Spectronaut 19.5.241126.62635
Computer Name: HALBARAD
User Domain Name: SPECTROMASSE
User Name: mouton
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 14-March-2025 10:51:23 UTC+0


[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 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
   │  ├─ Exclude Single Hit Proteins:	False
   │  ├─ 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
   │  ├─ 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
   │  └─ 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
   │  │     └─ Multi Channel Qvalue Filter:	Group Qvalue
   │  ├─ Quantification window:	Synchronized
   │  ├─ Interference Correction:	True
   │  │  ├─ Only Identified Peptides:	True
   │  │  ├─ Exclude All Multi-Channel Interferences:	True
   │  │  ├─ MS1 Min:	2
   │  │  └─ MS2 Min:	3
   │  ├─ Major (Protein) Grouping:	by Protein Group Id
   │  ├─ Minor (Peptide) Grouping:	by Stripped Sequence
   │  ├─ Major Group Quantity:	Mean peptide quantity
   │  ├─ Major Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Minor Group Quantity:	Mean precursor quantity
   │  ├─ Minor Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ DeepQuant Correction [Beta]:	False
   │  └─ Minimum Log2 Precursor Quantity:	0
   ├─ 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)
   │  │  └─ RT Sampling Reduction:	1
   │  └─ PTM Localization Filter:	False
   ├─ Pulsar Search\Labeling
   │  └─ Channels:	
   │     ├─ Channel 1:	False
   │     ├─ Channel 2:	False
   │     ├─ Channel 3:	False
   │     ├─ Channel 4:	False
   │     └─ Channel 5:	False
   ├─ Pulsar Search\Modifications
   │  ├─ Max Variable Modifications:	5
   │  └─ Select Modifications:	
   │     ├─ Fixed Modifications::	Carbamidomethyl (C)
   │     └─ Variable Modifications: :	Acetyl (Protein N-term), Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin/P
   │  ├─ Digest Type:	Specific
   │  ├─ 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: "\\tol-brandir\masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 1
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 09-January-2025 15:59:50 UTC+0
   │     ├─ Date Modified: 14-January-2025 17:51:28 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
   ├─ Path: "\\tol-brandir\masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 2
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 09-January-2025 15:59:50 UTC+0
   │     ├─ Date Modified: 14-January-2025 17:51:28 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
   ├─ Path: "\\tol-brandir\masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d\analysis.tdf"
   ├─ Condition: A
   ├─ Replicate: 3
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 09-January-2025 15:59:50 UTC+0
   │     ├─ Date Modified: 14-January-2025 17:51:28 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
   ├─ Path: "\\tol-brandir\masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 1
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 09-January-2025 15:59:50 UTC+0
   │     ├─ Date Modified: 14-January-2025 17:51:28 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
   ├─ Path: "\\tol-brandir\masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 2
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 09-January-2025 15:59:50 UTC+0
   │     ├─ Date Modified: 14-January-2025 17:51:28 UTC+0
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [400 - 425] - IM: 0.74
      ├─ [425 - 450] - IM: 0.75
      ├─ [450 - 475] - IM: 0.76
      ├─ [475 - 500] - IM: 0.77
      ├─ [500 - 525] - IM: 0.78
      ├─ [525 - 550] - IM: 0.79
      ├─ [550 - 575] - IM: 0.81
      ├─ [575 - 600] - IM: 0.82
      ├─ [600 - 625] - IM: 0.92
      ├─ [625 - 650] - IM: 0.94
      ├─ [650 - 675] - IM: 0.97
      ├─ [675 - 700] - IM: 0.99
      ├─ [700 - 725] - IM: 1.01
      ├─ [725 - 750] - IM: 1.03
      ├─ [750 - 775] - IM: 1.06
      ├─ [775 - 800] - IM: 1.08
      ├─ [800 - 825] - IM: 1.19
      ├─ [825 - 850] - IM: 1.21
      ├─ [850 - 875] - IM: 1.22
      ├─ [875 - 900] - IM: 1.23
      ├─ [900 - 925] - IM: 1.24
      ├─ [925 - 950] - IM: 1.25
      ├─ [950 - 975] - IM: 1.27
      └─ [975 - 1000] - IM: 1.28

Run: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
   ├─ Vendor: Bruker
   ├─ File: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
   ├─ Path: "\\tol-brandir\masse\Data timsTOF SCP\Karima Chaoui\ProteoBench_GhentSamples_diaPASEF\NewSamples_jan2025\25ng_injRep\ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d\analysis.tdf"
   ├─ Condition: B
   ├─ Replicate: 3
   ├─ HTRMS Version: 19.5.241126.62635
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_DDAQuantification
   │     ├─ Protein Entries: 31 889
   │     ├─ Original File: ProteoBenchFASTA_DDAQuantification.fasta
   │     ├─ Date Created: 09-January-2025 15:59:50 UTC+0
   │     ├─ Date Modified: 14-January-2025 17:51:28 UTC+0
   │     └─ 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:    [13/03/2025 10:06:12] -> Initializing Pipeline...
INFO:    [13/03/2025 10:06:12] -> Loading...
INFO:    [14/01/2025 10:30:41] -> Initializing Pipeline...
INFO:    [14/01/2025 10:30:41] -> Preprocessing Run #1 of 6...
INFO:    [14/01/2025 10:30:41] -> Searching DIA with Pulsar...
INFO:    [14/01/2025 10:30:43] -> Initialize Pipeline...
INFO:    [14/01/2025 10:30:44] -> Initialize Pipeline
INFO:    [14/01/2025 10:31:13] -> Initialize Pipeline...
