2026 10:08:26] -> Calculating Result Values at Run and Experiment Level...
INFO:    [01/08/2026 10:08:39] -> Pulsar identified 363893 PSMs, 79442 stripped sequences, 89812 peptide precursors, 9839 protein groups.
INFO:    [01/08/2026 10:08:39] -> Calculating Summary...
INFO:    [01/08/2026 10:08:52] -> Identifying Calibration Peptides...
INFO:    [01/08/2026 10:08:54] -> Performing directDIA+ Post Processing...
INFO:    [01/08/2026 10:13:36] -> Combining Protein-Group FDR Results...
INFO:    [01/08/2026 10:13:36] -> Combined Protein-Group Identifications at 1% Qvalue: 13 197
INFO:    [01/08/2026 10:13:36] -> Writing experiment store..
INFO:    [01/08/2026 10:14:01] -> Assigning iRT Source...
INFO:    [01/08/2026 10:14:01] -> Calculating iRT...
INFO:    [01/08/2026 10:14:02] -> Cleaning Up Experiment...
INFO:    [01/08/2026 10:14:02] -> Summarizing Identifications
INFO:    [01/08/2026 10:15:52] -> Predicting Ion Mobility
INFO:    [01/08/2026 10:18:03] -> Calculating Median iRT
INFO:    [01/08/2026 10:18:06] -> Building BGS Protein Grouping...
INFO:    [01/08/2026 10:18:08] -> Digesting Fasta...
INFO:    [01/08/2026 10:18:09] -> Annotating Proteins...
INFO:    [01/08/2026 10:18:10] -> Grouping Proteins...
INFO:    [01/08/2026 10:18:15] -> Calculating Run Summary Statistics...
INFO:    [01/08/2026 10:18:29] -> Building Consensus Fragment Spectra...
INFO:    [01/08/2026 10:18:56] -> Selecting best fragment ions
INFO:    [01/08/2026 10:18:56] -> Condensing Global Results...
INFO:    [01/08/2026 10:21:00] -> Protein Groups: 12553 (12703), Protein Id: 12689 (12885), Modified Peptides: 131008, Precursors: 151793, Peptides: 129693, Fragments: 906098
INFO:    [01/08/2026 10:22:16] -> Initializing Experiment...
INFO:    [01/08/2026 10:22:16] -> Loading Spectral Libraries...
INFO:    [01/08/2026 11:12:46] -> Initialize Scoring...
INFO:    [01/08/2026 11:12:46] -> Generating Scan Map...
INFO:    [01/08/2026 11:12:47] -> Initializing Workpackages...
INFO:    [01/08/2026 11:12:47] -> Performing Basic Calibration...
INFO:    [01/08/2026 11:12:49] -> Calibration successful
INFO:    [01/08/2026 11:12:49] -> Identifying Calibration Peptides...
INFO:    [01/08/2026 11:12:49] -> Calibration successful
INFO:    [01/08/2026 11:12:49] -> Correcting Gradient Fine Structure...
INFO:    [01/08/2026 11:12:59] -> Initializing Pipeline...
INFO:    [01/08/2026 11:12:59] -> Preprocessing Run #1 of 6...
INFO:    [01/08/2026 11:12:59] -> Initialize Scoring...
INFO:    [01/08/2026 11:12:59] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:14:28] -> Machine Learning...
INFO:    [01/08/2026 11:14:31] -> Pipeline executed in 1.53m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:14:32] -> Calibration successful
INFO:    [01/08/2026 11:14:40] -> Initializing Pipeline...
INFO:    [01/08/2026 11:14:40] -> Preprocessing Run #1 of 6...
INFO:    [01/08/2026 11:14:40] -> Initialize Scoring...
INFO:    [01/08/2026 11:14:40] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:16:55] -> Machine Learning...
INFO:    [01/08/2026 11:17:09] -> Pipeline executed in 2.48m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:17:27] -> Calibration successful
INFO:    [01/08/2026 11:17:27] -> Initialize Scoring...
INFO:    [01/08/2026 11:17:27] -> Preprocessing Run #2 of 6...
INFO:    [01/08/2026 11:17:27] -> Searching DIA with Pulsar...
INFO:    [01/08/2026 11:17:27] -> Initializing Experiment...
INFO:    [01/08/2026 11:17:27] -> Loading Spectral Libraries...
