Spectronaut 20.3.251119.92449
Computer Name: CBS-GC1414-STAR
User Domain Name: AD3
User Name: protcore
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 15-December-2025 15:13:10 UTC -08:00 


[BEGIN-SETTINGS]
Settings Used: BGS Factory Settings
   ├─ DIA Analysis\Calibration
   │  ├─ MZ Extraction Strategy:	Maximum Intensity
   │  ├─ Allow source specific iRT Calibration:	True
   │  ├─ Precision iRT:	True
   │  │  ├─ Exclude De-amidated Peptides:	True
   │  │  └─ iRT <-> RT Regression Type:	Local (Non-Linear) Regression
   │  ├─ MS1 Mass Tolerance Strategy:	System Default
   │  └─ MS2 Mass Tolerance Strategy:	System Default
   ├─ DIA Analysis\Identification
   │  ├─ Precursor Qvalue Cutoff:	0.01
   │  ├─ Precursor Qvalue Cutoff (Experiment):	0.01
   │  ├─ Precursor PEP Cutoff:	0.2
   │  ├─ Protein Qvalue Cutoff (Experiment):	0.01
   │  ├─ Protein Qvalue Cutoff (Run):	0.05
   │  ├─ Protein PEP Cutoff:	0.75
   │  ├─ Single Hit Definition:	By Stripped Sequence
   │  ├─ Single Hit Protein Rule:	Stratified Single Hit Protein FDR
   │  ├─ Run-Level Protein Scoring:	All Observations
   │  ├─ Exclude Duplicate Assays:	True
   │  ├─ Exclude Predicted Fragment Scores:	False
   │  ├─ Generate Decoys:	True
   │  │  ├─ Decoy Generation Method:	Mutated
   │  │  │  └─ Preferred Fragment Source:	NN Predicted Fragments
   │  │  └─ Decoy Limit Strategy:	Dynamic
   │  │     └─ Library Size Fraction:	0.1
   │  └─ Pvalue Estimator:	Kernel Density Estimator
   ├─ DIA Analysis\Pipeline Mode
   │  ├─ Export All XICs:	False
   │  ├─ 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\protcore\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\Workflow
   │  ├─ Method Evaluation:	False
   │  ├─ MS2 DeMultiplexing:	Automatic
   │  ├─ Multi-Channel Workflow Definition:	From Library Annotation
   │  │  └─ Fallback Option:	Labeled
   │  ├─ Profiling Strategy:	None
   │  ├─ Run Limit for directDIA Library:	-1
   │  ├─ Hybrid (DDA + DIA) Library:	False
   │  └─ Unify Peptide Peaks Strategy:	None
   ├─ DIA Analysis\XIC Extraction
   │  ├─ XIC IM Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ XIC RT Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ MS1 Mass Tolerance Strategy:	Dynamic
   │  │  └─ Correction Factor:	1
   │  └─ MS2 Mass Tolerance Strategy:	Dynamic
   │     └─ Correction Factor:	1
   ├─ Pulsar Search\Identification
   │  ├─ Grouped Peptide FDR:	None
   │  ├─ PSM FDR:	0.01
   │  ├─ Peptide FDR:	0.01
   │  ├─ Protein Group FDR:	0.01
   │  ├─ directDIA Workflow:	directDIA+ (Deep)
   │  │  ├─ IM Sampling Reduction:	7
   │  │  └─ RT Sampling Reduction:	1
   │  ├─ PTM Localization Filter:	False
   │  └─ 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
   │  └─ diaPASEF Pre-Processing:	Automatic
   ├─ Pulsar Search\Tolerances
   │  └─ Tolerance Parameters:	
   │     ├─ Thermo IonTrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     ├─ Thermo Orbitrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     └─ TOF:	
   │        ├─ Calibration Search:	Dynamic
   │        │  ├─ MS1 Correction Factor:	1
   │        │  └─ MS2 Correction Factor:	1
   │        └─ Main Search:	Dynamic
   │           ├─ MS1 Correction Factor:	1
   │           └─ MS2 Correction Factor:	1
   └─ Pulsar Search\Workflow
      ├─ Fragment Ion Selection Strategy:	Intensity Based
      ├─ In-Silico Generate Missing Channels:	False
      └─ Use DNN Predicted Ion Mobility:	Auto
[END-SETTINGS]

[BEGIN-SETUP]
Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
   ├─ Path: "B:\brett\proteobench\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 1
   ├─ HTRMS Version: 20.3.251119.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 15-December-2025 12:31:21 UTC -08:00 
   │     ├─ Date Modified: 15-December-2025 15:11:40 UTC -08:00 
   │     └─ 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: "B:\brett\proteobench\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 2
   ├─ HTRMS Version: 20.3.251119.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 15-December-2025 12:31:21 UTC -08:00 
   │     ├─ Date Modified: 15-December-2025 15:11:40 UTC -08:00 
   │     └─ 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: "B:\brett\proteobench\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 3
   ├─ HTRMS Version: 20.3.251119.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 15-December-2025 12:31:21 UTC -08:00 
   │     ├─ Date Modified: 15-December-2025 15:11:40 UTC -08:00 
   │     └─ 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: "B:\brett\proteobench\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 1
   ├─ HTRMS Version: 20.3.251119.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 15-December-2025 12:31:21 UTC -08:00 
   │     ├─ Date Modified: 15-December-2025 15:11:40 UTC -08:00 
   │     └─ 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: "B:\brett\proteobench\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 2
   ├─ HTRMS Version: 20.3.251119.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 15-December-2025 12:31:21 UTC -08:00 
   │     ├─ Date Modified: 15-December-2025 15:11:40 UTC -08:00 
   │     └─ 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: "B:\brett\proteobench\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 3
   ├─ HTRMS Version: 20.3.251119.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 15-December-2025 12:31:21 UTC -08:00 
   │     ├─ Date Modified: 15-December-2025 15:11:40 UTC -08:00 
   │     └─ 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:    [15/12/2025 12:34:15] -> Initializing Pipeline...