INFO:    [14/01/2025 10:31:13] -> Creating Experiment Environment
INFO:    [14/01/2025 10:31:13] -> SuperRun 1/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d)
INFO:    [14/01/2025 10:31:13] -> Run 1/6: Organizing Data from Run
INFO:    [14/01/2025 10:31:13] -> Run 1/6: Creating Calibration Search Space...
INFO:    [14/01/2025 10:31:15] -> Collecting Search Space Parameters...
INFO:    [14/01/2025 10:31:19] -> Creating the Search Space...
INFO:    [14/01/2025 10:31:20] -> Run 1/6: Creating Search Space...
INFO:    [14/01/2025 10:31:20] -> Collecting Search Space Parameters...
INFO:    [14/01/2025 10:31:39] -> Creating the Search Space...
INFO:    [14/01/2025 10:31:40] -> Size of search space [MB]: 0
INFO:    [14/01/2025 10:31:40] -> Number of IMPGs in search space: 0
INFO:    [14/01/2025 10:31:40] -> Run 1/6: MS2 Index Generation
INFO:    [14/01/2025 10:32:55] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [14/01/2025 10:33:00] -> Initializing...
INFO:    [14/01/2025 10:38:05] -> Finalizing HTRMS File...
INFO:    [14/01/2025 10:41:20] -> Processed in 8.3m
INFO:    [14/01/2025 10:41:23] -> Done
INFO:    [14/01/2025 10:41:23] -> Run 1/6: Process Raw File...
INFO:    [14/01/2025 10:41:58] -> Run 1/6: Preparing Partitions...
INFO:    [14/01/2025 10:41:58] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [14/01/2025 10:41:59] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [14/01/2025 10:42:16] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [14/01/2025 10:42:35] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3100 [19.2s]
INFO:    [14/01/2025 10:42:40] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [14/01/2025 10:42:41] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [14/01/2025 10:47:10] -> Extracting 317804 MS1 XICs
INFO:    [14/01/2025 10:50:59] -> Run 1/6: Cleaning Up Run..
INFO:    [14/01/2025 10:51:00] -> SuperRun 2/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d)
INFO:    [14/01/2025 10:51:00] -> Run 2/6: Organizing Data from Run
INFO:    [14/01/2025 10:51:00] -> Run 2/6: Creating Calibration Search Space...
INFO:    [14/01/2025 10:51:00] -> Run 2/6: Creating Search Space...
INFO:    [14/01/2025 10:51:00] -> Size of search space [MB]: 0
INFO:    [14/01/2025 10:51:00] -> Number of IMPGs in search space: 0
INFO:    [14/01/2025 10:51:00] -> Run 2/6: MS2 Index Generation
INFO:    [14/01/2025 10:51:02] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [14/01/2025 10:51:08] -> Initializing...
INFO:    [14/01/2025 10:56:00] -> Finalizing HTRMS File...
INFO:    [14/01/2025 10:59:34] -> Processed in 8.4m
INFO:    [14/01/2025 10:59:36] -> Done
INFO:    [14/01/2025 10:59:36] -> Run 2/6: Process Raw File...
INFO:    [14/01/2025 11:00:07] -> Run 2/6: Preparing Partitions...
INFO:    [14/01/2025 11:00:07] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [14/01/2025 11:00:08] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [14/01/2025 11:00:24] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [14/01/2025 11:00:45] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2980 [20.7s]
INFO:    [14/01/2025 11:00:49] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [14/01/2025 11:00:51] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [14/01/2025 11:05:17] -> Extracting 320692 MS1 XICs
INFO:    [14/01/2025 11:09:26] -> Run 2/6: Cleaning Up Run..
INFO:    [14/01/2025 11:09:28] -> SuperRun 3/6: Initializing (ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d)
INFO:    [14/01/2025 11:09:28] -> Run 3/6: Organizing Data from Run
INFO:    [14/01/2025 11:09:28] -> Run 3/6: Creating Calibration Search Space...
INFO:    [14/01/2025 11:09:28] -> Run 3/6: Creating Search Space...
INFO:    [14/01/2025 11:09:28] -> Size of search space [MB]: 0
INFO:    [14/01/2025 11:09:28] -> Number of IMPGs in search space: 0
INFO:    [14/01/2025 11:09:28] -> Run 3/6: MS2 Index Generation
INFO:    [14/01/2025 11:09:29] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [14/01/2025 11:09:36] -> Initializing...
INFO:    [14/01/2025 11:14:27] -> Finalizing HTRMS File...
INFO:    [14/01/2025 11:17:22] -> Processed in 7.8m
INFO:    [14/01/2025 11:17:24] -> Done
INFO:    [14/01/2025 11:17:24] -> Run 3/6: Process Raw File...
INFO:    [14/01/2025 11:17:57] -> Run 3/6: Preparing Partitions...
INFO:    [14/01/2025 11:17:57] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [14/01/2025 11:17:59] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [14/01/2025 11:18:16] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [14/01/2025 11:18:36] -> The number of PSMs identified during calibration with FDR <= 0.01 is 2942 [19.7s]
INFO:    [14/01/2025 11:18:40] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [14/01/2025 11:18:41] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [14/01/2025 11:23:11] -> Extracting 320968 MS1 XICs
INFO:    [14/01/2025 11:27:16] -> Run 3/6: Cleaning Up Run..
INFO:    [14/01/2025 11:27:18] -> SuperRun 4/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d)
INFO:    [14/01/2025 11:27:18] -> Run 4/6: Organizing Data from Run
INFO:    [14/01/2025 11:27:18] -> Run 4/6: Creating Calibration Search Space...
INFO:    [14/01/2025 11:27:18] -> Run 4/6: Creating Search Space...