INFO:    [01/08/2026 11:17:27] -> Initialize Scoring...
INFO:    [01/08/2026 11:17:27] -> Generating Scan Map...
INFO:    [01/08/2026 11:17:28] -> Initializing Workpackages...
INFO:    [01/08/2026 11:17:28] -> Performing Basic Calibration...
INFO:    [01/08/2026 11:17:28] -> Calibration successful
INFO:    [01/08/2026 11:17:28] -> Identifying Calibration Peptides...
INFO:    [01/08/2026 11:17:28] -> Calibration successful
INFO:    [01/08/2026 11:17:28] -> Correcting Gradient Fine Structure...
INFO:    [01/08/2026 11:17:34] -> Initializing Pipeline...
INFO:    [01/08/2026 11:17:34] -> Preprocessing Run #2 of 6...
INFO:    [01/08/2026 11:17:34] -> Initialize Scoring...
INFO:    [01/08/2026 11:17:34] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:19:17] -> Machine Learning...
INFO:    [01/08/2026 11:19:20] -> Pipeline executed in 1.77m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:19:21] -> Calibration successful
INFO:    [01/08/2026 11:19:31] -> Initializing Pipeline...
INFO:    [01/08/2026 11:19:31] -> Preprocessing Run #2 of 6...
INFO:    [01/08/2026 11:19:31] -> Initialize Scoring...
INFO:    [01/08/2026 11:19:31] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:22:29] -> Machine Learning...
INFO:    [01/08/2026 11:22:37] -> Pipeline executed in 3.1m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:22:46] -> Calibration successful
INFO:    [01/08/2026 11:22:46] -> Initialize Scoring...
INFO:    [01/08/2026 11:22:46] -> Preprocessing Run #3 of 6...
INFO:    [01/08/2026 11:22:46] -> Searching DIA with Pulsar...
INFO:    [01/08/2026 11:22:46] -> Initializing Experiment...
INFO:    [01/08/2026 11:22:46] -> Loading Spectral Libraries...
INFO:    [01/08/2026 11:22:46] -> Initialize Scoring...
INFO:    [01/08/2026 11:22:46] -> Generating Scan Map...
INFO:    [01/08/2026 11:22:46] -> Initializing Workpackages...
INFO:    [01/08/2026 11:22:46] -> Performing Basic Calibration...
INFO:    [01/08/2026 11:22:47] -> Calibration successful
INFO:    [01/08/2026 11:22:47] -> Identifying Calibration Peptides...
INFO:    [01/08/2026 11:22:47] -> Calibration successful
INFO:    [01/08/2026 11:22:47] -> Correcting Gradient Fine Structure...
INFO:    [01/08/2026 11:22:52] -> Initializing Pipeline...
INFO:    [01/08/2026 11:22:52] -> Preprocessing Run #3 of 6...
INFO:    [01/08/2026 11:22:52] -> Initialize Scoring...
INFO:    [01/08/2026 11:22:52] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:24:03] -> Machine Learning...
INFO:    [01/08/2026 11:24:05] -> Pipeline executed in 1.21m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:24:05] -> Calibration successful
INFO:    [01/08/2026 11:24:10] -> Initializing Pipeline...
INFO:    [01/08/2026 11:24:10] -> Preprocessing Run #3 of 6...
INFO:    [01/08/2026 11:24:10] -> Initialize Scoring...
INFO:    [01/08/2026 11:24:10] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:25:30] -> Machine Learning...
INFO:    [01/08/2026 11:25:38] -> Pipeline executed in 1.47m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:25:47] -> Calibration successful
INFO:    [01/08/2026 11:25:47] -> Initialize Scoring...
INFO:    [01/08/2026 11:25:47] -> Preprocessing Run #4 of 6...
INFO:    [01/08/2026 11:25:47] -> Searching DIA with Pulsar...
INFO:    [01/08/2026 11:25:47] -> Initializing Experiment...
INFO:    [01/08/2026 11:25:47] -> Loading Spectral Libraries...
INFO:    [01/08/2026 11:25:47] -> Initialize Scoring...
INFO:    [01/08/2026 11:25:47] -> Generating Scan Map...
INFO:    [01/08/2026 11:25:47] -> Initializing Workpackages...
INFO:    [01/08/2026 11:25:47] -> Performing Basic Calibration...
