Spectronaut 20.0.250606.92449
Computer Name: HALBARAD
User Domain Name: SPECTROMASSE
User Name: chaoui
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 11-July-2025 09:47:10 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
   │  ├─ 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):	0.01
   │  ├─ Protein PEP Cutoff:	0.75
   │  ├─ Single Hit Definition:	By Stripped Sequence
   │  ├─ Single Hit Protein Rule:	Stratified Single Hit Protein FDR
   │  ├─ Run-Level Protein Scoring:	Highest Scoring Observation (SN19 default)
   │  ├─ Exclude Duplicate Assays:	True
   │  ├─ Exclude Predicted Fragment Scores:	False
   │  ├─ Generate Decoys:	True
   │  │  ├─ Decoy Generation Method:	Mutated
   │  │  │  └─ Preferred Fragment Source:	NN Predicted Fragments
   │  │  └─ Decoy Limit Strategy:	Dynamic
   │  │     └─ Library Size Fraction:	0.1
   │  └─ Pvalue Estimator:	Kernel Density Estimator
   ├─ DIA Analysis\Pipeline Mode
   │  ├─ Export All XICs:	False
   │  ├─ Generate SNE File:	True
   │  │  └─ Store Ion traces in SNE:	True
   │  ├─ Post Analysis Reports:	
   │  │  ├─ Binned CVs:	False
   │  │  ├─ Binned Identification:	False
   │  │  ├─ CV Density Line Chart:	False
   │  │  ├─ CVs Below X Bar Chart:	False
   │  │  ├─ Data Completeness Bar Chart:	False
   │  │  ├─ Run Identifications Bar Chart:	False
   │  │  ├─ Scoring Histograms:	False
   │  │  └─ TIC Overlay:	False
   │  ├─ PTM Report Schema:	
   │  ├─ Report Schema:	BGS Factory Report (Normal)
   │  └─ Reporting Unit:	Across Experiment
   ├─ DIA Analysis\Post Analysis
   │  ├─ Differential Abundance Testing:	Unpaired t-test
   │  │  ├─ Assume Equal Variance:	False
   │  │  ├─ Group-Wise Testing Correction:	False
   │  │  ├─ Log2 Ratio Candidate Filter:	0.58
   │  │  └─ Confidence Candidate Filter:	Qvalue
   │  │     └─ Confidence:	0.05
   │  ├─ Differential Abundance Grouping:	Major Group (Quantification Settings)
   │  │  └─ Smallest Quantitative Unit:	Major Group (Quantification Settings)
   │  │     └─ Use All MS-Level Quantities:	True
   │  ├─ Calculate Explained TIC:	None
   │  ├─ Calculate Sample Correlation Matrix:	False
   │  ├─ Gene Ontology:	\\GANDALF\chaoui\AppData\Spectronaut\geneOntology\Ontologies\bgs_default_go-basic.obo
   │  └─ Hierarchical Clustering:	True
   │     ├─ Distance Metric:	Manhattan Distance
   │     ├─ Linkage Strategy:	Ward's Method
   │     ├─ Order Runs by Clustering:	True
   │     └─ Z-score Transformation:	False
   ├─ DIA Analysis\Protein Inference
   │  └─ Protein Inference Workflow:	Automatic
   │     └─ Inference Algorithm:	IDPicker
   ├─ DIA Analysis\PTM Workflow
   │  ├─ Input Normalization Strategy:	None
   │  └─ PTM Localization:	False
   ├─ DIA Analysis\Quantification
   │  ├─ Precursor Filtering:	Identified (Qvalue)
   │  │  ├─ Imputation Strategy:	None
   │  │  └─ Multi Channel Qvalue Filter:	Group Qvalue
   │  ├─ Proteotypicity Filter:	None
   │  ├─ Protein LFQ Method:	Automatic
   │  ├─ Quantity MS Level:	MS2
   │  ├─ Quantity Type:	Area
   │  ├─ Cross-Run Normalization:	True
   │  │  ├─ Normalization Filter Type:	None
   │  │  ├─ Normalization Strategy:	Automatic
   │  │  └─ Row Selection:	Automatic
   │  ├─ Perform background noise removal:	True
   │  ├─ Quantification window:	Synchronized
   │  ├─ Interference Correction:	True
   │  │  ├─ Only Identified Peptides:	True
   │  │  ├─ Exclude All Multi-Channel Interferences:	True
   │  │  ├─ MS1 Min:	2
   │  │  └─ MS2 Min:	3
   │  ├─ Major Group Quantity:	Mean peptide quantity
   │  ├─ Minor (Peptide) Grouping:	by Stripped Sequence
   │  ├─ Major (Protein) Grouping:	by Protein Group Id
   │  ├─ Major Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Minor Group Quantity:	Mean precursor quantity
   │  ├─ Minor Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Use Log2 Quantity Filter:	True
   │  │  └─ Minimum Log2 Precursor Quantity:	0
   │  └─ Perform IM Peak Picking for Quantification:	True
   ├─ DIA Analysis\Workflow
   │  ├─ Method Evaluation:	False
   │  ├─ MS2 DeMultiplexing:	Automatic
   │  ├─ Multi-Channel Workflow Definition:	From Library Annotation
   │  │  └─ Fallback Option:	Labeled
   │  ├─ Profiling Strategy:	None
   │  ├─ Run Limit for directDIA Library:	-1
   │  ├─ Hybrid (DDA + DIA) Library:	False
   │  └─ Unify Peptide Peaks Strategy:	None
   ├─ DIA Analysis\XIC Extraction
   │  ├─ XIC IM Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ XIC RT Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ MS1 Mass Tolerance Strategy:	Dynamic
   │  │  └─ Correction Factor:	1
   │  └─ MS2 Mass Tolerance Strategy:	Dynamic
   │     └─ Correction Factor:	1
   ├─ Pulsar Search\Identification
   │  ├─ PSM FDR:	0.01
   │  ├─ Peptide FDR:	0.01
   │  ├─ Protein Group FDR:	0.01
   │  ├─ directDIA Workflow:	directDIA+ (Deep)
   │  └─ PTM Localization Filter:	False
   ├─ Pulsar Search\iRT Calibration
   │  ├─ Calibrate from Empirical RT:	False
   │  ├─ Auto-assign iRT source:	True
   │  ├─ iRT Reference Strategy:	Deep Learning Assisted iRT Regression
   │  ├─ Use Source Specific iRT:	Auto
   │  └─ Minimum Rsquare:	0.8
   ├─ Pulsar Search\Labeling
   │  └─ Channels:	
   │     ├─ Channel 1:	False
   │     ├─ Channel 2:	False
   │     ├─ Channel 3:	False
   │     ├─ Channel 4:	False
   │     └─ Channel 5:	False
   ├─ Pulsar Search\Modifications
   │  └─ Search Mode:	Closed Search
   │     ├─ Max Variable Modifications:	1
   │     ├─ Fixed Modifications::	Carbamidomethyl (C)
   │     └─ Variable Modifications::	Acetyl (Protein N-term), Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin/P
   │  ├─ Digest Type:	Specific
   │  ├─ Decoy Generation Rule:	KR