INFO:    [15/12/2025 12:34:15] -> Preprocessing Run #1 of 6...
INFO:    [15/12/2025 12:34:15] -> Searching DIA with Pulsar...
INFO:    [15/12/2025 12:34:15] -> Initialize Pipeline...
INFO:    [15/12/2025 12:34:15] -> Initialize Pipeline
INFO:    [15/12/2025 12:34:21] -> Initialize Pipeline...
INFO:    [15/12/2025 12:34:21] -> Creating Experiment Environment
INFO:    [15/12/2025 12:34:21] -> SuperRun 1/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d)
INFO:    [15/12/2025 12:34:21] -> Run 1/6: Organizing Data from Run
INFO:    [15/12/2025 12:34:21] -> Run 1/6: Creating Calibration Search Space...
INFO:    [15/12/2025 12:34:22] -> Collecting Search Space Parameters...
INFO:    [15/12/2025 12:34:23] -> Creating the Search Space...
INFO:    [15/12/2025 12:34:24] -> Run 1/6: Creating Search Space...
INFO:    [15/12/2025 12:34:24] -> Collecting Search Space Parameters...
INFO:    [15/12/2025 12:34:32] -> Creating the Search Space...
INFO:    [15/12/2025 12:34:33] -> Size of search space [MB]: 0
INFO:    [15/12/2025 12:34:33] -> Number of IMPGs in search space: 0
INFO:    [15/12/2025 12:34:33] -> Run 1/6: MS2 Index Generation
INFO:    [15/12/2025 12:34:59] -> MS2 Index Generation Time: 25.87s
INFO:    [15/12/2025 12:34:59] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [15/12/2025 12:35:01] -> Initializing...
INFO:    [15/12/2025 12:36:41] -> Finalizing HTRMS File...
INFO:    [15/12/2025 12:40:56] -> Processed in 5.9m
INFO:    [15/12/2025 12:40:57] -> Done
INFO:    [15/12/2025 12:40:57] -> Run 1/6: Process Raw File...
INFO:    [15/12/2025 12:41:11] -> Run 1/6: Preparing Partitions...
INFO:    [15/12/2025 12:41:11] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [15/12/2025 12:41:11] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [15/12/2025 12:41:19] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [15/12/2025 12:41:33] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3120 [13.9s]
INFO:    [15/12/2025 12:41:36] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [15/12/2025 12:41:36] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [15/12/2025 12:45:19] -> Extracting 343646 MS1 XICs
INFO:    [15/12/2025 12:47:56] -> Run 1/6: Cleaning Up Run...
INFO:    [15/12/2025 12:47:56] -> SuperRun 2/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d)
INFO:    [15/12/2025 12:47:56] -> Run 2/6: Organizing Data from Run
INFO:    [15/12/2025 12:47:56] -> Run 2/6: Creating Calibration Search Space...
INFO:    [15/12/2025 12:47:56] -> Run 2/6: Creating Search Space...
INFO:    [15/12/2025 12:47:56] -> Size of search space [MB]: 0
INFO:    [15/12/2025 12:47:56] -> Number of IMPGs in search space: 0
INFO:    [15/12/2025 12:47:56] -> Run 2/6: MS2 Index Generation
INFO:    [15/12/2025 12:47:57] -> MS2 Index Generation Time: 450.97ms
INFO:    [15/12/2025 12:47:57] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [15/12/2025 12:47:58] -> Initializing...
INFO:    [15/12/2025 12:49:37] -> Finalizing HTRMS File...
INFO:    [15/12/2025 12:53:52] -> Processed in 5.9m
INFO:    [15/12/2025 12:53:53] -> Done
INFO:    [15/12/2025 12:53:53] -> Run 2/6: Process Raw File...
INFO:    [15/12/2025 12:54:07] -> Run 2/6: Preparing Partitions...
INFO:    [15/12/2025 12:54:07] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [15/12/2025 12:54:07] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [15/12/2025 12:54:14] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [15/12/2025 12:54:29] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3099 [14.2s]
INFO:    [15/12/2025 12:54:31] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [15/12/2025 12:54:32] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [15/12/2025 12:58:02] -> Extracting 326310 MS1 XICs
INFO:    [15/12/2025 13:00:26] -> Run 2/6: Cleaning Up Run...
INFO:    [15/12/2025 13:00:27] -> SuperRun 3/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d)
INFO:    [15/12/2025 13:00:27] -> Run 3/6: Organizing Data from Run
INFO:    [15/12/2025 13:00:27] -> Run 3/6: Creating Calibration Search Space...
INFO:    [15/12/2025 13:00:27] -> Run 3/6: Creating Search Space...