INFO:    [01/08/2026 11:25:48] -> Calibration successful
INFO:    [01/08/2026 11:25:48] -> Identifying Calibration Peptides...
INFO:    [01/08/2026 11:25:48] -> Calibration successful
INFO:    [01/08/2026 11:25:48] -> Correcting Gradient Fine Structure...
INFO:    [01/08/2026 11:25:52] -> Initializing Pipeline...
INFO:    [01/08/2026 11:25:52] -> Preprocessing Run #4 of 6...
INFO:    [01/08/2026 11:25:52] -> Initialize Scoring...
INFO:    [01/08/2026 11:25:52] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:26:50] -> Machine Learning...
INFO:    [01/08/2026 11:26:51] -> Pipeline executed in 58.95s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:26:52] -> Calibration successful
INFO:    [01/08/2026 11:26:56] -> Initializing Pipeline...
INFO:    [01/08/2026 11:26:56] -> Preprocessing Run #4 of 6...
INFO:    [01/08/2026 11:26:56] -> Initialize Scoring...
INFO:    [01/08/2026 11:26:56] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:29:21] -> Machine Learning...
INFO:    [01/08/2026 11:29:42] -> Pipeline executed in 2.76m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:30:04] -> Calibration successful
INFO:    [01/08/2026 11:30:04] -> Initialize Scoring...
INFO:    [01/08/2026 11:30:04] -> Preprocessing Run #5 of 6...
INFO:    [01/08/2026 11:30:04] -> Searching DIA with Pulsar...
INFO:    [01/08/2026 11:30:04] -> Initializing Experiment...
INFO:    [01/08/2026 11:30:04] -> Loading Spectral Libraries...
INFO:    [01/08/2026 11:30:04] -> Initialize Scoring...
INFO:    [01/08/2026 11:30:04] -> Generating Scan Map...
INFO:    [01/08/2026 11:30:05] -> Initializing Workpackages...
INFO:    [01/08/2026 11:30:05] -> Performing Basic Calibration...
INFO:    [01/08/2026 11:30:06] -> Calibration successful
INFO:    [01/08/2026 11:30:06] -> Identifying Calibration Peptides...
INFO:    [01/08/2026 11:30:06] -> Calibration successful
INFO:    [01/08/2026 11:30:06] -> Correcting Gradient Fine Structure...
INFO:    [01/08/2026 11:30:17] -> Initializing Pipeline...
INFO:    [01/08/2026 11:30:17] -> Preprocessing Run #5 of 6...
INFO:    [01/08/2026 11:30:17] -> Initialize Scoring...
INFO:    [01/08/2026 11:30:17] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:31:37] -> Machine Learning...
INFO:    [01/08/2026 11:31:40] -> Pipeline executed in 1.38m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:31:40] -> Calibration successful
INFO:    [01/08/2026 11:31:51] -> Initializing Pipeline...
INFO:    [01/08/2026 11:31:51] -> Preprocessing Run #5 of 6...
INFO:    [01/08/2026 11:31:51] -> Initialize Scoring...
INFO:    [01/08/2026 11:31:52] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:34:01] -> Machine Learning...
INFO:    [01/08/2026 11:34:10] -> Pipeline executed in 2.32m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:34:21] -> Calibration successful
INFO:    [01/08/2026 11:34:21] -> Initialize Scoring...
INFO:    [01/08/2026 11:34:21] -> Preprocessing Run #6 of 6...
INFO:    [01/08/2026 11:34:21] -> Searching DIA with Pulsar...
INFO:    [01/08/2026 11:34:21] -> Initializing Experiment...
INFO:    [01/08/2026 11:34:21] -> Loading Spectral Libraries...
INFO:    [01/08/2026 11:34:21] -> Initialize Scoring...
INFO:    [01/08/2026 11:34:21] -> Generating Scan Map...
INFO:    [01/08/2026 11:34:21] -> Initializing Workpackages...
INFO:    [01/08/2026 11:34:21] -> Performing Basic Calibration...
INFO:    [01/08/2026 11:34:22] -> Calibration successful
INFO:    [01/08/2026 11:34:22] -> Identifying Calibration Peptides...
INFO:    [01/08/2026 11:34:22] -> Calibration successful
INFO:    [01/08/2026 11:34:22] -> Correcting Gradient Fine Structure...