   │  ├─ Max Peptide Length:	30
   │  ├─ Min Peptide Length:	6
   │  ├─ Missed Cleavages:	1
   │  └─ Toggle N-terminal M:	True
   ├─ Pulsar Search\Result Filters
   │  ├─ Fragment Ions:	
   │  │  ├─ Ion AA Length:	True
   │  │  │  └─ N:	3
   │  │  ├─ Ion Charge:	False
   │  │  ├─ Ion Loss Type:	False
   │  │  ├─ Ion Type:	False
   │  │  ├─ m/z :	True
   │  │  │  ├─ Max:	2000
   │  │  │  └─ Min:	50
   │  │  ├─ Overlapping between Channels:	False
   │  │  └─ Relative Intensity:	True
   │  │     └─ Min:	1
   │  └─ Precursors:	
   │     ├─ Amino Acids:	False
   │     ├─ Best N Fragments per Peptide:	True
   │     │  ├─ Max:	6
   │     │  └─ Min:	3
   │     ├─ Best N Peptides per Protein Group:	False
   │     ├─ Channel Count:	False
   │     ├─ FASTA Matched:	False
   │     ├─ Missed Cleavage:	False
   │     ├─ Modifications:	None
   │     ├─ Peptide Charge:	False
   │     └─ Proteotypicity:	False
   ├─ Pulsar Search\Speed-Up
   │  ├─ MS2 Index:	Automatic
   │  └─ diaPASEF Pre-Processing:	Automatic
   ├─ Pulsar Search\Tolerances
   │  └─ Tolerance Parameters:	
   │     ├─ Thermo IonTrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     ├─ Thermo Orbitrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     └─ TOF:	
   │        ├─ Calibration Search:	Dynamic
   │        │  ├─ MS1 Correction Factor:	1
   │        │  └─ MS2 Correction Factor:	1
   │        └─ Main Search:	Dynamic
   │           ├─ MS1 Correction Factor:	1
   │           └─ MS2 Correction Factor:	1
   └─ Pulsar Search\Workflow
      ├─ Fragment Ion Selection Strategy:	Intensity Based
      ├─ In-Silico Generate Missing Channels:	False
      └─ Use DNN Predicted Ion Mobility:	Auto
[END-SETTINGS]

[BEGIN-SETUP]
Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 1
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 11-July-2025 09:41:42 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 2
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 11-July-2025 09:41:42 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 3
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 11-July-2025 09:41:42 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 4
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 11-July-2025 09:41:42 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 5
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 11-July-2025 09:41:42 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
   ├─ Path: "\\tol-brandir\Masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d\analysis.tdf"
   ├─ Condition: Not Defined
   ├─ Replicate: 6
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 20-November-2024 09:08:03 UTC +01:00 
   │     ├─ Date Modified: 11-July-2025 09:41:42 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

[END-SETUP]

[BEGIN-LOG]
INFO:    [07/07/2025 12:01:20] -> Initializing Pipeline...
INFO:    [07/07/2025 12:01:20] -> Loading...
INFO:    [07/07/2025 12:01:20] -> Loading SNE File: D:/Utilisateurs/Emma/spectronaut results/automatic SNE storage/20250512_143152_ttSCP_Protebench_Param_Robbe.sne
INFO:    [12/05/2025 14:31:53] -> Initializing Pipeline...
INFO:    [12/05/2025 14:31:53] -> Preprocessing Run #1 of 6...
INFO:    [12/05/2025 14:31:53] -> Searching DIA with Pulsar...
INFO:    [12/05/2025 14:31:55] -> Initialize Pipeline...
INFO:    [12/05/2025 14:31:55] -> Initialize Pipeline
INFO:    [12/05/2025 14:33:32] -> Initialize Pipeline...
INFO:    [12/05/2025 14:33:32] -> Creating Experiment Environment
INFO:    [12/05/2025 14:33:32] -> SuperRun 1/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d)
INFO:    [12/05/2025 14:33:32] -> Run 1/6: Organizing Data from Run
INFO:    [12/05/2025 14:33:32] -> Run 1/6: Creating Calibration Search Space...
INFO:    [12/05/2025 14:33:34] -> Run 1/6: Creating Search Space...
INFO:    [12/05/2025 14:33:34] -> Size of search space [MB]: 0
INFO:    [12/05/2025 14:33:34] -> Number of IMPGs in search space: 0
INFO:    [12/05/2025 14:33:34] -> Run 1/6: MS2 Index Generation
INFO:    [12/05/2025 14:33:35] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [12/05/2025 14:33:48] -> Initializing...
INFO:    [12/05/2025 14:38:49] -> Finalizing HTRMS File...
INFO:    [12/05/2025 14:41:58] -> Processed in 8.2m
INFO:    [12/05/2025 14:42:12] -> Done
INFO:    [12/05/2025 14:42:12] -> Run 1/6: Process Raw File...
INFO:    [12/05/2025 14:42:53] -> Run 1/6: Preparing Partitions...
INFO:    [12/05/2025 14:42:53] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [12/05/2025 14:42:55] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [12/05/2025 14:43:11] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [12/05/2025 14:43:27] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3019 [16s]
INFO:    [12/05/2025 14:43:31] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [12/05/2025 14:43:32] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [12/05/2025 14:47:12] -> Extracting 317506 MS1 XICs
INFO:    [12/05/2025 14:51:22] -> Run 1/6: Cleaning Up Run..
INFO:    [12/05/2025 14:51:29] -> SuperRun 2/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d)
INFO:    [12/05/2025 14:51:29] -> Run 2/6: Organizing Data from Run
INFO:    [12/05/2025 14:51:29] -> Run 2/6: Creating Calibration Search Space...
INFO:    [12/05/2025 14:51:29] -> Run 2/6: Creating Search Space...
INFO:    [12/05/2025 14:51:29] -> Size of search space [MB]: 0
INFO:    [12/05/2025 14:51:29] -> Number of IMPGs in search space: 0
INFO:    [12/05/2025 14:51:29] -> Run 2/6: MS2 Index Generation
INFO:    [12/05/2025 14:51:30] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [12/05/2025 14:51:45] -> Initializing...