INFO:    [15/12/2025 13:00:27] -> Size of search space [MB]: 0
INFO:    [15/12/2025 13:00:27] -> Number of IMPGs in search space: 0
INFO:    [15/12/2025 13:00:27] -> Run 3/6: MS2 Index Generation
INFO:    [15/12/2025 13:00:27] -> MS2 Index Generation Time: 540.76ms
INFO:    [15/12/2025 13:00:27] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [15/12/2025 13:00:29] -> Initializing...
INFO:    [15/12/2025 13:02:10] -> Finalizing HTRMS File...
INFO:    [15/12/2025 13:06:27] -> Processed in 6m
INFO:    [15/12/2025 13:06:27] -> Done
INFO:    [15/12/2025 13:06:27] -> Run 3/6: Process Raw File...
INFO:    [15/12/2025 13:06:41] -> Run 3/6: Preparing Partitions...
INFO:    [15/12/2025 13:06:41] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [15/12/2025 13:06:42] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [15/12/2025 13:06:49] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [15/12/2025 13:07:03] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2915 [14.1s]
INFO:    [15/12/2025 13:07:06] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [15/12/2025 13:07:06] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [15/12/2025 13:10:35] -> Extracting 326679 MS1 XICs
INFO:    [15/12/2025 13:12:59] -> Run 3/6: Cleaning Up Run...
INFO:    [15/12/2025 13:13:00] -> SuperRun 4/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d)
INFO:    [15/12/2025 13:13:00] -> Run 4/6: Organizing Data from Run
INFO:    [15/12/2025 13:13:00] -> Run 4/6: Creating Calibration Search Space...
INFO:    [15/12/2025 13:13:00] -> Run 4/6: Creating Search Space...
INFO:    [15/12/2025 13:13:00] -> Size of search space [MB]: 0
INFO:    [15/12/2025 13:13:00] -> Number of IMPGs in search space: 0
INFO:    [15/12/2025 13:13:00] -> Run 4/6: MS2 Index Generation
INFO:    [15/12/2025 13:13:00] -> MS2 Index Generation Time: 489.09ms
INFO:    [15/12/2025 13:13:00] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [15/12/2025 13:13:02] -> Initializing...
INFO:    [15/12/2025 13:14:38] -> Finalizing HTRMS File...
INFO:    [15/12/2025 13:18:56] -> Processed in 5.9m
INFO:    [15/12/2025 13:18:57] -> Done
INFO:    [15/12/2025 13:18:57] -> Run 4/6: Process Raw File...
INFO:    [15/12/2025 13:19:11] -> Run 4/6: Preparing Partitions...
INFO:    [15/12/2025 13:19:11] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [15/12/2025 13:19:12] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [15/12/2025 13:19:18] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [15/12/2025 13:19:31] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3212 [12s]
INFO:    [15/12/2025 13:19:33] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [15/12/2025 13:19:34] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [15/12/2025 13:22:58] -> Extracting 340851 MS1 XICs
INFO:    [15/12/2025 13:25:24] -> Run 4/6: Cleaning Up Run...
INFO:    [15/12/2025 13:25:24] -> SuperRun 5/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d)
INFO:    [15/12/2025 13:25:24] -> Run 5/6: Organizing Data from Run
INFO:    [15/12/2025 13:25:24] -> Run 5/6: Creating Calibration Search Space...
INFO:    [15/12/2025 13:25:24] -> Run 5/6: Creating Search Space...
INFO:    [15/12/2025 13:25:24] -> Size of search space [MB]: 0
INFO:    [15/12/2025 13:25:24] -> Number of IMPGs in search space: 0
INFO:    [15/12/2025 13:25:24] -> Run 5/6: MS2 Index Generation
INFO:    [15/12/2025 13:25:25] -> MS2 Index Generation Time: 452.15ms
INFO:    [15/12/2025 13:25:25] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [15/12/2025 13:25:27] -> Initializing...
INFO:    [15/12/2025 13:27:04] -> Finalizing HTRMS File...
INFO:    [15/12/2025 13:31:19] -> Processed in 5.9m
INFO:    [15/12/2025 13:31:19] -> Done
INFO:    [15/12/2025 13:31:19] -> Run 5/6: Process Raw File...
INFO:    [15/12/2025 13:31:34] -> Run 5/6: Preparing Partitions...
INFO:    [15/12/2025 13:31:34] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [15/12/2025 13:31:34] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [15/12/2025 13:31:41] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [15/12/2025 13:31:54] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3425 [12.3s]
INFO:    [15/12/2025 13:31:56] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [15/12/2025 13:31:57] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [15/12/2025 13:35:13] -> Extracting 321646 MS1 XICs
INFO:    [15/12/2025 13:37:32] -> Run 5/6: Cleaning Up Run...
INFO:    [15/12/2025 13:37:33] -> SuperRun 6/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d)
INFO:    [15/12/2025 13:37:33] -> Run 6/6: Organizing Data from Run
INFO:    [15/12/2025 13:37:33] -> Run 6/6: Creating Calibration Search Space...
INFO:    [15/12/2025 13:37:33] -> Run 6/6: Creating Search Space...
INFO:    [15/12/2025 13:37:33] -> Size of search space [MB]: 0
INFO:    [15/12/2025 13:37:33] -> Number of IMPGs in search space: 0
INFO:    [15/12/2025 13:37:33] -> Run 6/6: MS2 Index Generation
INFO:    [15/12/2025 13:37:33] -> MS2 Index Generation Time: 521.46ms
INFO:    [15/12/2025 13:37:33] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [15/12/2025 13:37:36] -> Initializing...