INFO:    [01/08/2026 11:34:28] -> Initializing Pipeline...
INFO:    [01/08/2026 11:34:28] -> Preprocessing Run #6 of 6...
INFO:    [01/08/2026 11:34:28] -> Initialize Scoring...
INFO:    [01/08/2026 11:34:28] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:35:54] -> Machine Learning...
INFO:    [01/08/2026 11:35:58] -> Pipeline executed in 1.5m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:35:59] -> Calibration successful
INFO:    [01/08/2026 11:36:08] -> Initializing Pipeline...
INFO:    [01/08/2026 11:36:08] -> Preprocessing Run #6 of 6...
INFO:    [01/08/2026 11:36:08] -> Initialize Scoring...
INFO:    [01/08/2026 11:36:08] -> Extracting Ion Currents...
INFO:    [01/08/2026 11:37:58] -> Machine Learning...
INFO:    [01/08/2026 11:38:08] -> Pipeline executed in 2m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [01/08/2026 11:38:20] -> Calibration successful
INFO:    [01/08/2026 11:38:20] -> Initialize Scoring...
INFO:    [01/08/2026 11:38:20] -> Initializing QC...
INFO:    [01/08/2026 11:38:20] -> Determining Calibration Parameter...
INFO:    [01/08/2026 11:38:20] -> Assigning ML Features...
INFO:    [01/08/2026 11:38:21] -> Generating Decoys...
INFO:    [01/08/2026 11:49:47] -> Extracting Ion Currents...
ERROR:   [01/08/2026 11:50:10] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:50:21] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:50:32] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:50:43] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:50:56] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:04] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:12] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:20] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:26] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:32] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:38] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:43] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:47] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:52] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:51:57] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:02] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:07] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:10] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:13] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:15] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:17] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:19] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:21] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:52:22] -> Exporting all XIC Data...: unable to open database file
INFO:    [01/08/2026 11:52:22] -> Releasing Raw Files...
INFO:    [01/08/2026 11:52:22] -> Machine Learning...
INFO:    [01/08/2026 11:55:54] -> Initializing HTRMS...
INFO:    [01/08/2026 11:55:54] -> Releasing Run Resources...
INFO:    [01/08/2026 11:55:55] -> Reducing Score Cache...
INFO:    [01/08/2026 11:55:59] -> Calculating Qvalues...
INFO:    [01/08/2026 11:56:05] -> Unique precursors: 144 255 of 151 793 | modified peptides: 125 623 of 131 008 | peptides: 124 353 of 129 693 |  protein groups: 12 272 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d]
INFO:    [01/08/2026 11:56:05] -> Calibration successful
INFO:    [01/08/2026 11:56:05] -> Annotating In-Source Fragmentation...
INFO:    [01/08/2026 11:56:06] -> Collapsing Search Tree...
INFO:    [01/08/2026 11:56:06] -> Processed in 17.78m
INFO:    [01/08/2026 11:56:08] -> Initializing QC...
INFO:    [01/08/2026 11:56:08] -> Determining Calibration Parameter...
INFO:    [01/08/2026 11:56:08] -> Assigning ML Features...
INFO:    [01/08/2026 11:56:09] -> Generating Decoys...
INFO:    [01/08/2026 11:56:09] -> Extracting Ion Currents...
ERROR:   [01/08/2026 11:56:15] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:56:26] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:56:33] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:56:41] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:56:50] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:56:58] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:07] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:13] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:19] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:25] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:30] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:36] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:40] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:45] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:52] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:57:57] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:01] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:04] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:07] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:10] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:12] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:13] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:15] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 11:58:16] -> Exporting all XIC Data...: unable to open database file
INFO:    [01/08/2026 11:58:16] -> Releasing Raw Files...
INFO:    [01/08/2026 11:58:16] -> Machine Learning...
INFO:    [01/08/2026 12:01:02] -> Initializing HTRMS...
INFO:    [01/08/2026 12:01:02] -> Releasing Run Resources...
INFO:    [01/08/2026 12:01:03] -> Reducing Score Cache...
INFO:    [01/08/2026 12:01:07] -> Calculating Qvalues...