INFO:    [12/05/2025 14:56:59] -> Finalizing HTRMS File...
INFO:    [12/05/2025 14:59:54] -> Processed in 8.2m
INFO:    [12/05/2025 15:00:02] -> Done
INFO:    [12/05/2025 15:00:02] -> Run 2/6: Process Raw File...
INFO:    [12/05/2025 15:00:49] -> Run 2/6: Preparing Partitions...
INFO:    [12/05/2025 15:00:49] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [12/05/2025 15:00:50] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [12/05/2025 15:01:08] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [12/05/2025 15:01:24] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3069 [15.4s]
INFO:    [12/05/2025 15:01:27] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [12/05/2025 15:01:28] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [12/05/2025 15:05:04] -> Extracting 320755 MS1 XICs
INFO:    [12/05/2025 15:09:07] -> Run 2/6: Cleaning Up Run..
INFO:    [12/05/2025 15:09:10] -> SuperRun 3/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d)
INFO:    [12/05/2025 15:09:10] -> Run 3/6: Organizing Data from Run
INFO:    [12/05/2025 15:09:10] -> Run 3/6: Creating Calibration Search Space...
INFO:    [12/05/2025 15:09:10] -> Run 3/6: Creating Search Space...
INFO:    [12/05/2025 15:09:10] -> Size of search space [MB]: 0
INFO:    [12/05/2025 15:09:10] -> Number of IMPGs in search space: 0
INFO:    [12/05/2025 15:09:10] -> Run 3/6: MS2 Index Generation
INFO:    [12/05/2025 15:09:11] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [12/05/2025 15:09:36] -> Initializing...
INFO:    [12/05/2025 15:14:58] -> Finalizing HTRMS File...
INFO:    [12/05/2025 15:17:47] -> Processed in 8.2m
INFO:    [12/05/2025 15:17:59] -> Done
INFO:    [12/05/2025 15:17:59] -> Run 3/6: Process Raw File...
INFO:    [12/05/2025 15:18:49] -> Run 3/6: Preparing Partitions...
INFO:    [12/05/2025 15:18:49] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [12/05/2025 15:18:50] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [12/05/2025 15:19:07] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [12/05/2025 15:19:22] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2854 [14.3s]
INFO:    [12/05/2025 15:19:26] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [12/05/2025 15:19:27] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [12/05/2025 15:23:05] -> Extracting 320652 MS1 XICs
INFO:    [12/05/2025 15:26:29] -> Run 3/6: Cleaning Up Run..
INFO:    [12/05/2025 15:26:31] -> SuperRun 4/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d)
INFO:    [12/05/2025 15:26:31] -> Run 4/6: Organizing Data from Run
INFO:    [12/05/2025 15:26:31] -> Run 4/6: Creating Calibration Search Space...
INFO:    [12/05/2025 15:26:31] -> Run 4/6: Creating Search Space...
INFO:    [12/05/2025 15:26:31] -> Size of search space [MB]: 0
INFO:    [12/05/2025 15:26:31] -> Number of IMPGs in search space: 0
INFO:    [12/05/2025 15:26:31] -> Run 4/6: MS2 Index Generation
INFO:    [12/05/2025 15:26:32] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [12/05/2025 15:26:43] -> Initializing...
INFO:    [12/05/2025 15:31:39] -> Finalizing HTRMS File...
INFO:    [12/05/2025 15:34:26] -> Processed in 7.7m
INFO:    [12/05/2025 15:34:40] -> Done
INFO:    [12/05/2025 15:34:40] -> Run 4/6: Process Raw File...
INFO:    [12/05/2025 15:35:17] -> Run 4/6: Preparing Partitions...
INFO:    [12/05/2025 15:35:17] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [12/05/2025 15:35:18] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [12/05/2025 15:35:34] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [12/05/2025 15:35:49] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3283 [14s]
INFO:    [12/05/2025 15:35:53] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [12/05/2025 15:35:54] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [12/05/2025 15:39:23] -> Extracting 309830 MS1 XICs
INFO:    [12/05/2025 15:43:09] -> Run 4/6: Cleaning Up Run..
INFO:    [12/05/2025 15:43:16] -> SuperRun 5/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d)
INFO:    [12/05/2025 15:43:16] -> Run 5/6: Organizing Data from Run
INFO:    [12/05/2025 15:43:16] -> Run 5/6: Creating Calibration Search Space...
INFO:    [12/05/2025 15:43:16] -> Run 5/6: Creating Search Space...
INFO:    [12/05/2025 15:43:16] -> Size of search space [MB]: 0
INFO:    [12/05/2025 15:43:16] -> Number of IMPGs in search space: 0
INFO:    [12/05/2025 15:43:16] -> Run 5/6: MS2 Index Generation
INFO:    [12/05/2025 15:43:17] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [12/05/2025 15:43:32] -> Initializing...
INFO:    [12/05/2025 15:48:22] -> Finalizing HTRMS File...
INFO:    [12/05/2025 15:50:58] -> Processed in 7.4m
INFO:    [12/05/2025 15:51:06] -> Done
INFO:    [12/05/2025 15:51:06] -> Run 5/6: Process Raw File...
INFO:    [12/05/2025 15:51:54] -> Run 5/6: Preparing Partitions...
INFO:    [12/05/2025 15:51:54] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [12/05/2025 15:51:55] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [12/05/2025 15:52:13] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [12/05/2025 15:52:26] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3203 [12.8s]
INFO:    [12/05/2025 15:52:30] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [12/05/2025 15:52:31] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [12/05/2025 15:55:57] -> Extracting 312450 MS1 XICs
INFO:    [12/05/2025 15:59:31] -> Run 5/6: Cleaning Up Run..
INFO:    [12/05/2025 15:59:33] -> SuperRun 6/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d)
INFO:    [12/05/2025 15:59:33] -> Run 6/6: Organizing Data from Run
INFO:    [12/05/2025 15:59:33] -> Run 6/6: Creating Calibration Search Space...
INFO:    [12/05/2025 15:59:33] -> Run 6/6: Creating Search Space...
INFO:    [12/05/2025 15:59:33] -> Size of search space [MB]: 0
INFO:    [12/05/2025 15:59:33] -> Number of IMPGs in search space: 0
INFO:    [12/05/2025 15:59:33] -> Run 6/6: MS2 Index Generation
INFO:    [12/05/2025 15:59:35] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [12/05/2025 15:59:49] -> Initializing...
INFO:    [12/05/2025 16:04:51] -> Finalizing HTRMS File...