INFO:    [15/12/2025 13:39:13] -> Finalizing HTRMS File...
INFO:    [15/12/2025 13:43:23] -> Processed in 5.8m
INFO:    [15/12/2025 13:43:24] -> Done
INFO:    [15/12/2025 13:43:24] -> Run 6/6: Process Raw File...
INFO:    [15/12/2025 13:43:38] -> Run 6/6: Preparing Partitions...
INFO:    [15/12/2025 13:43:38] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [15/12/2025 13:43:38] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [15/12/2025 13:43:45] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [15/12/2025 13:43:58] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3403 [13.2s]
INFO:    [15/12/2025 13:44:01] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [15/12/2025 13:44:01] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [15/12/2025 13:47:33] -> Extracting 339673 MS1 XICs
INFO:    [15/12/2025 13:50:05] -> Run 6/6: Cleaning Up Run...
INFO:    [15/12/2025 13:50:11] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [15/12/2025 13:50:11] -> Score Post-Processing
INFO:    [15/12/2025 13:51:03] -> Score Post-Processing: 52.56s
INFO:    [15/12/2025 13:51:03] -> PSM FDR...
INFO:    [15/12/2025 13:51:20] -> PSM FDR: 16.28s
INFO:    [15/12/2025 13:51:20] -> Converting to non-redundant data structure...
INFO:    [15/12/2025 13:51:28] -> Performing Peptide FDR...
INFO:    [15/12/2025 13:51:30] -> Performing Protein Inference...
INFO:    [15/12/2025 13:51:31] -> Performing Protein FDR...
INFO:    [15/12/2025 13:51:31] -> Calculating Result Values at Run and Experiment Level...
INFO:    [15/12/2025 13:51:37] -> Pulsar identified 358744 PSMs, 76710 stripped sequences, 86935 peptide precursors, 9511 protein groups.
INFO:    [15/12/2025 13:51:37] -> iRT Calibration...
INFO:    [15/12/2025 13:51:41] -> Performing directDIA+ search fine tuning...
INFO:    [15/12/2025 13:55:39] -> Performing directDIA+ search...
INFO:    [15/12/2025 13:55:39] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
INFO:    [15/12/2025 14:02:55] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
INFO:    [15/12/2025 14:10:31] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
INFO:    [15/12/2025 14:18:08] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
INFO:    [15/12/2025 14:25:22] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
INFO:    [15/12/2025 14:32:47] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
INFO:    [15/12/2025 14:39:32] -> Total nr of Searched Peptides: 2,465,438 of 2,465,438
INFO:    [15/12/2025 14:39:33] -> Initializing Combined Protein Inference...
INFO:    [15/12/2025 14:39:36] -> Performing Protein Inference...
INFO:    [15/12/2025 14:39:38] -> Performing Protein FDR...
INFO:    [15/12/2025 14:39:39] -> Calculating Result Values at Run and Experiment Level...
INFO:    [15/12/2025 14:39:44] -> Pulsar identified 358745 PSMs, 76710 stripped sequences, 86935 peptide precursors, 9530 protein groups.
INFO:    [15/12/2025 14:39:44] -> Calculating Summary...
INFO:    [15/12/2025 14:39:46] -> Identifying Calibration Peptides...
INFO:    [15/12/2025 14:39:47] -> Performing directDIA+ Post Processing...
INFO:    [15/12/2025 14:39:52] -> Combining Protein-Group FDR Results...
INFO:    [15/12/2025 14:39:52] -> Combined Protein-Group Identifications at 1% Qvalue: 11,530
INFO:    [15/12/2025 14:39:52] -> Writing experiment store..
INFO:    [15/12/2025 14:39:56] -> Assigning iRT Source...
INFO:    [15/12/2025 14:39:56] -> Calculating iRT...
INFO:    [15/12/2025 14:39:57] -> Cleaning Up Experiment...
INFO:    [15/12/2025 14:39:57] -> Summarizing Identifications
INFO:    [15/12/2025 14:40:48] -> Identifiying Significant Precursors...
INFO:    [15/12/2025 14:40:58] -> Predicting Ion Mobility
INFO:    [15/12/2025 14:41:03] -> Calculating Median iRT
INFO:    [15/12/2025 14:41:04] -> Building BGS Protein Grouping...
INFO:    [15/12/2025 14:41:04] -> Digesting Fasta...
INFO:    [15/12/2025 14:41:04] -> Annotating Proteins...
INFO:    [15/12/2025 14:41:04] -> Grouping Proteins...
INFO:    [15/12/2025 14:41:06] -> Calculating Run Summary Statistics...
INFO:    [15/12/2025 14:41:22] -> Building Consensus Fragment Spectra...
INFO:    [15/12/2025 14:41:50] -> Selecting best fragment ions
INFO:    [15/12/2025 14:43:27] -> Initializing Experiment...
INFO:    [15/12/2025 14:43:27] -> Loading Spectral Libraries...
INFO:    [15/12/2025 14:43:56] -> Initialize Scoring...
INFO:    [15/12/2025 14:43:56] -> Generating Scan Map...
INFO:    [15/12/2025 14:43:57] -> Initializing Workpackages...
INFO:    [15/12/2025 14:43:57] -> Performing Basic Calibration...
INFO:    [15/12/2025 14:43:58] -> Identifying Calibration Peptides...
INFO:    [15/12/2025 14:43:58] -> Correcting Gradient Fine Structure...
INFO:    [15/12/2025 14:44:01] -> Initializing Pipeline...