INFO:    [01/08/2026 12:01:14] -> Unique precursors: 145 569 of 151 793 | modified peptides: 126 631 of 131 008 | peptides: 125 354 of 129 693 |  protein groups: 12 309 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d]
INFO:    [01/08/2026 12:01:14] -> Calibration successful
INFO:    [01/08/2026 12:01:15] -> Annotating In-Source Fragmentation...
INFO:    [01/08/2026 12:01:16] -> Collapsing Search Tree...
INFO:    [01/08/2026 12:01:16] -> Processed in 5.15m
INFO:    [01/08/2026 12:01:17] -> Initializing QC...
INFO:    [01/08/2026 12:01:17] -> Determining Calibration Parameter...
INFO:    [01/08/2026 12:01:17] -> Assigning ML Features...
INFO:    [01/08/2026 12:01:17] -> Generating Decoys...
INFO:    [01/08/2026 12:01:18] -> Extracting Ion Currents...
ERROR:   [01/08/2026 12:01:26] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:01:37] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:01:45] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:01:52] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:01:59] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:09] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:17] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:23] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:29] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:35] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:40] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:46] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:51] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:02:56] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:03] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:08] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:11] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:15] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:19] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:25] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:29] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:32] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:35] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:03:37] -> Exporting all XIC Data...: unable to open database file
INFO:    [01/08/2026 12:03:37] -> Releasing Raw Files...
INFO:    [01/08/2026 12:03:37] -> Machine Learning...
INFO:    [01/08/2026 12:07:00] -> Initializing HTRMS...
INFO:    [01/08/2026 12:07:00] -> Releasing Run Resources...
INFO:    [01/08/2026 12:07:01] -> Reducing Score Cache...
INFO:    [01/08/2026 12:07:06] -> Calculating Qvalues...
INFO:    [01/08/2026 12:07:11] -> Unique precursors: 145 584 of 151 793 | modified peptides: 126 670 of 131 008 | peptides: 125 397 of 129 693 |  protein groups: 12 292 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d]
INFO:    [01/08/2026 12:07:11] -> Calibration successful
INFO:    [01/08/2026 12:07:11] -> Annotating In-Source Fragmentation...
INFO:    [01/08/2026 12:07:13] -> Collapsing Search Tree...
INFO:    [01/08/2026 12:07:13] -> Processed in 5.94m
INFO:    [01/08/2026 12:07:15] -> Initializing QC...
INFO:    [01/08/2026 12:07:16] -> Determining Calibration Parameter...
INFO:    [01/08/2026 12:07:16] -> Assigning ML Features...
INFO:    [01/08/2026 12:07:16] -> Generating Decoys...
INFO:    [01/08/2026 12:07:17] -> Extracting Ion Currents...
ERROR:   [01/08/2026 12:07:24] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:07:31] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:07:39] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:07:48] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:07:55] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:02] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:10] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:17] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:23] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:30] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:38] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:43] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:48] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:52] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:08:56] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:01] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:06] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:08] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:11] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:14] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:16] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:18] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:19] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:09:20] -> Exporting all XIC Data...: unable to open database file
INFO:    [01/08/2026 12:09:21] -> Releasing Raw Files...
INFO:    [01/08/2026 12:09:21] -> Machine Learning...
INFO:    [01/08/2026 12:12:54] -> Initializing HTRMS...
INFO:    [01/08/2026 12:12:54] -> Releasing Run Resources...
INFO:    [01/08/2026 12:12:55] -> Reducing Score Cache...
INFO:    [01/08/2026 12:12:59] -> Calculating Qvalues...
INFO:    [01/08/2026 12:13:03] -> Unique precursors: 145 457 of 151 793 | modified peptides: 126 493 of 131 008 | peptides: 125 206 of 129 693 |  protein groups: 12 374 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d]
INFO:    [01/08/2026 12:13:03] -> Calibration successful
INFO:    [01/08/2026 12:13:05] -> Annotating In-Source Fragmentation...
INFO:    [01/08/2026 12:13:07] -> Collapsing Search Tree...
INFO:    [01/08/2026 12:13:07] -> Processed in 5.87m
INFO:    [01/08/2026 12:13:10] -> Initializing QC...
INFO:    [01/08/2026 12:13:10] -> Determining Calibration Parameter...
INFO:    [01/08/2026 12:13:10] -> Assigning ML Features...
INFO:    [01/08/2026 12:13:10] -> Generating Decoys...