INFO:    [14/01/2025 11:27:18] -> Size of search space [MB]: 0
INFO:    [14/01/2025 11:27:18] -> Number of IMPGs in search space: 0
INFO:    [14/01/2025 11:27:18] -> Run 4/6: MS2 Index Generation
INFO:    [14/01/2025 11:27:20] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [14/01/2025 11:27:24] -> Initializing...
INFO:    [14/01/2025 11:33:10] -> Finalizing HTRMS File...
INFO:    [14/01/2025 11:36:48] -> Processed in 9.4m
INFO:    [14/01/2025 11:36:51] -> Done
INFO:    [14/01/2025 11:36:51] -> Run 4/6: Process Raw File...
INFO:    [14/01/2025 11:37:23] -> Run 4/6: Preparing Partitions...
INFO:    [14/01/2025 11:37:23] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [14/01/2025 11:37:24] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [14/01/2025 11:37:42] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [14/01/2025 11:38:06] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3193 [23.9s]
INFO:    [14/01/2025 11:38:11] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [14/01/2025 11:38:12] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [14/01/2025 11:43:06] -> Extracting 312942 MS1 XICs
INFO:    [14/01/2025 11:46:41] -> Run 4/6: Cleaning Up Run..
INFO:    [14/01/2025 11:46:43] -> SuperRun 5/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d)
INFO:    [14/01/2025 11:46:43] -> Run 5/6: Organizing Data from Run
INFO:    [14/01/2025 11:46:43] -> Run 5/6: Creating Calibration Search Space...
INFO:    [14/01/2025 11:46:43] -> Run 5/6: Creating Search Space...
INFO:    [14/01/2025 11:46:43] -> Size of search space [MB]: 0
INFO:    [14/01/2025 11:46:43] -> Number of IMPGs in search space: 0
INFO:    [14/01/2025 11:46:43] -> Run 5/6: MS2 Index Generation
INFO:    [14/01/2025 11:46:44] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [14/01/2025 11:46:52] -> Initializing...
INFO:    [14/01/2025 11:51:22] -> Finalizing HTRMS File...
INFO:    [14/01/2025 11:54:07] -> Processed in 7.2m
INFO:    [14/01/2025 11:54:10] -> Done
INFO:    [14/01/2025 11:54:10] -> Run 5/6: Process Raw File...
INFO:    [14/01/2025 11:54:40] -> Run 5/6: Preparing Partitions...
INFO:    [14/01/2025 11:54:40] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [14/01/2025 11:54:42] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [14/01/2025 11:54:57] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [14/01/2025 11:55:15] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3311 [17.8s]
INFO:    [14/01/2025 11:55:20] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [14/01/2025 11:55:21] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [14/01/2025 11:59:51] -> Extracting 309811 MS1 XICs
INFO:    [14/01/2025 12:03:12] -> Run 5/6: Cleaning Up Run..
INFO:    [14/01/2025 12:03:15] -> SuperRun 6/6: Initializing (ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d)
INFO:    [14/01/2025 12:03:15] -> Run 6/6: Organizing Data from Run
INFO:    [14/01/2025 12:03:15] -> Run 6/6: Creating Calibration Search Space...
INFO:    [14/01/2025 12:03:15] -> Run 6/6: Creating Search Space...
INFO:    [14/01/2025 12:03:15] -> Size of search space [MB]: 0
INFO:    [14/01/2025 12:03:15] -> Number of IMPGs in search space: 0
INFO:    [14/01/2025 12:03:15] -> Run 6/6: MS2 Index Generation
INFO:    [14/01/2025 12:03:16] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [14/01/2025 12:03:22] -> Initializing...
INFO:    [14/01/2025 12:08:04] -> Finalizing HTRMS File...
INFO:    [14/01/2025 12:10:49] -> Processed in 7.4m
INFO:    [14/01/2025 12:10:55] -> Done
INFO:    [14/01/2025 12:10:55] -> Run 6/6: Process Raw File...
INFO:    [14/01/2025 12:11:24] -> Run 6/6: Preparing Partitions...
INFO:    [14/01/2025 12:11:24] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [14/01/2025 12:11:26] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [14/01/2025 12:11:42] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [14/01/2025 12:12:01] -> The number of PSMs identified during calibration with FDR <= 0.01 is 3224 [18.6s]
INFO:    [14/01/2025 12:12:06] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [14/01/2025 12:12:07] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [14/01/2025 12:16:40] -> Extracting 313121 MS1 XICs
INFO:    [14/01/2025 12:20:06] -> Run 6/6: Cleaning Up Run..
INFO:    [14/01/2025 12:20:18] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [14/01/2025 12:20:19] -> Score Post-Processing
INFO:    [14/01/2025 12:22:26] -> Score Post-Processing: 2.11m
INFO:    [14/01/2025 12:22:26] -> PSM FDR...
INFO:    [14/01/2025 12:23:05] -> PSM FDR: 38.7s
INFO:    [14/01/2025 12:23:05] -> Converting to non-redundant data structure...
INFO:    [14/01/2025 12:23:28] -> Performing Peptide FDR...
INFO:    [14/01/2025 12:23:34] -> Performing Protein Inference...
INFO:    [14/01/2025 12:23:37] -> Performing Protein FDR...
INFO:    [14/01/2025 12:23:38] -> Calculating Result Values at Run and Experiment Level...
INFO:    [14/01/2025 12:23:55] -> Pulsar identified 344152 PSMs, 72061 stripped sequences, 81510 peptide precursors, 9008 protein groups.
INFO:    [14/01/2025 12:23:55] -> Calculating Summary...
INFO:    [14/01/2025 12:24:00] -> Identifying Calibration Peptides...