INFO:    [12/05/2025 16:07:30] -> Processed in 7.7m
INFO:    [12/05/2025 16:07:33] -> Done
INFO:    [12/05/2025 16:07:33] -> Run 6/6: Process Raw File...
INFO:    [12/05/2025 16:08:11] -> Run 6/6: Preparing Partitions...
INFO:    [12/05/2025 16:08:11] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [12/05/2025 16:08:12] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [12/05/2025 16:08:29] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [12/05/2025 16:08:43] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3215 [14s]
INFO:    [12/05/2025 16:08:47] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [12/05/2025 16:08:48] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [12/05/2025 16:12:30] -> Extracting 332197 MS1 XICs
INFO:    [12/05/2025 16:16:14] -> Run 6/6: Cleaning Up Run..
INFO:    [12/05/2025 16:16:26] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [12/05/2025 16:16:32] -> Score Post-Processing
INFO:    [12/05/2025 16:18:28] -> Score Post-Processing: 1.94m
INFO:    [12/05/2025 16:18:28] -> PSM FDR...
INFO:    [12/05/2025 16:19:00] -> PSM FDR: 31.94s
INFO:    [12/05/2025 16:19:00] -> Converting to non-redundant data structure...
INFO:    [12/05/2025 16:19:25] -> Performing Peptide FDR...
INFO:    [12/05/2025 16:19:30] -> Performing Protein Inference...
INFO:    [12/05/2025 16:19:33] -> Performing Protein FDR...
INFO:    [12/05/2025 16:19:34] -> Calculating Result Values at Run and Experiment Level...
INFO:    [12/05/2025 16:19:49] -> Pulsar identified 351972 PSMs, 74115 stripped sequences, 83948 peptide precursors, 9253 protein groups.
INFO:    [12/05/2025 16:19:49] -> Calculating Summary...
INFO:    [12/05/2025 16:19:53] -> Identifying Calibration Peptides...
INFO:    [12/05/2025 16:19:55] -> iRT Calibration...
INFO:    [12/05/2025 16:20:00] -> Performing directDIA+ search...
INFO:    [12/05/2025 16:20:54] -> Generating directDIA+ search space
INFO:    [12/05/2025 16:23:29] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
INFO:    [12/05/2025 16:32:08] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
INFO:    [12/05/2025 16:40:56] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
INFO:    [12/05/2025 16:49:35] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
INFO:    [12/05/2025 16:58:18] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
INFO:    [12/05/2025 17:06:36] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
INFO:    [12/05/2025 17:15:24] -> Performing directDIA+ Post Processing...
INFO:    [12/05/2025 17:15:35] -> Writing experiment store..
INFO:    [12/05/2025 17:15:44] -> Assigning iRT Source...
INFO:    [12/05/2025 17:15:44] -> Calculating iRT...
INFO:    [12/05/2025 17:15:45] -> Cleaning Up Experiment...
INFO:    [12/05/2025 17:15:45] -> Summarizing Identifications
INFO:    [12/05/2025 17:17:43] -> Identifiying Significant Precursors...
INFO:    [12/05/2025 17:18:07] -> Predicting Ion Mobility
INFO:    [12/05/2025 17:18:22] -> Calculating Median iRT
INFO:    [12/05/2025 17:18:24] -> Building BGS Protein Grouping...
INFO:    [12/05/2025 17:18:24] -> Digesting Fasta...
INFO:    [12/05/2025 17:18:25] -> Annotating Proteins...
INFO:    [12/05/2025 17:18:25] -> Grouping Proteins...
INFO:    [12/05/2025 17:18:28] -> Calculating Run Summary Statistics...
INFO:    [12/05/2025 17:19:09] -> Building Consensus Fragment Spectra...
INFO:    [12/05/2025 17:20:17] -> Selecting best fragment ions
INFO:    [12/05/2025 17:24:51] -> Initializing Experiment...
INFO:    [12/05/2025 17:24:51] -> Loading Spectral Libraries...
INFO:    [12/05/2025 17:26:10] -> Initialize Scoring...
INFO:    [12/05/2025 17:26:10] -> Generating Scan Map...
INFO:    [12/05/2025 17:26:10] -> Initializing Workpackages...
INFO:    [12/05/2025 17:26:10] -> Performing Basic Calibration...
INFO:    [12/05/2025 17:26:12] -> Identifying Calibration Peptides...
INFO:    [12/05/2025 17:26:12] -> Correcting Gradient Fine Structure...
INFO:    [12/05/2025 17:26:17] -> Initializing Pipeline...
INFO:    [12/05/2025 17:26:17] -> Preprocessing Run #1 of 6...
INFO:    [12/05/2025 17:26:17] -> Initialize Scoring...
INFO:    [12/05/2025 17:26:17] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:27:00] -> Machine Learning...
INFO:    [12/05/2025 17:27:02] -> Pipeline executed in 44.93s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:27:08] -> Initializing Pipeline...
INFO:    [12/05/2025 17:27:08] -> Preprocessing Run #1 of 6...
INFO:    [12/05/2025 17:27:08] -> Initialize Scoring...
INFO:    [12/05/2025 17:27:08] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:28:14] -> Machine Learning...
INFO:    [12/05/2025 17:28:18] -> Pipeline executed in 1.17m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:28:34] -> Initialize Scoring...
INFO:    [12/05/2025 17:28:34] -> Preprocessing Run #2 of 6...
INFO:    [12/05/2025 17:28:34] -> Searching DIA with Pulsar...
INFO:    [12/05/2025 17:28:34] -> Initializing Experiment...
INFO:    [12/05/2025 17:28:34] -> Loading Spectral Libraries...
INFO:    [12/05/2025 17:28:34] -> Initialize Scoring...
INFO:    [12/05/2025 17:28:34] -> Generating Scan Map...
INFO:    [12/05/2025 17:28:34] -> Initializing Workpackages...
INFO:    [12/05/2025 17:28:34] -> Performing Basic Calibration...
INFO:    [12/05/2025 17:28:36] -> Identifying Calibration Peptides...
INFO:    [12/05/2025 17:28:36] -> Correcting Gradient Fine Structure...
INFO:    [12/05/2025 17:28:40] -> Initializing Pipeline...
INFO:    [12/05/2025 17:28:40] -> Preprocessing Run #2 of 6...
INFO:    [12/05/2025 17:28:40] -> Initialize Scoring...
INFO:    [12/05/2025 17:28:40] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:29:20] -> Machine Learning...
INFO:    [12/05/2025 17:29:21] -> Pipeline executed in 41.1s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:29:28] -> Initializing Pipeline...