INFO:    [15/12/2025 14:44:01] -> Preprocessing Run #1 of 6...
INFO:    [15/12/2025 14:44:01] -> Initialize Scoring...
INFO:    [15/12/2025 14:44:01] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:44:28] -> Machine Learning...
INFO:    [15/12/2025 14:44:28] -> Pipeline executed in 27.35s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:44:32] -> Initializing Pipeline...
INFO:    [15/12/2025 14:44:32] -> Preprocessing Run #1 of 6...
INFO:    [15/12/2025 14:44:32] -> Initialize Scoring...
INFO:    [15/12/2025 14:44:32] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:45:23] -> Machine Learning...
INFO:    [15/12/2025 14:45:26] -> Pipeline executed in 53.55s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:45:32] -> Initialize Scoring...
INFO:    [15/12/2025 14:45:32] -> Preprocessing Run #2 of 6...
INFO:    [15/12/2025 14:45:32] -> Searching DIA with Pulsar...
INFO:    [15/12/2025 14:45:32] -> Initializing Experiment...
INFO:    [15/12/2025 14:45:32] -> Loading Spectral Libraries...
INFO:    [15/12/2025 14:45:32] -> Initialize Scoring...
INFO:    [15/12/2025 14:45:32] -> Generating Scan Map...
INFO:    [15/12/2025 14:45:32] -> Initializing Workpackages...
INFO:    [15/12/2025 14:45:32] -> Performing Basic Calibration...
INFO:    [15/12/2025 14:45:33] -> Identifying Calibration Peptides...
INFO:    [15/12/2025 14:45:33] -> Correcting Gradient Fine Structure...
INFO:    [15/12/2025 14:45:36] -> Initializing Pipeline...
INFO:    [15/12/2025 14:45:36] -> Preprocessing Run #2 of 6...
INFO:    [15/12/2025 14:45:36] -> Initialize Scoring...
INFO:    [15/12/2025 14:45:36] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:46:03] -> Machine Learning...
INFO:    [15/12/2025 14:46:03] -> Pipeline executed in 27.42s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:46:07] -> Initializing Pipeline...
INFO:    [15/12/2025 14:46:07] -> Preprocessing Run #2 of 6...
INFO:    [15/12/2025 14:46:07] -> Initialize Scoring...
INFO:    [15/12/2025 14:46:07] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:46:58] -> Machine Learning...
INFO:    [15/12/2025 14:47:02] -> Pipeline executed in 54.58s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:47:07] -> Initialize Scoring...
INFO:    [15/12/2025 14:47:07] -> Preprocessing Run #3 of 6...
INFO:    [15/12/2025 14:47:07] -> Searching DIA with Pulsar...
INFO:    [15/12/2025 14:47:07] -> Initializing Experiment...
INFO:    [15/12/2025 14:47:07] -> Loading Spectral Libraries...
INFO:    [15/12/2025 14:47:07] -> Initialize Scoring...
INFO:    [15/12/2025 14:47:07] -> Generating Scan Map...
INFO:    [15/12/2025 14:47:07] -> Initializing Workpackages...
INFO:    [15/12/2025 14:47:07] -> Performing Basic Calibration...
INFO:    [15/12/2025 14:47:08] -> Identifying Calibration Peptides...
INFO:    [15/12/2025 14:47:08] -> Correcting Gradient Fine Structure...
INFO:    [15/12/2025 14:47:11] -> Initializing Pipeline...
INFO:    [15/12/2025 14:47:11] -> Preprocessing Run #3 of 6...
INFO:    [15/12/2025 14:47:11] -> Initialize Scoring...
INFO:    [15/12/2025 14:47:11] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:47:37] -> Machine Learning...
INFO:    [15/12/2025 14:47:38] -> Pipeline executed in 26.75s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:47:42] -> Initializing Pipeline...
INFO:    [15/12/2025 14:47:42] -> Preprocessing Run #3 of 6...
INFO:    [15/12/2025 14:47:42] -> Initialize Scoring...
INFO:    [15/12/2025 14:47:42] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:48:33] -> Machine Learning...
INFO:    [15/12/2025 14:48:36] -> Pipeline executed in 54.42s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:48:42] -> Initialize Scoring...
INFO:    [15/12/2025 14:48:42] -> Preprocessing Run #4 of 6...
INFO:    [15/12/2025 14:48:42] -> Searching DIA with Pulsar...
INFO:    [15/12/2025 14:48:42] -> Initializing Experiment...
INFO:    [15/12/2025 14:48:42] -> Loading Spectral Libraries...
INFO:    [15/12/2025 14:48:42] -> Initialize Scoring...
INFO:    [15/12/2025 14:48:42] -> Generating Scan Map...
INFO:    [15/12/2025 14:48:42] -> Initializing Workpackages...
INFO:    [15/12/2025 14:48:42] -> Performing Basic Calibration...
INFO:    [15/12/2025 14:48:43] -> Identifying Calibration Peptides...
INFO:    [15/12/2025 14:48:43] -> Correcting Gradient Fine Structure...
INFO:    [15/12/2025 14:48:46] -> Initializing Pipeline...
INFO:    [15/12/2025 14:48:46] -> Preprocessing Run #4 of 6...
INFO:    [15/12/2025 14:48:46] -> Initialize Scoring...
INFO:    [15/12/2025 14:48:46] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:49:12] -> Machine Learning...