INFO:    [14/01/2025 12:24:01] -> iRT Calibration...
INFO:    [14/01/2025 12:24:06] -> Performing directDIA+ search...
INFO:    [14/01/2025 12:25:03] -> Generating directDIA+ search space
INFO:    [14/01/2025 12:27:50] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
INFO:    [14/01/2025 12:40:00] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
INFO:    [14/01/2025 12:50:08] -> directDIA+ search: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
INFO:    [14/01/2025 13:11:11] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
INFO:    [14/01/2025 13:39:24] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
INFO:    [14/01/2025 14:08:41] -> directDIA+ search: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
INFO:    [14/01/2025 14:52:25] -> Performing directDIA+ Post Processing...
INFO:    [14/01/2025 14:52:52] -> Writing experiment store..
INFO:    [14/01/2025 14:53:12] -> Assigning iRT Source...
INFO:    [14/01/2025 14:53:12] -> Calculating iRT...
INFO:    [14/01/2025 14:53:13] -> Cleaning Up Experiment...
INFO:    [14/01/2025 14:53:13] -> Summarizing Identifications
INFO:    [14/01/2025 14:57:23] -> Identifiying Significant Precursors...
INFO:    [14/01/2025 14:58:01] -> Predicting Ion Mobility
INFO:    [14/01/2025 14:58:23] -> Calculating Median iRT
INFO:    [14/01/2025 14:58:28] -> Building BGS Protein Grouping...
INFO:    [14/01/2025 14:58:30] -> Digesting Fasta...
INFO:    [14/01/2025 14:58:31] -> Annotating Proteins...
INFO:    [14/01/2025 14:58:32] -> Grouping Proteins...
INFO:    [14/01/2025 14:58:38] -> Calculating Run Summary Statistics...
INFO:    [14/01/2025 14:59:58] -> Building Consensus Fragment Spectra...
INFO:    [14/01/2025 15:02:37] -> Selecting best fragment ions
INFO:    [14/01/2025 15:11:36] -> Initializing Experiment...
INFO:    [14/01/2025 15:11:36] -> Loading Spectral Libraries...
INFO:    [14/01/2025 15:13:59] -> Initialize Scoring...
INFO:    [14/01/2025 15:13:59] -> Generating Scan Map...
INFO:    [14/01/2025 15:13:59] -> Initializing Workpackages...
INFO:    [14/01/2025 15:13:59] -> Performing Basic Calibration...
INFO:    [14/01/2025 15:14:03] -> Identifying Calibration Peptides...
INFO:    [14/01/2025 15:14:03] -> Correcting Gradient Fine Structure...
INFO:    [14/01/2025 15:14:14] -> Initializing Pipeline...
INFO:    [14/01/2025 15:14:14] -> Preprocessing Run #1 of 6...
INFO:    [14/01/2025 15:14:14] -> Initialize Scoring...
ERROR:   [14/01/2025 15:14:35] -> Error during peak detection: Object reference not set to an instance of an object.
INFO:    [14/01/2025 15:14:35] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:16:43] -> Machine Learning...
INFO:    [14/01/2025 15:16:45] -> Pipeline executed in 2.53m - Current Experiment had 0 Warnings and 1 Errors.
INFO:    [14/01/2025 15:16:56] -> Initializing Pipeline...
INFO:    [14/01/2025 15:16:56] -> Preprocessing Run #1 of 6...
INFO:    [14/01/2025 15:16:56] -> Initialize Scoring...
INFO:    [14/01/2025 15:16:56] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:19:28] -> Machine Learning...
INFO:    [14/01/2025 15:19:38] -> Pipeline executed in 2.7m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:20:02] -> Initialize Scoring...
INFO:    [14/01/2025 15:20:02] -> Preprocessing Run #2 of 6...
INFO:    [14/01/2025 15:20:02] -> Searching DIA with Pulsar...
INFO:    [14/01/2025 15:20:02] -> Initializing Experiment...
INFO:    [14/01/2025 15:20:02] -> Loading Spectral Libraries...
INFO:    [14/01/2025 15:20:02] -> Initialize Scoring...
INFO:    [14/01/2025 15:20:02] -> Generating Scan Map...
INFO:    [14/01/2025 15:20:02] -> Initializing Workpackages...
INFO:    [14/01/2025 15:20:02] -> Performing Basic Calibration...
INFO:    [14/01/2025 15:20:05] -> Identifying Calibration Peptides...
INFO:    [14/01/2025 15:20:05] -> Correcting Gradient Fine Structure...
INFO:    [14/01/2025 15:20:11] -> Initializing Pipeline...
INFO:    [14/01/2025 15:20:11] -> Preprocessing Run #2 of 6...
INFO:    [14/01/2025 15:20:11] -> Initialize Scoring...
INFO:    [14/01/2025 15:20:11] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:21:53] -> Machine Learning...
INFO:    [14/01/2025 15:21:55] -> Pipeline executed in 1.73m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:22:10] -> Initializing Pipeline...
INFO:    [14/01/2025 15:22:10] -> Preprocessing Run #2 of 6...
INFO:    [14/01/2025 15:22:10] -> Initialize Scoring...
INFO:    [14/01/2025 15:22:10] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:24:58] -> Machine Learning...
INFO:    [14/01/2025 15:25:07] -> Pipeline executed in 2.94m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:25:31] -> Initialize Scoring...
INFO:    [14/01/2025 15:25:31] -> Preprocessing Run #3 of 6...
INFO:    [14/01/2025 15:25:31] -> Searching DIA with Pulsar...
INFO:    [14/01/2025 15:25:31] -> Initializing Experiment...
INFO:    [14/01/2025 15:25:31] -> Loading Spectral Libraries...