INFO:    [12/05/2025 17:29:28] -> Preprocessing Run #2 of 6...
INFO:    [12/05/2025 17:29:28] -> Initialize Scoring...
INFO:    [12/05/2025 17:29:28] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:30:34] -> Machine Learning...
INFO:    [12/05/2025 17:30:38] -> Pipeline executed in 1.17m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:30:54] -> Initialize Scoring...
INFO:    [12/05/2025 17:30:54] -> Preprocessing Run #3 of 6...
INFO:    [12/05/2025 17:30:54] -> Searching DIA with Pulsar...
INFO:    [12/05/2025 17:30:54] -> Initializing Experiment...
INFO:    [12/05/2025 17:30:54] -> Loading Spectral Libraries...
INFO:    [12/05/2025 17:30:54] -> Initialize Scoring...
INFO:    [12/05/2025 17:30:54] -> Generating Scan Map...
INFO:    [12/05/2025 17:30:54] -> Initializing Workpackages...
INFO:    [12/05/2025 17:30:54] -> Performing Basic Calibration...
INFO:    [12/05/2025 17:30:56] -> Identifying Calibration Peptides...
INFO:    [12/05/2025 17:30:56] -> Correcting Gradient Fine Structure...
INFO:    [12/05/2025 17:31:00] -> Initializing Pipeline...
INFO:    [12/05/2025 17:31:00] -> Preprocessing Run #3 of 6...
INFO:    [12/05/2025 17:31:00] -> Initialize Scoring...
INFO:    [12/05/2025 17:31:00] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:31:41] -> Machine Learning...
INFO:    [12/05/2025 17:31:42] -> Pipeline executed in 42.19s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:31:49] -> Initializing Pipeline...
INFO:    [12/05/2025 17:31:49] -> Preprocessing Run #3 of 6...
INFO:    [12/05/2025 17:31:49] -> Initialize Scoring...
INFO:    [12/05/2025 17:31:49] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:32:56] -> Machine Learning...
INFO:    [12/05/2025 17:33:01] -> Pipeline executed in 1.19m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:33:16] -> Initialize Scoring...
INFO:    [12/05/2025 17:33:16] -> Preprocessing Run #4 of 6...
INFO:    [12/05/2025 17:33:16] -> Searching DIA with Pulsar...
INFO:    [12/05/2025 17:33:16] -> Initializing Experiment...
INFO:    [12/05/2025 17:33:16] -> Loading Spectral Libraries...
INFO:    [12/05/2025 17:33:16] -> Initialize Scoring...
INFO:    [12/05/2025 17:33:16] -> Generating Scan Map...
INFO:    [12/05/2025 17:33:16] -> Initializing Workpackages...
INFO:    [12/05/2025 17:33:16] -> Performing Basic Calibration...
INFO:    [12/05/2025 17:33:18] -> Identifying Calibration Peptides...
INFO:    [12/05/2025 17:33:18] -> Correcting Gradient Fine Structure...
INFO:    [12/05/2025 17:33:22] -> Initializing Pipeline...
INFO:    [12/05/2025 17:33:22] -> Preprocessing Run #4 of 6...
INFO:    [12/05/2025 17:33:22] -> Initialize Scoring...
INFO:    [12/05/2025 17:33:22] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:34:03] -> Machine Learning...
INFO:    [12/05/2025 17:34:04] -> Pipeline executed in 41.7s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:34:11] -> Initializing Pipeline...
INFO:    [12/05/2025 17:34:11] -> Preprocessing Run #4 of 6...
INFO:    [12/05/2025 17:34:11] -> Initialize Scoring...
INFO:    [12/05/2025 17:34:11] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:35:15] -> Machine Learning...
INFO:    [12/05/2025 17:35:20] -> Pipeline executed in 1.15m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:35:35] -> Initialize Scoring...
INFO:    [12/05/2025 17:35:35] -> Preprocessing Run #5 of 6...
INFO:    [12/05/2025 17:35:35] -> Searching DIA with Pulsar...
INFO:    [12/05/2025 17:35:35] -> Initializing Experiment...
INFO:    [12/05/2025 17:35:35] -> Loading Spectral Libraries...
INFO:    [12/05/2025 17:35:35] -> Initialize Scoring...
INFO:    [12/05/2025 17:35:35] -> Generating Scan Map...
INFO:    [12/05/2025 17:35:35] -> Initializing Workpackages...
INFO:    [12/05/2025 17:35:35] -> Performing Basic Calibration...
INFO:    [12/05/2025 17:35:37] -> Identifying Calibration Peptides...
INFO:    [12/05/2025 17:35:37] -> Correcting Gradient Fine Structure...
INFO:    [12/05/2025 17:35:41] -> Initializing Pipeline...
INFO:    [12/05/2025 17:35:41] -> Preprocessing Run #5 of 6...
INFO:    [12/05/2025 17:35:41] -> Initialize Scoring...
INFO:    [12/05/2025 17:35:41] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:36:21] -> Machine Learning...
INFO:    [12/05/2025 17:36:22] -> Pipeline executed in 41.16s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:36:29] -> Initializing Pipeline...
INFO:    [12/05/2025 17:36:29] -> Preprocessing Run #5 of 6...
INFO:    [12/05/2025 17:36:29] -> Initialize Scoring...
INFO:    [12/05/2025 17:36:29] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:37:34] -> Machine Learning...
INFO:    [12/05/2025 17:37:38] -> Pipeline executed in 1.16m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:37:52] -> Initialize Scoring...
INFO:    [12/05/2025 17:37:52] -> Preprocessing Run #6 of 6...
INFO:    [12/05/2025 17:37:52] -> Searching DIA with Pulsar...
INFO:    [12/05/2025 17:37:52] -> Initializing Experiment...
INFO:    [12/05/2025 17:37:52] -> Loading Spectral Libraries...
INFO:    [12/05/2025 17:37:52] -> Initialize Scoring...
INFO:    [12/05/2025 17:37:52] -> Generating Scan Map...
INFO:    [12/05/2025 17:37:52] -> Initializing Workpackages...
INFO:    [12/05/2025 17:37:52] -> Performing Basic Calibration...
INFO:    [12/05/2025 17:37:53] -> Identifying Calibration Peptides...
INFO:    [12/05/2025 17:37:53] -> Correcting Gradient Fine Structure...
INFO:    [12/05/2025 17:37:58] -> Initializing Pipeline...
INFO:    [12/05/2025 17:37:58] -> Preprocessing Run #6 of 6...
INFO:    [12/05/2025 17:37:58] -> Initialize Scoring...