INFO:    [01/08/2026 12:13:11] -> Extracting Ion Currents...
ERROR:   [01/08/2026 12:13:18] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:13:28] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:13:35] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:13:44] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:13:52] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:13:59] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:06] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:13] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:20] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:26] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:35] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:41] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:46] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:51] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:55] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:14:59] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:02] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:06] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:08] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:11] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:12] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:14] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:16] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:15:17] -> Exporting all XIC Data...: unable to open database file
INFO:    [01/08/2026 12:15:17] -> Releasing Raw Files...
INFO:    [01/08/2026 12:15:18] -> Machine Learning...
INFO:    [01/08/2026 12:18:29] -> Initializing HTRMS...
INFO:    [01/08/2026 12:18:29] -> Releasing Run Resources...
INFO:    [01/08/2026 12:18:30] -> Reducing Score Cache...
INFO:    [01/08/2026 12:18:34] -> Calculating Qvalues...
INFO:    [01/08/2026 12:18:41] -> Unique precursors: 145 958 of 151 793 | modified peptides: 126 925 of 131 008 | peptides: 125 642 of 129 693 |  protein groups: 12 386 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d]
INFO:    [01/08/2026 12:18:41] -> Calibration successful
INFO:    [01/08/2026 12:18:41] -> Annotating In-Source Fragmentation...
INFO:    [01/08/2026 12:18:42] -> Collapsing Search Tree...
INFO:    [01/08/2026 12:18:42] -> Processed in 5.54m
INFO:    [01/08/2026 12:18:42] -> Initializing QC...
INFO:    [01/08/2026 12:18:42] -> Determining Calibration Parameter...
INFO:    [01/08/2026 12:18:43] -> Assigning ML Features...
INFO:    [01/08/2026 12:18:43] -> Generating Decoys...
INFO:    [01/08/2026 12:18:44] -> Extracting Ion Currents...
ERROR:   [01/08/2026 12:18:54] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:05] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:12] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:22] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:29] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:36] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:42] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:49] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:19:56] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:03] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:09] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:14] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:19] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:23] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:28] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:33] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:41] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:48] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:53] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:20:57] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:21:00] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:21:03] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:21:05] -> Exporting all XIC Data...: unable to open database file
ERROR:   [01/08/2026 12:21:07] -> Exporting all XIC Data...: unable to open database file
INFO:    [01/08/2026 12:21:07] -> Releasing Raw Files...
INFO:    [01/08/2026 12:21:08] -> Machine Learning...
INFO:    [01/08/2026 12:24:37] -> Initializing HTRMS...
INFO:    [01/08/2026 12:24:37] -> Releasing Run Resources...
INFO:    [01/08/2026 12:24:38] -> Reducing Score Cache...
INFO:    [01/08/2026 12:24:42] -> Calculating Qvalues...
INFO:    [01/08/2026 12:24:45] -> Unique precursors: 146 267 of 151 793 | modified peptides: 127 109 of 131 008 | peptides: 125 826 of 129 693 |  protein groups: 12 405 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d]
INFO:    [01/08/2026 12:24:45] -> Calibration successful
INFO:    [01/08/2026 12:24:46] -> Annotating In-Source Fragmentation...
INFO:    [01/08/2026 12:24:46] -> Collapsing Search Tree...
INFO:    [01/08/2026 12:24:47] -> Processed in 6.07m
INFO:    [01/08/2026 12:24:47] -> Normalizing Cscores...
INFO:    [01/08/2026 12:24:48] -> Calculating Global CVs
INFO:    [01/08/2026 12:24:50] -> Calculating Profile Qvalues...
INFO:    [01/08/2026 12:24:53] -> Initializing Protein Groups...
INFO:    [01/08/2026 12:25:19] -> Correcting Interferences...
INFO:    [01/08/2026 12:25:49] -> Calculating Global CVs
INFO:    [01/08/2026 12:25:52] -> Calculating Precursor Quantities...
INFO:    [01/08/2026 12:25:52] -> Normalizing Quantification...
INFO:    [01/08/2026 12:25:55] -> Performing Local Normalization...
INFO:    [01/08/2026 12:25:58] -> Calculating Global CVs
INFO:    [01/08/2026 12:26:01] -> Calculating Condition CVs
INFO:    [01/08/2026 12:26:06] -> Excluding Library Duplicates...