INFO:    [14/01/2025 15:25:31] -> Initialize Scoring...
INFO:    [14/01/2025 15:25:31] -> Generating Scan Map...
INFO:    [14/01/2025 15:25:31] -> Initializing Workpackages...
INFO:    [14/01/2025 15:25:31] -> Performing Basic Calibration...
INFO:    [14/01/2025 15:25:35] -> Identifying Calibration Peptides...
INFO:    [14/01/2025 15:25:35] -> Correcting Gradient Fine Structure...
INFO:    [14/01/2025 15:25:41] -> Initializing Pipeline...
INFO:    [14/01/2025 15:25:41] -> Preprocessing Run #3 of 6...
INFO:    [14/01/2025 15:25:41] -> Initialize Scoring...
INFO:    [14/01/2025 15:25:42] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:27:58] -> Machine Learning...
INFO:    [14/01/2025 15:28:00] -> Pipeline executed in 2.31m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:28:14] -> Initializing Pipeline...
INFO:    [14/01/2025 15:28:14] -> Preprocessing Run #3 of 6...
INFO:    [14/01/2025 15:28:14] -> Initialize Scoring...
INFO:    [14/01/2025 15:28:14] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:31:17] -> Machine Learning...
INFO:    [14/01/2025 15:31:29] -> Pipeline executed in 3.25m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:32:01] -> Initialize Scoring...
INFO:    [14/01/2025 15:32:01] -> Preprocessing Run #4 of 6...
INFO:    [14/01/2025 15:32:01] -> Searching DIA with Pulsar...
INFO:    [14/01/2025 15:32:01] -> Initializing Experiment...
INFO:    [14/01/2025 15:32:01] -> Loading Spectral Libraries...
INFO:    [14/01/2025 15:32:01] -> Initialize Scoring...
INFO:    [14/01/2025 15:32:01] -> Generating Scan Map...
INFO:    [14/01/2025 15:32:01] -> Initializing Workpackages...
INFO:    [14/01/2025 15:32:01] -> Performing Basic Calibration...
INFO:    [14/01/2025 15:32:06] -> Identifying Calibration Peptides...
INFO:    [14/01/2025 15:32:06] -> Correcting Gradient Fine Structure...
INFO:    [14/01/2025 15:32:16] -> Initializing Pipeline...
INFO:    [14/01/2025 15:32:16] -> Preprocessing Run #4 of 6...
INFO:    [14/01/2025 15:32:16] -> Initialize Scoring...
INFO:    [14/01/2025 15:32:16] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:34:15] -> Machine Learning...
INFO:    [14/01/2025 15:34:17] -> Pipeline executed in 2.01m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:34:28] -> Initializing Pipeline...
INFO:    [14/01/2025 15:34:28] -> Preprocessing Run #4 of 6...
INFO:    [14/01/2025 15:34:28] -> Initialize Scoring...
INFO:    [14/01/2025 15:34:28] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:37:50] -> Machine Learning...
INFO:    [14/01/2025 15:37:58] -> Pipeline executed in 3.5m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:38:22] -> Initialize Scoring...
INFO:    [14/01/2025 15:38:22] -> Preprocessing Run #5 of 6...
INFO:    [14/01/2025 15:38:22] -> Searching DIA with Pulsar...
INFO:    [14/01/2025 15:38:22] -> Initializing Experiment...
INFO:    [14/01/2025 15:38:22] -> Loading Spectral Libraries...
INFO:    [14/01/2025 15:38:22] -> Initialize Scoring...
INFO:    [14/01/2025 15:38:22] -> Generating Scan Map...
INFO:    [14/01/2025 15:38:22] -> Initializing Workpackages...
INFO:    [14/01/2025 15:38:22] -> Performing Basic Calibration...
INFO:    [14/01/2025 15:38:25] -> Identifying Calibration Peptides...
INFO:    [14/01/2025 15:38:25] -> Correcting Gradient Fine Structure...
INFO:    [14/01/2025 15:38:33] -> Initializing Pipeline...
INFO:    [14/01/2025 15:38:33] -> Preprocessing Run #5 of 6...
INFO:    [14/01/2025 15:38:33] -> Initialize Scoring...
INFO:    [14/01/2025 15:38:33] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:40:47] -> Machine Learning...
INFO:    [14/01/2025 15:40:48] -> Pipeline executed in 2.26m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:40:56] -> Initializing Pipeline...
INFO:    [14/01/2025 15:40:56] -> Preprocessing Run #5 of 6...
INFO:    [14/01/2025 15:40:56] -> Initialize Scoring...
INFO:    [14/01/2025 15:40:56] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:43:31] -> Machine Learning...
INFO:    [14/01/2025 15:43:49] -> Pipeline executed in 2.88m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:44:12] -> Initialize Scoring...
INFO:    [14/01/2025 15:44:12] -> Preprocessing Run #6 of 6...
INFO:    [14/01/2025 15:44:12] -> Searching DIA with Pulsar...
INFO:    [14/01/2025 15:44:12] -> Initializing Experiment...
INFO:    [14/01/2025 15:44:12] -> Loading Spectral Libraries...
INFO:    [14/01/2025 15:44:12] -> Initialize Scoring...
INFO:    [14/01/2025 15:44:12] -> Generating Scan Map...
INFO:    [14/01/2025 15:44:12] -> Initializing Workpackages...
INFO:    [14/01/2025 15:44:12] -> Performing Basic Calibration...
INFO:    [14/01/2025 15:44:16] -> Identifying Calibration Peptides...
INFO:    [14/01/2025 15:44:16] -> Correcting Gradient Fine Structure...
INFO:    [14/01/2025 15:44:23] -> Initializing Pipeline...