INFO:    [12/05/2025 17:37:58] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:38:39] -> Machine Learning...
INFO:    [12/05/2025 17:38:41] -> Pipeline executed in 42.74s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:38:47] -> Initializing Pipeline...
INFO:    [12/05/2025 17:38:47] -> Preprocessing Run #6 of 6...
INFO:    [12/05/2025 17:38:47] -> Initialize Scoring...
INFO:    [12/05/2025 17:38:47] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:39:53] -> Machine Learning...
INFO:    [12/05/2025 17:39:58] -> Pipeline executed in 1.17m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 17:40:13] -> Initialize Scoring...
INFO:    [12/05/2025 17:40:13] -> Initializing QC...
INFO:    [12/05/2025 17:40:13] -> Determining Calibration Parameter...
INFO:    [12/05/2025 17:40:14] -> Assigning ML Features...
INFO:    [12/05/2025 17:40:14] -> Generating Decoys...
INFO:    [12/05/2025 17:40:25] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:42:27] -> Releasing Raw Files...
INFO:    [12/05/2025 17:42:27] -> Machine Learning...
INFO:    [12/05/2025 17:43:35] -> Initializing HTRMS...
INFO:    [12/05/2025 17:43:35] -> Releasing Run Resources...
INFO:    [12/05/2025 17:43:36] -> Reducing Score Cache...
INFO:    [12/05/2025 17:43:42] -> Calculating Qvalues...
INFO:    [12/05/2025 17:43:43] -> Unique precursors: 125 554 of 139 010 | modified peptides: 109 610 of 119 204 | peptides: 107 375 of 116 597 |  protein groups: 11 489 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d]
INFO:    [12/05/2025 17:43:43] -> Collapsing Search Tree...
INFO:    [12/05/2025 17:43:43] -> Processed in 3.5m
INFO:    [12/05/2025 17:43:43] -> Initializing QC...
INFO:    [12/05/2025 17:43:43] -> Determining Calibration Parameter...
INFO:    [12/05/2025 17:43:44] -> Assigning ML Features...
INFO:    [12/05/2025 17:43:44] -> Generating Decoys...
INFO:    [12/05/2025 17:43:44] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:45:27] -> Releasing Raw Files...
INFO:    [12/05/2025 17:45:27] -> Machine Learning...
INFO:    [12/05/2025 17:46:36] -> Initializing HTRMS...
INFO:    [12/05/2025 17:46:36] -> Releasing Run Resources...
INFO:    [12/05/2025 17:46:37] -> Reducing Score Cache...
INFO:    [12/05/2025 17:46:44] -> Calculating Qvalues...
INFO:    [12/05/2025 17:46:45] -> Unique precursors: 126 470 of 139 010 | modified peptides: 110 460 of 119 204 | peptides: 108 198 of 116 597 |  protein groups: 11 453 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d]
INFO:    [12/05/2025 17:46:45] -> Collapsing Search Tree...
INFO:    [12/05/2025 17:46:45] -> Processed in 3.04m
INFO:    [12/05/2025 17:46:46] -> Initializing QC...
INFO:    [12/05/2025 17:46:46] -> Determining Calibration Parameter...
INFO:    [12/05/2025 17:46:46] -> Assigning ML Features...
INFO:    [12/05/2025 17:46:46] -> Generating Decoys...
INFO:    [12/05/2025 17:46:47] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:48:29] -> Releasing Raw Files...
INFO:    [12/05/2025 17:48:29] -> Machine Learning...
INFO:    [12/05/2025 17:49:36] -> Initializing HTRMS...
INFO:    [12/05/2025 17:49:36] -> Releasing Run Resources...
INFO:    [12/05/2025 17:49:37] -> Reducing Score Cache...
INFO:    [12/05/2025 17:49:43] -> Calculating Qvalues...
INFO:    [12/05/2025 17:49:44] -> Unique precursors: 123 428 of 139 010 | modified peptides: 108 440 of 119 204 | peptides: 106 247 of 116 597 |  protein groups: 11 226 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d]
INFO:    [12/05/2025 17:49:44] -> Collapsing Search Tree...
INFO:    [12/05/2025 17:49:44] -> Processed in 2.98m
INFO:    [12/05/2025 17:49:44] -> Initializing QC...
INFO:    [12/05/2025 17:49:44] -> Determining Calibration Parameter...
INFO:    [12/05/2025 17:49:45] -> Assigning ML Features...
INFO:    [12/05/2025 17:49:45] -> Generating Decoys...
INFO:    [12/05/2025 17:49:45] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:51:28] -> Releasing Raw Files...
INFO:    [12/05/2025 17:51:28] -> Machine Learning...
INFO:    [12/05/2025 17:52:29] -> Initializing HTRMS...
INFO:    [12/05/2025 17:52:29] -> Releasing Run Resources...
INFO:    [12/05/2025 17:52:30] -> Reducing Score Cache...
INFO:    [12/05/2025 17:52:37] -> Calculating Qvalues...
INFO:    [12/05/2025 17:52:38] -> Unique precursors: 124 171 of 139 010 | modified peptides: 108 891 of 119 204 | peptides: 106 645 of 116 597 |  protein groups: 11 275 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d]
INFO:    [12/05/2025 17:52:38] -> Collapsing Search Tree...
INFO:    [12/05/2025 17:52:38] -> Processed in 2.89m
INFO:    [12/05/2025 17:52:38] -> Initializing QC...
INFO:    [12/05/2025 17:52:38] -> Determining Calibration Parameter...
INFO:    [12/05/2025 17:52:38] -> Assigning ML Features...
INFO:    [12/05/2025 17:52:38] -> Generating Decoys...
INFO:    [12/05/2025 17:52:39] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:54:20] -> Releasing Raw Files...
INFO:    [12/05/2025 17:54:20] -> Machine Learning...
INFO:    [12/05/2025 17:55:27] -> Initializing HTRMS...
INFO:    [12/05/2025 17:55:28] -> Releasing Run Resources...
INFO:    [12/05/2025 17:55:28] -> Reducing Score Cache...
INFO:    [12/05/2025 17:55:35] -> Calculating Qvalues...
INFO:    [12/05/2025 17:55:36] -> Unique precursors: 125 909 of 139 010 | modified peptides: 110 059 of 119 204 | peptides: 107 773 of 116 597 |  protein groups: 11 463 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d]
INFO:    [12/05/2025 17:55:36] -> Collapsing Search Tree...
INFO:    [12/05/2025 17:55:36] -> Processed in 2.97m
INFO:    [12/05/2025 17:55:36] -> Initializing QC...