INFO:    [15/12/2025 14:49:13] -> Pipeline executed in 27.46s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:49:17] -> Initializing Pipeline...
INFO:    [15/12/2025 14:49:17] -> Preprocessing Run #4 of 6...
INFO:    [15/12/2025 14:49:17] -> Initialize Scoring...
INFO:    [15/12/2025 14:49:17] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:50:07] -> Machine Learning...
INFO:    [15/12/2025 14:50:10] -> Pipeline executed in 53.64s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:50:16] -> Initialize Scoring...
INFO:    [15/12/2025 14:50:16] -> Preprocessing Run #5 of 6...
INFO:    [15/12/2025 14:50:16] -> Searching DIA with Pulsar...
INFO:    [15/12/2025 14:50:16] -> Initializing Experiment...
INFO:    [15/12/2025 14:50:16] -> Loading Spectral Libraries...
INFO:    [15/12/2025 14:50:16] -> Initialize Scoring...
INFO:    [15/12/2025 14:50:16] -> Generating Scan Map...
INFO:    [15/12/2025 14:50:16] -> Initializing Workpackages...
INFO:    [15/12/2025 14:50:16] -> Performing Basic Calibration...
INFO:    [15/12/2025 14:50:17] -> Identifying Calibration Peptides...
INFO:    [15/12/2025 14:50:17] -> Correcting Gradient Fine Structure...
INFO:    [15/12/2025 14:50:20] -> Initializing Pipeline...
INFO:    [15/12/2025 14:50:20] -> Preprocessing Run #5 of 6...
INFO:    [15/12/2025 14:50:20] -> Initialize Scoring...
INFO:    [15/12/2025 14:50:20] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:50:46] -> Machine Learning...
INFO:    [15/12/2025 14:50:47] -> Pipeline executed in 26.96s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:50:51] -> Initializing Pipeline...
INFO:    [15/12/2025 14:50:51] -> Preprocessing Run #5 of 6...
INFO:    [15/12/2025 14:50:51] -> Initialize Scoring...
INFO:    [15/12/2025 14:50:51] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:51:41] -> Machine Learning...
INFO:    [15/12/2025 14:51:44] -> Pipeline executed in 53.3s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:51:50] -> Initialize Scoring...
INFO:    [15/12/2025 14:51:50] -> Preprocessing Run #6 of 6...
INFO:    [15/12/2025 14:51:50] -> Searching DIA with Pulsar...
INFO:    [15/12/2025 14:51:50] -> Initializing Experiment...
INFO:    [15/12/2025 14:51:50] -> Loading Spectral Libraries...
INFO:    [15/12/2025 14:51:50] -> Initialize Scoring...
INFO:    [15/12/2025 14:51:50] -> Generating Scan Map...
INFO:    [15/12/2025 14:51:50] -> Initializing Workpackages...
INFO:    [15/12/2025 14:51:50] -> Performing Basic Calibration...
INFO:    [15/12/2025 14:51:51] -> Identifying Calibration Peptides...
INFO:    [15/12/2025 14:51:51] -> Correcting Gradient Fine Structure...
INFO:    [15/12/2025 14:51:54] -> Initializing Pipeline...
INFO:    [15/12/2025 14:51:54] -> Preprocessing Run #6 of 6...
INFO:    [15/12/2025 14:51:54] -> Initialize Scoring...
INFO:    [15/12/2025 14:51:54] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:52:20] -> Machine Learning...
INFO:    [15/12/2025 14:52:21] -> Pipeline executed in 27.33s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:52:25] -> Initializing Pipeline...
INFO:    [15/12/2025 14:52:25] -> Preprocessing Run #6 of 6...
INFO:    [15/12/2025 14:52:25] -> Initialize Scoring...
INFO:    [15/12/2025 14:52:25] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:53:16] -> Machine Learning...
INFO:    [15/12/2025 14:53:19] -> Pipeline executed in 54.55s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 14:53:25] -> Initialize Scoring...
INFO:    [15/12/2025 14:53:25] -> Initializing QC...
INFO:    [15/12/2025 14:53:25] -> Determining Calibration Parameter...
INFO:    [15/12/2025 14:53:25] -> Assigning ML Features...
INFO:    [15/12/2025 14:53:25] -> Generating Decoys...
INFO:    [15/12/2025 14:53:36] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:55:14] -> Releasing Raw Files...
INFO:    [15/12/2025 14:55:14] -> Machine Learning...
INFO:    [15/12/2025 14:55:37] -> Initializing HTRMS...
INFO:    [15/12/2025 14:55:37] -> Releasing Run Resources...
INFO:    [15/12/2025 14:55:38] -> Reducing Score Cache...
INFO:    [15/12/2025 14:55:41] -> Calculating Qvalues...
INFO:    [15/12/2025 14:55:42] -> Unique precursors: 132,577 of 141,506 | modified peptides: 116,984 of 124,120 | peptides: 115,746 of 122,806 |  protein groups: 11,320 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d]
INFO:    [15/12/2025 14:55:42] -> Collapsing Search Tree...
INFO:    [15/12/2025 14:55:42] -> Processed in 2.29m
INFO:    [15/12/2025 14:55:42] -> Initializing QC...
INFO:    [15/12/2025 14:55:42] -> Determining Calibration Parameter...
INFO:    [15/12/2025 14:55:42] -> Assigning ML Features...
INFO:    [15/12/2025 14:55:42] -> Generating Decoys...