INFO:    [14/01/2025 15:44:23] -> Preprocessing Run #6 of 6...
INFO:    [14/01/2025 15:44:23] -> Initialize Scoring...
INFO:    [14/01/2025 15:44:24] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:46:49] -> Machine Learning...
INFO:    [14/01/2025 15:46:52] -> Pipeline executed in 2.47m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:47:02] -> Initializing Pipeline...
INFO:    [14/01/2025 15:47:02] -> Preprocessing Run #6 of 6...
INFO:    [14/01/2025 15:47:02] -> Initialize Scoring...
INFO:    [14/01/2025 15:47:02] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:49:45] -> Machine Learning...
INFO:    [14/01/2025 15:49:53] -> Pipeline executed in 2.84m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [14/01/2025 15:50:19] -> Initialize Scoring...
INFO:    [14/01/2025 15:50:19] -> Initializing QC...
INFO:    [14/01/2025 15:50:19] -> Determining Calibration Parameter...
INFO:    [14/01/2025 15:50:19] -> Assigning ML Features...
INFO:    [14/01/2025 15:50:20] -> Generating Decoys...
INFO:    [14/01/2025 15:50:36] -> Extracting Ion Currents...
INFO:    [14/01/2025 15:55:22] -> Releasing Raw Files...
INFO:    [14/01/2025 15:55:22] -> Machine Learning...
INFO:    [14/01/2025 16:10:35] -> Initializing HTRMS...
INFO:    [14/01/2025 16:10:35] -> Releasing Run Resources...
INFO:    [14/01/2025 16:10:37] -> Reducing Score Cache...
INFO:    [14/01/2025 16:10:41] -> Calculating Qvalues...
INFO:    [14/01/2025 16:10:44] -> Unique precursors: 124 396 of 132 925 | modified peptides: 109 951 of 116 881 | peptides: 107 533 of 114 219 |  protein groups: 11 105 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d]
INFO:    [14/01/2025 16:10:44] -> Collapsing Search Tree...
INFO:    [14/01/2025 16:10:44] -> Processed in 20.43m
INFO:    [14/01/2025 16:10:44] -> Initializing QC...
INFO:    [14/01/2025 16:10:45] -> Determining Calibration Parameter...
INFO:    [14/01/2025 16:10:47] -> Assigning ML Features...
INFO:    [14/01/2025 16:10:47] -> Generating Decoys...
INFO:    [14/01/2025 16:10:49] -> Extracting Ion Currents...
INFO:    [14/01/2025 16:14:19] -> Releasing Raw Files...
INFO:    [14/01/2025 16:14:19] -> Machine Learning...
INFO:    [14/01/2025 16:28:36] -> Initializing HTRMS...
INFO:    [14/01/2025 16:28:36] -> Releasing Run Resources...
INFO:    [14/01/2025 16:28:37] -> Reducing Score Cache...
INFO:    [14/01/2025 16:28:43] -> Calculating Qvalues...
INFO:    [14/01/2025 16:28:44] -> Unique precursors: 125 654 of 132 925 | modified peptides: 111 054 of 116 881 | peptides: 108 676 of 114 219 |  protein groups: 11 112 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d]
INFO:    [14/01/2025 16:28:44] -> Collapsing Search Tree...
INFO:    [14/01/2025 16:28:44] -> Processed in 18m
INFO:    [14/01/2025 16:28:45] -> Initializing QC...
INFO:    [14/01/2025 16:28:45] -> Determining Calibration Parameter...
INFO:    [14/01/2025 16:28:45] -> Assigning ML Features...
INFO:    [14/01/2025 16:28:46] -> Generating Decoys...
INFO:    [14/01/2025 16:28:48] -> Extracting Ion Currents...
INFO:    [14/01/2025 16:32:52] -> Releasing Raw Files...
INFO:    [14/01/2025 16:32:52] -> Machine Learning...
INFO:    [14/01/2025 16:46:34] -> Initializing HTRMS...
INFO:    [14/01/2025 16:46:34] -> Releasing Run Resources...
INFO:    [14/01/2025 16:46:36] -> Reducing Score Cache...
INFO:    [14/01/2025 16:46:46] -> Calculating Qvalues...
INFO:    [14/01/2025 16:46:50] -> Unique precursors: 126 008 of 132 925 | modified peptides: 111 405 of 116 881 | peptides: 108 967 of 114 219 |  protein groups: 11 120 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d]
INFO:    [14/01/2025 16:46:50] -> Collapsing Search Tree...
INFO:    [14/01/2025 16:46:51] -> Processed in 18.11m
INFO:    [14/01/2025 16:46:54] -> Initializing QC...
INFO:    [14/01/2025 16:46:55] -> Determining Calibration Parameter...
INFO:    [14/01/2025 16:46:56] -> Assigning ML Features...
INFO:    [14/01/2025 16:46:56] -> Generating Decoys...
INFO:    [14/01/2025 16:46:58] -> Extracting Ion Currents...
INFO:    [14/01/2025 16:51:39] -> Releasing Raw Files...
INFO:    [14/01/2025 16:51:39] -> Machine Learning...
INFO:    [14/01/2025 17:06:25] -> Initializing HTRMS...
INFO:    [14/01/2025 17:06:25] -> Releasing Run Resources...
INFO:    [14/01/2025 17:06:26] -> Reducing Score Cache...
INFO:    [14/01/2025 17:06:31] -> Calculating Qvalues...
INFO:    [14/01/2025 17:06:39] -> Unique precursors: 127 490 of 132 925 | modified peptides: 112 576 of 116 881 | peptides: 110 077 of 114 219 |  protein groups: 11 176 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d]
INFO:    [14/01/2025 17:06:39] -> Collapsing Search Tree...