INFO:    [12/05/2025 17:55:36] -> Determining Calibration Parameter...
INFO:    [12/05/2025 17:55:36] -> Assigning ML Features...
INFO:    [12/05/2025 17:55:36] -> Generating Decoys...
INFO:    [12/05/2025 17:55:37] -> Extracting Ion Currents...
INFO:    [12/05/2025 17:57:21] -> Releasing Raw Files...
INFO:    [12/05/2025 17:57:21] -> Machine Learning...
INFO:    [12/05/2025 17:59:27] -> Initializing HTRMS...
INFO:    [12/05/2025 17:59:27] -> Releasing Run Resources...
INFO:    [12/05/2025 17:59:28] -> Reducing Score Cache...
INFO:    [12/05/2025 17:59:31] -> Calculating Qvalues...
INFO:    [12/05/2025 17:59:32] -> Unique precursors: 127 359 of 139 010 | modified peptides: 111 323 of 119 204 | peptides: 108 997 of 116 597 |  protein groups: 11 494 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d]
INFO:    [12/05/2025 17:59:32] -> Collapsing Search Tree...
INFO:    [12/05/2025 17:59:32] -> Processed in 3.94m
INFO:    [12/05/2025 17:59:33] -> Normalizing Cscores...
INFO:    [12/05/2025 17:59:33] -> Initializing Protein Groups...
INFO:    [12/05/2025 17:59:53] -> Correcting Interferences...
INFO:    [12/05/2025 18:00:18] -> Calculating Global CVs
INFO:    [12/05/2025 18:00:20] -> Calculating Precursor Quantities...
INFO:    [12/05/2025 18:00:20] -> Normalizing Quantification...
INFO:    [12/05/2025 18:00:21] -> Performing Local Normalization...
INFO:    [12/05/2025 18:00:28] -> Calculating Global CVs
INFO:    [12/05/2025 18:00:29] -> Calculating Condition CVs
INFO:    [12/05/2025 18:00:33] -> Excluding Library Duplicates...
INFO:    [12/05/2025 18:00:33] -> Calculating Global CVs
INFO:    [12/05/2025 18:00:35] -> Building Protein Groups...
INFO:    [12/05/2025 18:00:50] -> Calculating Run-Wise Protein Group FDR...
INFO:    [12/05/2025 18:00:53] -> Annotating Protein Single Hits...
INFO:    [12/05/2025 18:00:55] -> Calculating Global CVs
INFO:    [12/05/2025 18:00:56] -> Updating Identification Counts...
INFO:    [12/05/2025 18:00:58] -> Resetting existing imputation...
INFO:    [12/05/2025 18:00:58] -> Calculating Protein Quantities...
INFO:    [12/05/2025 18:00:59] -> Calculating Protein Quantities...
INFO:    [12/05/2025 18:00:59] -> Calculating MaxLFQ Protein Quantities...
INFO:    [12/05/2025 18:01:09] -> Collapsing PTM-Locations...
INFO:    [12/05/2025 18:01:09] -> PTM Stoichiometry calculation...
INFO:    [12/05/2025 18:01:09] -> Creating Protein Map...
INFO:    [12/05/2025 18:01:09] -> Compiling Run Summary Information...
INFO:    [12/05/2025 18:01:09] -> Running Post Analysis Processes...
INFO:    [12/05/2025 18:01:46] -> Saving Qc Data...
INFO:    [12/05/2025 18:01:53] -> Writing Summary Information...
INFO:    [12/05/2025 18:01:53] -> Unique precursors: 124 428 of 139 010 | modified peptides: 108 490 of 119 204 | peptides: 106 256 of 116 597 |  protein groups: 10 513 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [12/05/2025 18:01:53] -> Unique precursors: 125 384 of 139 010 | modified peptides: 109 385 of 119 204 | peptides: 107 124 of 116 597 |  protein groups: 10 515 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [12/05/2025 18:01:53] -> Unique precursors: 122 602 of 139 010 | modified peptides: 107 619 of 119 204 | peptides: 105 427 of 116 597 |  protein groups: 10 485 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [12/05/2025 18:01:53] -> Unique precursors: 123 381 of 139 010 | modified peptides: 108 110 of 119 204 | peptides: 105 865 of 116 597 |  protein groups: 10 573 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [12/05/2025 18:01:53] -> Unique precursors: 124 941 of 139 010 | modified peptides: 109 099 of 119 204 | peptides: 106 814 of 116 597 |  protein groups: 10 607 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [12/05/2025 18:01:53] -> Unique precursors: 126 299 of 139 010 | modified peptides: 110 274 of 119 204 | peptides: 107 952 of 116 597 |  protein groups: 10 570 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [12/05/2025 18:01:53] -> Unique precursors: 133 941 of 139 010 | modified peptides: 115 329 of 119 204 | peptides: 112 808 of 116 597 |  protein groups: 10 728 (Qvalue <= 0.01) for whole experiment "ttSCP_Protebench_Param_Robbe"

INFO:    [12/05/2025 18:01:53] -> Saving SNE File...
INFO:    [12/05/2025 18:01:53] -> Automatic SNE storage disabled
INFO:    [12/05/2025 18:01:53] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [12/05/2025 18:01:53] -> Pipeline executed in 3.5h - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/05/2025 09:05:47] -> Initializing Pipeline...
INFO:    [13/05/2025 09:05:47] -> Calculating Qvalues...
INFO:    [13/05/2025 09:05:47] -> Saving...
INFO:    [07/07/2025 12:01:34] -> Applying settings to loaded experiment...
INFO:    [07/07/2025 12:01:34] -> Updating the condition setup for the experiment
INFO:    [07/07/2025 12:01:34] -> Updating Quantities...
INFO:    [07/07/2025 12:01:34] -> Unifying Meta...
INFO:    [07/07/2025 12:01:34] -> Normalizing Cscores...
INFO:    [07/07/2025 12:01:34] -> Calculating Global CVs
INFO:    [07/07/2025 12:01:36] -> Calculating Profile Qvalues...
INFO:    [07/07/2025 12:01:38] -> Linking References...
INFO:    [07/07/2025 12:01:41] -> Initializing Protein Groups...
INFO:    [07/07/2025 12:01:56] -> Building Protein Groups...
INFO:    [07/07/2025 12:01:59] -> Calculating Run-Wise Protein Group FDR...
INFO:    [07/07/2025 12:02:05] -> Annotating Protein Single Hits...
INFO:    [07/07/2025 12:02:06] -> Normalizing Quantification...