INFO:    [15/12/2025 14:55:43] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:57:18] -> Releasing Raw Files...
INFO:    [15/12/2025 14:57:18] -> Machine Learning...
INFO:    [15/12/2025 14:57:42] -> Initializing HTRMS...
INFO:    [15/12/2025 14:57:42] -> Releasing Run Resources...
INFO:    [15/12/2025 14:57:43] -> Reducing Score Cache...
INFO:    [15/12/2025 14:57:46] -> Calculating Qvalues...
INFO:    [15/12/2025 14:57:47] -> Unique precursors: 133,181 of 141,506 | modified peptides: 117,500 of 124,120 | peptides: 116,252 of 122,806 |  protein groups: 11,342 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d]
INFO:    [15/12/2025 14:57:47] -> Collapsing Search Tree...
INFO:    [15/12/2025 14:57:47] -> Processed in 2.08m
INFO:    [15/12/2025 14:57:47] -> Initializing QC...
INFO:    [15/12/2025 14:57:47] -> Determining Calibration Parameter...
INFO:    [15/12/2025 14:57:47] -> Assigning ML Features...
INFO:    [15/12/2025 14:57:47] -> Generating Decoys...
INFO:    [15/12/2025 14:57:47] -> Extracting Ion Currents...
INFO:    [15/12/2025 14:59:22] -> Releasing Raw Files...
INFO:    [15/12/2025 14:59:22] -> Machine Learning...
INFO:    [15/12/2025 14:59:47] -> Initializing HTRMS...
INFO:    [15/12/2025 14:59:47] -> Releasing Run Resources...
INFO:    [15/12/2025 14:59:47] -> Reducing Score Cache...
INFO:    [15/12/2025 14:59:50] -> Calculating Qvalues...
INFO:    [15/12/2025 14:59:52] -> Unique precursors: 132,778 of 141,506 | modified peptides: 117,190 of 124,120 | peptides: 115,953 of 122,806 |  protein groups: 11,320 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d]
INFO:    [15/12/2025 14:59:52] -> Collapsing Search Tree...
INFO:    [15/12/2025 14:59:52] -> Processed in 2.08m
INFO:    [15/12/2025 14:59:52] -> Initializing QC...
INFO:    [15/12/2025 14:59:52] -> Determining Calibration Parameter...
INFO:    [15/12/2025 14:59:52] -> Assigning ML Features...
INFO:    [15/12/2025 14:59:52] -> Generating Decoys...
INFO:    [15/12/2025 14:59:52] -> Extracting Ion Currents...
INFO:    [15/12/2025 15:01:27] -> Releasing Raw Files...
INFO:    [15/12/2025 15:01:27] -> Machine Learning...
INFO:    [15/12/2025 15:01:53] -> Initializing HTRMS...
INFO:    [15/12/2025 15:01:53] -> Releasing Run Resources...
INFO:    [15/12/2025 15:01:53] -> Reducing Score Cache...
INFO:    [15/12/2025 15:01:56] -> Calculating Qvalues...
INFO:    [15/12/2025 15:01:58] -> Unique precursors: 133,343 of 141,506 | modified peptides: 117,677 of 124,120 | peptides: 116,421 of 122,806 |  protein groups: 11,390 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d]
INFO:    [15/12/2025 15:01:58] -> Collapsing Search Tree...
INFO:    [15/12/2025 15:01:58] -> Processed in 2.1m
INFO:    [15/12/2025 15:01:58] -> Initializing QC...
INFO:    [15/12/2025 15:01:58] -> Determining Calibration Parameter...
INFO:    [15/12/2025 15:01:58] -> Assigning ML Features...
INFO:    [15/12/2025 15:01:58] -> Generating Decoys...
INFO:    [15/12/2025 15:01:58] -> Extracting Ion Currents...
INFO:    [15/12/2025 15:03:30] -> Releasing Raw Files...
INFO:    [15/12/2025 15:03:30] -> Machine Learning...
INFO:    [15/12/2025 15:03:53] -> Initializing HTRMS...
INFO:    [15/12/2025 15:03:53] -> Releasing Run Resources...
INFO:    [15/12/2025 15:03:54] -> Reducing Score Cache...
INFO:    [15/12/2025 15:03:57] -> Calculating Qvalues...
INFO:    [15/12/2025 15:03:58] -> Unique precursors: 134,578 of 141,506 | modified peptides: 118,777 of 124,120 | peptides: 117,527 of 122,806 |  protein groups: 11,407 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d]
INFO:    [15/12/2025 15:03:58] -> Collapsing Search Tree...
INFO:    [15/12/2025 15:03:58] -> Processed in 2.01m
INFO:    [15/12/2025 15:03:58] -> Initializing QC...
INFO:    [15/12/2025 15:03:58] -> Determining Calibration Parameter...
INFO:    [15/12/2025 15:03:58] -> Assigning ML Features...
INFO:    [15/12/2025 15:03:58] -> Generating Decoys...
INFO:    [15/12/2025 15:03:59] -> Extracting Ion Currents...
INFO:    [15/12/2025 15:05:30] -> Releasing Raw Files...
INFO:    [15/12/2025 15:05:30] -> Machine Learning...
INFO:    [15/12/2025 15:05:53] -> Initializing HTRMS...
INFO:    [15/12/2025 15:05:53] -> Releasing Run Resources...
INFO:    [15/12/2025 15:05:54] -> Reducing Score Cache...
INFO:    [15/12/2025 15:05:55] -> Calculating Qvalues...