INFO:    [14/01/2025 17:06:39] -> Processed in 19.75m
INFO:    [14/01/2025 17:06:40] -> Initializing QC...
INFO:    [14/01/2025 17:06:40] -> Determining Calibration Parameter...
INFO:    [14/01/2025 17:06:40] -> Assigning ML Features...
INFO:    [14/01/2025 17:06:41] -> Generating Decoys...
INFO:    [14/01/2025 17:06:42] -> Extracting Ion Currents...
INFO:    [14/01/2025 17:11:20] -> Releasing Raw Files...
INFO:    [14/01/2025 17:11:20] -> Machine Learning...
INFO:    [14/01/2025 17:24:39] -> Initializing HTRMS...
INFO:    [14/01/2025 17:24:39] -> Releasing Run Resources...
INFO:    [14/01/2025 17:24:40] -> Reducing Score Cache...
INFO:    [14/01/2025 17:24:45] -> Calculating Qvalues...
INFO:    [14/01/2025 17:24:47] -> Unique precursors: 125 538 of 132 925 | modified peptides: 110 941 of 116 881 | peptides: 108 499 of 114 219 |  protein groups: 11 105 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d]
INFO:    [14/01/2025 17:24:47] -> Collapsing Search Tree...
INFO:    [14/01/2025 17:24:47] -> Processed in 18.12m
INFO:    [14/01/2025 17:24:47] -> Initializing QC...
INFO:    [14/01/2025 17:24:48] -> Determining Calibration Parameter...
INFO:    [14/01/2025 17:24:49] -> Assigning ML Features...
INFO:    [14/01/2025 17:24:50] -> Generating Decoys...
INFO:    [14/01/2025 17:24:53] -> Extracting Ion Currents...
INFO:    [14/01/2025 17:28:59] -> Releasing Raw Files...
INFO:    [14/01/2025 17:28:59] -> Machine Learning...
INFO:    [14/01/2025 17:45:53] -> Initializing HTRMS...
INFO:    [14/01/2025 17:45:53] -> Releasing Run Resources...
INFO:    [14/01/2025 17:45:54] -> Reducing Score Cache...
INFO:    [14/01/2025 17:45:59] -> Calculating Qvalues...
INFO:    [14/01/2025 17:46:00] -> Unique precursors: 125 974 of 132 925 | modified peptides: 111 347 of 116 881 | peptides: 108 900 of 114 219 |  protein groups: 11 112 (Qvalue <= 0.01) [ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d]
INFO:    [14/01/2025 17:46:00] -> Collapsing Search Tree...
INFO:    [14/01/2025 17:46:00] -> Processed in 21.22m
INFO:    [14/01/2025 17:46:02] -> Normalizing Cscores...
INFO:    [14/01/2025 17:46:03] -> Initializing Protein Groups...
INFO:    [14/01/2025 17:47:47] -> Correcting Interferences...
INFO:    [14/01/2025 17:48:49] -> Calculating Global CVs
INFO:    [14/01/2025 17:48:51] -> Calculating Precursor Quantities...
INFO:    [14/01/2025 17:48:51] -> Normalizing Quantification...
INFO:    [14/01/2025 17:48:55] -> Performing Local Normalization...
INFO:    [14/01/2025 17:49:08] -> Calculating Global CVs
INFO:    [14/01/2025 17:49:10] -> Calculating Condition CVs
INFO:    [14/01/2025 17:49:18] -> Excluding Library Duplicates...
INFO:    [14/01/2025 17:49:19] -> Calculating Global CVs
INFO:    [14/01/2025 17:49:21] -> Building Protein Groups...
INFO:    [14/01/2025 17:49:47] -> Calculating Run-Wise Protein Group FDR...
INFO:    [14/01/2025 17:49:52] -> Annotating Protein Single Hits...
INFO:    [14/01/2025 17:49:53] -> Calculating Global CVs
INFO:    [14/01/2025 17:49:55] -> Updating Identification Counts...
INFO:    [14/01/2025 17:49:58] -> Resetting existing imputation...
INFO:    [14/01/2025 17:49:58] -> Calculating Protein Quantities...
INFO:    [14/01/2025 17:50:01] -> Calculating Protein Quantities...
INFO:    [14/01/2025 17:50:01] -> Calculating MaxLFQ Protein Quantities...
INFO:    [14/01/2025 17:50:15] -> Collapsing PTM-Locations...
INFO:    [14/01/2025 17:50:16] -> PTM Stoichiometry calculation...
INFO:    [14/01/2025 17:50:16] -> Creating Protein Map...
INFO:    [14/01/2025 17:50:16] -> Compiling Run Summary Information...
INFO:    [14/01/2025 17:50:17] -> Running Post Analysis Processes...
INFO:    [14/01/2025 17:51:15] -> Saving Qc Data...
INFO:    [14/01/2025 17:51:27] -> Writing Summary Information...