INFO:    [07/07/2025 12:02:06] -> Calculating Global CVs
INFO:    [07/07/2025 12:02:07] -> Updating Identification Counts...
INFO:    [07/07/2025 12:02:09] -> Resetting existing imputation...
INFO:    [07/07/2025 12:02:09] -> Calculating Protein Quantities...
INFO:    [07/07/2025 12:02:11] -> Calculating Protein Quantities...
INFO:    [07/07/2025 12:02:11] -> Calculating MaxLFQ Protein Quantities...
INFO:    [07/07/2025 12:02:20] -> Collapsing PTM-Locations...
INFO:    [07/07/2025 12:02:20] -> PTM Stoichiometry calculation...
INFO:    [07/07/2025 12:02:20] -> Calculating Condition CVs
INFO:    [07/07/2025 12:02:23] -> Creating Protein Map...
INFO:    [07/07/2025 12:02:23] -> Compiling Run Summary Information...
INFO:    [07/07/2025 12:02:23] -> Running Post Analysis Processes...
INFO:    [07/07/2025 12:03:00] -> Writing Summary Information...
INFO:    [07/07/2025 12:03:00] -> Unique precursors: 119 200 of 139 010 | modified peptides: 105 262 of 119 204 | peptides: 103 167 of 116 597 |  protein groups: 10 424 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [07/07/2025 12:03:00] -> Unique precursors: 120 288 of 139 010 | modified peptides: 106 238 of 119 204 | peptides: 104 141 of 116 597 |  protein groups: 10 427 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [07/07/2025 12:03:00] -> Unique precursors: 118 989 of 139 010 | modified peptides: 105 196 of 119 204 | peptides: 103 100 of 116 597 |  protein groups: 10 403 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [07/07/2025 12:03:00] -> Unique precursors: 119 693 of 139 010 | modified peptides: 105 685 of 119 204 | peptides: 103 548 of 116 597 |  protein groups: 10 488 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [07/07/2025 12:03:00] -> Unique precursors: 120 157 of 139 010 | modified peptides: 106 106 of 119 204 | peptides: 103 947 of 116 597 |  protein groups: 10 517 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [07/07/2025 12:03:00] -> Unique precursors: 121 310 of 139 010 | modified peptides: 107 090 of 119 204 | peptides: 104 933 of 116 597 |  protein groups: 10 488 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [07/07/2025 12:03:00] -> Unique precursors: 124 267 of 139 010 | modified peptides: 109 518 of 119 204 | peptides: 107 272 of 116 597 |  protein groups: 10 624 (Qvalue <= 0.01) for whole experiment "ttSCP_Protebench_Param_Robbe"

INFO:    [07/07/2025 12:03:01] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [07/07/2025 12:03:01] -> Pipeline executed in 1.67m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [11/07/2025 09:34:48] -> Initializing Pipeline...
INFO:    [11/07/2025 09:34:48] -> Calculating Global CVs
INFO:    [11/07/2025 09:34:49] -> Calculating Profile Qvalues...
INFO:    [11/07/2025 09:34:51] -> Updating Quantities...
INFO:    [11/07/2025 09:35:00] -> Subtracting background noise...
INFO:    [11/07/2025 09:35:00] -> Calculating Precursor Quantities...
INFO:    [11/07/2025 09:35:00] -> Normalizing Quantification...
INFO:    [11/07/2025 09:35:02] -> Performing Local Normalization...
INFO:    [11/07/2025 09:35:04] -> Resetting existing imputation...
INFO:    [11/07/2025 09:35:04] -> Calculating Run-Wise Protein Group FDR...
INFO:    [11/07/2025 09:35:12] -> Calculating Protein Quantities...
INFO:    [11/07/2025 09:35:14] -> Calculating Protein Quantities...
INFO:    [11/07/2025 09:35:14] -> Calculating MaxLFQ Protein Quantities...
INFO:    [11/07/2025 09:35:22] -> Collapsing PTM-Locations...
INFO:    [11/07/2025 09:35:22] -> PTM Stoichiometry calculation...
INFO:    [11/07/2025 09:35:22] -> Annotating Protein Single Hits...
INFO:    [11/07/2025 09:35:23] -> Calculating Global CVs
INFO:    [11/07/2025 09:35:24] -> Updating Identification Counts...
INFO:    [11/07/2025 09:35:27] -> Calculating Condition CVs
INFO:    [11/07/2025 09:35:30] -> Creating Protein Map...
INFO:    [11/07/2025 09:35:30] -> Running Post Analysis Processes...
INFO:    [11/07/2025 09:36:06] -> Writing Summary Information...
INFO:    [11/07/2025 09:36:06] -> Unique precursors: 119 139 of 139 010 | modified peptides: 105 204 of 119 204 | peptides: 103 109 of 116 597 |  protein groups: 10 385 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [11/07/2025 09:36:06] -> Unique precursors: 120 217 of 139 010 | modified peptides: 106 168 of 119 204 | peptides: 104 071 of 116 597 |  protein groups: 10 386 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [11/07/2025 09:36:06] -> Unique precursors: 118 910 of 139 010 | modified peptides: 105 119 of 119 204 | peptides: 103 023 of 116 597 |  protein groups: 10 347 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [11/07/2025 09:36:06] -> Unique precursors: 119 625 of 139 010 | modified peptides: 105 617 of 119 204 | peptides: 103 480 of 116 597 |  protein groups: 10 438 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [11/07/2025 09:36:06] -> Unique precursors: 120 073 of 139 010 | modified peptides: 106 022 of 119 204 | peptides: 103 863 of 116 597 |  protein groups: 10 451 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [11/07/2025 09:36:06] -> Unique precursors: 121 266 of 139 010 | modified peptides: 107 047 of 119 204 | peptides: 104 890 of 116 597 |  protein groups: 10 457 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [11/07/2025 09:36:06] -> Unique precursors: 124 267 of 139 010 | modified peptides: 109 518 of 119 204 | peptides: 107 272 of 116 597 |  protein groups: 10 624 (Qvalue <= 0.01) for whole experiment "ttSCP_Protebench_Param_Robbe"

INFO:    [11/07/2025 09:36:07] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [11/07/2025 09:36:07] -> Pipeline executed in 1.33m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [11/07/2025 09:41:41] -> Initializing Pipeline...
INFO:    [11/07/2025 09:41:41] -> Calculating Qvalues...
INFO:    [11/07/2025 09:41:42] -> Saving...
INFO:    [11/07/2025 09:41:55] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [11/07/2025 09:41:55] -> Pipeline executed in 14.04s - Current Experiment had 0 Warnings and 0 Errors.
[END-LOG]