INFO:    [15/12/2025 15:05:56] -> Unique precursors: 133,876 of 141,506 | modified peptides: 117,976 of 124,120 | peptides: 116,729 of 122,806 |  protein groups: 11,408 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d]
INFO:    [15/12/2025 15:05:56] -> Collapsing Search Tree...
INFO:    [15/12/2025 15:05:56] -> Processed in 1.97m
INFO:    [15/12/2025 15:05:56] -> Normalizing Cscores...
INFO:    [15/12/2025 15:05:57] -> Calculating Global CVs
INFO:    [15/12/2025 15:05:57] -> Calculating Profile Qvalues...
INFO:    [15/12/2025 15:05:58] -> Initializing Protein Groups...
INFO:    [15/12/2025 15:06:07] -> Correcting Interferences...
INFO:    [15/12/2025 15:06:18] -> Calculating Global CVs
INFO:    [15/12/2025 15:06:18] -> Calculating Precursor Quantities...
INFO:    [15/12/2025 15:06:18] -> Normalizing Quantification...
INFO:    [15/12/2025 15:06:19] -> Performing Local Normalization...
INFO:    [15/12/2025 15:06:20] -> Calculating Global CVs
INFO:    [15/12/2025 15:06:21] -> Calculating Condition CVs
INFO:    [15/12/2025 15:06:22] -> Excluding Library Duplicates...
INFO:    [15/12/2025 15:06:23] -> Calculating Global CVs
INFO:    [15/12/2025 15:06:23] -> Building Protein Groups...
INFO:    [15/12/2025 15:06:30] -> Calculating Run-Wise Protein Group FDR...
INFO:    [15/12/2025 15:06:33] -> Annotating Protein Single Hits...
INFO:    [15/12/2025 15:06:34] -> Calculating Global CVs
INFO:    [15/12/2025 15:06:34] -> Updating Identification Counts...
INFO:    [15/12/2025 15:06:35] -> Subtracting background noise...
INFO:    [15/12/2025 15:06:38] -> Resetting existing imputation...
INFO:    [15/12/2025 15:06:38] -> Calculating Protein Quantities...
INFO:    [15/12/2025 15:06:39] -> Calculating Protein Quantities...
INFO:    [15/12/2025 15:06:39] -> Calculating MaxLFQ Protein Quantities...
INFO:    [15/12/2025 15:06:43] -> Collapsing PTM-Locations...
INFO:    [15/12/2025 15:06:43] -> PTM Stoichiometry calculation...
INFO:    [15/12/2025 15:06:43] -> Creating Protein Map...
INFO:    [15/12/2025 15:06:43] -> Compiling Run Summary Information...
INFO:    [15/12/2025 15:06:43] -> Running Post Analysis Processes...
INFO:    [15/12/2025 15:06:54] -> Saving Qc Data...
INFO:    [15/12/2025 15:06:57] -> Writing Summary Information...
INFO:    [15/12/2025 15:06:57] -> Unique precursors: 126,777 of 141,506 | modified peptides: 112,356 of 124,120 | peptides: 111,169 of 122,806 |  protein groups: 11,099 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [15/12/2025 15:06:57] -> Unique precursors: 127,589 of 141,506 | modified peptides: 113,060 of 124,120 | peptides: 111,866 of 122,806 |  protein groups: 11,130 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [15/12/2025 15:06:57] -> Unique precursors: 127,381 of 141,506 | modified peptides: 112,892 of 124,120 | peptides: 111,702 of 122,806 |  protein groups: 11,114 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [15/12/2025 15:06:57] -> Unique precursors: 127,813 of 141,506 | modified peptides: 113,219 of 124,120 | peptides: 112,014 of 122,806 |  protein groups: 11,206 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [15/12/2025 15:06:57] -> Unique precursors: 128,236 of 141,506 | modified peptides: 113,586 of 124,120 | peptides: 112,392 of 122,806 |  protein groups: 11,220 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [15/12/2025 15:06:57] -> Unique precursors: 128,438 of 141,506 | modified peptides: 113,742 of 124,120 | peptides: 112,542 of 122,806 |  protein groups: 11,215 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [15/12/2025 15:06:57] -> Unique precursors: 130,775 of 141,506 | modified peptides: 115,646 of 124,120 | peptides: 114,433 of 122,806 |  protein groups: 11,270 (Qvalue <= 0.01) for whole experiment "Proteobench"

INFO:    [15/12/2025 15:06:57] -> Saving SNE File...
INFO:    [15/12/2025 15:06:57] -> Storing SNE File: S:\sne_storage\20251215_123414_Proteobench.sne
INFO:    [15/12/2025 15:06:57] -> Initializing Pipeline...
INFO:    [15/12/2025 15:06:57] -> Calculating Qvalues...
INFO:    [15/12/2025 15:06:57] -> Saving...
INFO:    [15/12/2025 15:07:12] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 15:07:12] -> Pipeline executed in 14.2s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 15:07:12] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 15:07:12] -> Pipeline executed in 2.55h - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 15:11:40] -> Initializing Pipeline...
INFO:    [15/12/2025 15:11:40] -> Calculating Qvalues...
INFO:    [15/12/2025 15:11:40] -> Saving...
INFO:    [15/12/2025 15:11:53] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [15/12/2025 15:11:53] -> Pipeline executed in 13.09s - Current Experiment had 0 Warnings and 0 Errors.
[END-LOG]