INFO:    [01/08/2026 12:26:07] -> Calculating Global CVs
INFO:    [01/08/2026 12:26:09] -> Building Protein Groups...
INFO:    [01/08/2026 12:26:29] -> Calculating Run-Wise Protein Group FDR...
INFO:    [01/08/2026 12:26:36] -> Annotating Protein Single Hits...
INFO:    [01/08/2026 12:26:39] -> Calculating Global CVs
INFO:    [01/08/2026 12:26:41] -> Updating Identification Counts...
INFO:    [01/08/2026 12:26:48] -> Subtracting background noise...
INFO:    [01/08/2026 12:26:56] -> Resetting existing imputation...
INFO:    [01/08/2026 12:26:56] -> Calculating Protein Quantities...
INFO:    [01/08/2026 12:26:58] -> Calculating Protein Quantities...
INFO:    [01/08/2026 12:26:58] -> Calculating MaxLFQ Protein Quantities...
INFO:    [01/08/2026 12:27:13] -> Collapsing PTM-Locations...
INFO:    [01/08/2026 12:27:13] -> PTM Stoichiometry calculation...
INFO:    [01/08/2026 12:27:13] -> Creating Protein Map...
INFO:    [01/08/2026 12:27:13] -> Compiling Run Summary Information...
INFO:    [01/08/2026 12:27:14] -> Running Post Analysis Processes...
INFO:    [01/08/2026 12:28:06] -> Saving Qc Data...
INFO:    [01/08/2026 12:28:14] -> Generating Output
INFO:    [01/08/2026 12:28:14] -> Generating Experiment Report
INFO:    [01/08/2026 12:30:03] -> 20260731_Quant_diaPASEFl_DIA_defaultParams_forRobbe_Report_BGS Factory Report (Normal).tsv
INFO:    [01/08/2026 12:30:03] -> Generating RT Recalibration Report
INFO:    [01/08/2026 12:30:03] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d_1_iRTCalibration.tsv
INFO:    [01/08/2026 12:30:03] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d_2_iRTCalibration.tsv
INFO:    [01/08/2026 12:30:03] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d_3_iRTCalibration.tsv
INFO:    [01/08/2026 12:30:03] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d_4_iRTCalibration.tsv
INFO:    [01/08/2026 12:30:03] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d_5_iRTCalibration.tsv
INFO:    [01/08/2026 12:30:03] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d_6_iRTCalibration.tsv
INFO:    [01/08/2026 12:30:03] -> Generating Run Meta Report
INFO:    [01/08/2026 12:30:05] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d_1_RunOverview.tsv
INFO:    [01/08/2026 12:30:05] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d_2_RunOverview.tsv
INFO:    [01/08/2026 12:30:05] -> ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d_3_RunOverview.tsv
INFO:    [01/08/2026 12:30:05] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d_4_RunOverview.tsv
INFO:    [01/08/2026 12:30:05] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d_5_RunOverview.tsv
INFO:    [01/08/2026 12:30:05] -> ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d_6_RunOverview.tsv
INFO:    [01/08/2026 12:30:05] -> Generating Post Analysis Reports
INFO:    [01/08/2026 12:30:06] -> 20260731_Quant_diaPASEFl_DIA_defaultParams_forRobbe_AnalyisOverview.txt
INFO:    [01/08/2026 12:30:06] -> ProteinFDR-Histogram.pdf
INFO:    [01/08/2026 12:30:06] -> Heatmap.png
INFO:    [01/08/2026 12:30:06] -> Generating Normalization Report
INFO:    [01/08/2026 12:30:10] -> 20260731_Quant_diaPASEFl_DIA_defaultParams_forRobbe_Normalization.pdf
INFO:    [01/08/2026 12:30:10] -> Generating Condition Setup Report
INFO:    [01/08/2026 12:30:10] -> 20260731_Quant_diaPASEFl_DIA_defaultParams_forRobbe_ConditionSetup.tsv
INFO:    [01/08/2026 12:30:10] -> Generating Memory Consumption Report
INFO:    [01/08/2026 12:30:10] -> 20260731_Quant_diaPASEFl_DIA_defaultParams_forRobbe_MemoryConsumption.tsv
INFO:    [01/08/2026 12:30:10] -> Generating Experiment Settings Report
[END-LOG]