INFO:    [14/01/2025 17:51:27] -> Unique precursors: 123 931 of 132 925 | modified peptides: 109 491 of 116 881 | peptides: 107 073 of 114 219 |  protein groups: 10 697 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [14/01/2025 17:51:27] -> Unique precursors: 125 160 of 132 925 | modified peptides: 110 567 of 116 881 | peptides: 108 189 of 114 219 |  protein groups: 10 689 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [14/01/2025 17:51:27] -> Unique precursors: 125 476 of 132 925 | modified peptides: 110 878 of 116 881 | peptides: 108 440 of 114 219 |  protein groups: 10 675 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [14/01/2025 17:51:27] -> Unique precursors: 126 992 of 132 925 | modified peptides: 112 082 of 116 881 | peptides: 109 583 of 114 219 |  protein groups: 10 742 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [14/01/2025 17:51:27] -> Unique precursors: 125 111 of 132 925 | modified peptides: 110 518 of 116 881 | peptides: 108 076 of 114 219 |  protein groups: 10 739 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [14/01/2025 17:51:27] -> Unique precursors: 125 535 of 132 925 | modified peptides: 110 913 of 116 881 | peptides: 108 466 of 114 219 |  protein groups: 10 730 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [14/01/2025 17:51:27] -> Unique precursors: 131 920 of 132 925 | modified peptides: 116 040 of 116 881 | peptides: 113 395 of 114 219 |  protein groups: 10 857 (Qvalue <= 0.01) for whole experiment "proteobench-diaPASEF-KAC_condA_B-Alpha-3rep"

INFO:    [14/01/2025 17:51:27] -> Saving SNE File...
INFO:    [14/01/2025 17:51:27] -> Storing SNE File: D:\Utilisateurs\Emma\spectronaut results\automatic SNE storage\20250114_103040_proteobench-diaPASEF-KAC_condA_B-Alpha-3rep.sne
INFO:    [14/01/2025 17:51:27] -> Initializing Pipeline...
INFO:    [14/01/2025 17:51:27] -> Calculating Qvalues...
INFO:    [14/01/2025 17:51:28] -> Saving...
INFO:    [13/03/2025 10:06:30] -> Applying settings to loaded experiment...
INFO:    [13/03/2025 10:06:30] -> Updating the condition setup for the experiment
INFO:    [13/03/2025 10:06:31] -> Updating Quantities...
INFO:    [13/03/2025 10:06:31] -> Unifying Meta...
INFO:    [13/03/2025 10:06:31] -> Normalizing Cscores...
INFO:    [13/03/2025 10:06:32] -> Calculating Global CVs
INFO:    [13/03/2025 10:06:33] -> Linking References...
INFO:    [13/03/2025 10:06:35] -> Initializing Protein Groups...
INFO:    [13/03/2025 10:06:46] -> Building Protein Groups...
INFO:    [13/03/2025 10:06:48] -> Calculating Run-Wise Protein Group FDR...
INFO:    [13/03/2025 10:06:52] -> Annotating Protein Single Hits...
INFO:    [13/03/2025 10:06:53] -> Normalizing Quantification...
INFO:    [13/03/2025 10:06:54] -> Calculating Global CVs
INFO:    [13/03/2025 10:06:55] -> Updating Identification Counts...
INFO:    [13/03/2025 10:06:59] -> Resetting existing imputation...
INFO:    [13/03/2025 10:06:59] -> Calculating Protein Quantities...
INFO:    [13/03/2025 10:07:00] -> Calculating Protein Quantities...
INFO:    [13/03/2025 10:07:00] -> Calculating MaxLFQ Protein Quantities...
INFO:    [13/03/2025 10:07:09] -> Collapsing PTM-Locations...
INFO:    [13/03/2025 10:07:09] -> PTM Stoichiometry calculation...
INFO:    [13/03/2025 10:07:09] -> Calculating Condition CVs
INFO:    [13/03/2025 10:07:12] -> Creating Protein Map...
INFO:    [13/03/2025 10:07:12] -> Compiling Run Summary Information...
INFO:    [13/03/2025 10:07:12] -> Running Post Analysis Processes...
INFO:    [13/03/2025 10:07:50] -> Writing Summary Information...
INFO:    [13/03/2025 10:07:50] -> Unique precursors: 123 931 of 132 925 | modified peptides: 109 491 of 116 881 | peptides: 107 073 of 114 219 |  protein groups: 10 697 (Qvalue <= 0.01) for run #1 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d"
INFO:    [13/03/2025 10:07:50] -> Unique precursors: 125 160 of 132 925 | modified peptides: 110 567 of 116 881 | peptides: 108 189 of 114 219 |  protein groups: 10 689 (Qvalue <= 0.01) for run #2 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d"
INFO:    [13/03/2025 10:07:50] -> Unique precursors: 125 476 of 132 925 | modified peptides: 110 878 of 116 881 | peptides: 108 440 of 114 219 |  protein groups: 10 675 (Qvalue <= 0.01) for run #3 "ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d"
INFO:    [13/03/2025 10:07:50] -> Unique precursors: 126 992 of 132 925 | modified peptides: 112 082 of 116 881 | peptides: 109 583 of 114 219 |  protein groups: 10 742 (Qvalue <= 0.01) for run #4 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d"
INFO:    [13/03/2025 10:07:50] -> Unique precursors: 125 111 of 132 925 | modified peptides: 110 518 of 116 881 | peptides: 108 076 of 114 219 |  protein groups: 10 739 (Qvalue <= 0.01) for run #5 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d"
INFO:    [13/03/2025 10:07:50] -> Unique precursors: 125 535 of 132 925 | modified peptides: 110 913 of 116 881 | peptides: 108 466 of 114 219 |  protein groups: 10 730 (Qvalue <= 0.01) for run #6 "ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d"
INFO:    [13/03/2025 10:07:50] -> Unique precursors: 131 920 of 132 925 | modified peptides: 116 040 of 116 881 | peptides: 113 395 of 114 219 |  protein groups: 10 857 (Qvalue <= 0.01) for whole experiment "proteobench-diaPASEF-KAC_condA_B-Alpha-3rep"

INFO:    [13/03/2025 10:07:50] -> Current Experiment had 0 Warnings and 1 Errors.
INFO:    [13/03/2025 10:07:50] -> Pipeline executed in 1.64m - Current Experiment had 0 Warnings and 1 Errors.
[END-LOG]
