Spectronaut 17.3.230224.55965 Computer Name: NBM-DPT-E0051 User Domain Name: DYC User Name: joaquin.fernandez Analysis Mode: UI Analysis Type: directDIA Analysis Date: 17-March-2023 13:56:35 +01:00 [BEGIN-SETTINGS] Settings Used: NB settings no-norm ├─ 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 │ ├─ Generate SNE File: True │ │ └─ Store Ion traces in SNE: True │ ├─ Post Analysis Reports: │ │ ├─ CV Density Line Chart: True │ │ ├─ CVs Below X Bar Chart: True │ │ ├─ Data Completeness Bar Chart: True │ │ ├─ Run Identifications Bar Chart: True │ │ └─ Scoring Histograms: True │ ├─ PTM Report Schema: │ ├─ Report Schema: MSStats Report (v 3.7.3) (Normal), Peptide Quant (Normal), Peptide Quant (Pivot), Peptide_QC (Normal), Prot Quant Proteomics (Normal), Protein Quant (Normal), Protein Quant (Pivot), Run_summary (Normal), BGS Factory Report (Normal) │ └─ Reporting Unit: Per Run ├─ DIA Analysis\Post Analysis │ ├─ Differential Abundance Testing: Unpaired t-test │ │ ├─ Assume Equal Variance: False │ │ └─ Group-Wise Testing Correction: False │ ├─ Differential Abundance Grouping: Major Group (Quantification Settings) │ │ └─ Smallest Quantitative Unit: Major Group (Quantification Settings) │ │ └─ Use All MS-Level Quantities: True │ ├─ Calculate Explained TIC: Extensive │ ├─ Calculate Sample Correlation Matrix: True │ └─ Hierarchical Clustering: True │ ├─ Distance Metric: Manhattan Distance │ ├─ Linkage Strategy: Ward's Method │ ├─ Order Runs by Clustering: True │ └─ Z-score Transformation: True ├─ DIA Analysis\Protein Inference │ └─ Protein Inference Workflow: Automatic │ └─ Inference Algorithm: IDPicker ├─ DIA Analysis\PTM Workflow │ └─ PTM Localization: False ├─ DIA Analysis\Quantification │ ├─ Precursor Filtering: Identified (Qvalue) │ │ └─ Imputation Strategy: None │ ├─ Proteotypicity Filter: Only Protein Group Specific │ ├─ Protein LFQ Method: Automatic │ ├─ Quantity MS Level: MS2 │ ├─ Quantity Type: Area │ ├─ Cross-Run Normalization: False │ ├─ 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: Sum peptide quantity │ ├─ Major Group Top N: False │ ├─ Minor Group Quantity: Sum precursor quantity │ └─ Minor Group Top N: False ├─ DIA Analysis\Workflow │ ├─ Method Evaluation: False │ ├─ MS2 DeMultiplexing: Automatic │ ├─ Profiling Strategy: None │ ├─ Run Limit for directDIA Library: -1 │ └─ 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\Labeling │ └─ Channels: │ ├─ Channel 1: False │ ├─ Channel 2: False │ └─ Channel 3: False ├─ Pulsar Search\Modifications │ ├─ Max Variable Modifications: 3 │ └─ Select Modifications: │ ├─ Fixed Modifications:: Carbamidomethyl (C) │ └─ Variable Modifications: : Acetyl (Protein N-term), Deamidation (N), Gln->pyro-Glu, 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: 1800 │ │ │ └─ Min: 300 │ │ └─ Relative Intensity: True │ │ └─ Min: 5 │ └─ Precursors: │ ├─ Amino Acids: False │ ├─ Best N Fragments per Peptide: True │ │ ├─ Max: 6 │ │ └─ Min: 3 │ ├─ Best N Peptides per Protein Group: False │ ├─ Channel Count: False │ ├─ FASTA Matched: False │ ├─ Missed Cleavage: False │ ├─ Modifications: None │ ├─ Peptide Charge: True │ │ ├─ Max Charge: 4 │ │ └─ Min Charge: 2 │ └─ Proteotypicity: False ├─ Pulsar Search\Speed-Up │ └─ MS2 Index: 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: H510_Dox_total_200ng_04.htrms ├─ Vendor: Thermo ├─ File: H510_Dox_total_200ng_04 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Dox_total_200ng_04.htrms" ├─ Condition: Dox ├─ Replicate: 1 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] Run: H510_Dox_total_200ng_03.htrms ├─ Vendor: Thermo ├─ File: H510_Dox_total_200ng_03 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Dox_total_200ng_03.htrms" ├─ Condition: Dox ├─ Replicate: 2 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] Run: H510_Dox_total_200ng_02.htrms ├─ Vendor: Thermo ├─ File: H510_Dox_total_200ng_02 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Dox_total_200ng_02.htrms" ├─ Condition: Dox ├─ Replicate: 3 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] Run: H510_Dox_total_200ng_01.htrms ├─ Vendor: Thermo ├─ File: H510_Dox_total_200ng_01 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Dox_total_200ng_01.htrms" ├─ Condition: Dox ├─ Replicate: 4 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] Run: H510_Control_total_200ng_04.htrms ├─ Vendor: Thermo ├─ File: H510_Control_total_200ng_04 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Control_total_200ng_04.htrms" ├─ Condition: Control ├─ Replicate: 1 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] Run: H510_Control_total_200ng_03.htrms ├─ Vendor: Thermo ├─ File: H510_Control_total_200ng_03 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Control_total_200ng_03.htrms" ├─ Condition: Control ├─ Replicate: 2 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] Run: H510_Control_total_200ng_02.htrms ├─ Vendor: Thermo ├─ File: H510_Control_total_200ng_02 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Control_total_200ng_02.htrms" ├─ Condition: Control ├─ Replicate: 3 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] Run: H510_Control_total_200ng_01.htrms ├─ Vendor: Thermo ├─ File: H510_Control_total_200ng_01 ├─ Path: "D:\Proyectos\278-Mirja\Ez-Exploris_SP_Isoforms_Human_Total\H510_Control_total_200ng_01.htrms" ├─ Condition: Control ├─ Replicate: 4 ├─ HTRMS Version: 17.3.230224.55965 ├─ Protein Databases Used │ └─ Homo_Sapiens_SP_2022_03_plus_isoforms_cRAPs │ ├─ Protein Entries: 42,480 │ ├─ Original File: Homo_Sapiens_SP_2022_03_plus_isoforms_cRAP.fasta │ ├─ Date Created: 27-September-2022 09:36:30 +02:00 │ ├─ Date Modified: 17-March-2023 00:23:57 +01:00 │ └─ Parsing Rule: UniProt FASTA └─ MS2 Method ├─ [399.4 - 420.4] ├─ [419.4 - 440.5] ├─ [439.4 - 460.5] ├─ [459.5 - 480.5] ├─ [479.5 - 500.5] ├─ [499.5 - 520.5] ├─ [519.5 - 540.5] ├─ [539.5 - 560.5] ├─ [559.5 - 580.5] ├─ [579.5 - 600.5] ├─ [599.5 - 620.5] ├─ [619.5 - 640.5] ├─ [639.5 - 660.6] ├─ [659.5 - 680.6] ├─ [679.6 - 700.6] ├─ [699.6 - 720.6] ├─ [719.6 - 740.6] ├─ [739.6 - 760.6] ├─ [759.6 - 780.6] ├─ [779.6 - 800.6] ├─ [799.6 - 820.6] ├─ [819.6 - 840.6] ├─ [839.6 - 860.6] ├─ [859.6 - 880.7] └─ [879.6 - 900.7] [END-SETUP] [BEGIN-LOG] INFO: [16/03/2023 22:46:18] -> Initializing Pipeline... INFO: [16/03/2023 22:46:18] -> Preprocessing Run #1 of 8... INFO: [16/03/2023 22:46:18] -> Searching DIA with Pulsar... INFO: [16/03/2023 22:46:19] -> Initialize Pipeline... INFO: [16/03/2023 22:46:19] -> Initialize Pipeline INFO: [16/03/2023 22:46:19] -> Initialize Pipeline... INFO: [16/03/2023 22:46:19] -> Creating Experiment Environment INFO: [16/03/2023 22:46:19] -> SuperRun 1/8: Initializing (H510_Dox_total_200ng_04.htrms) INFO: [16/03/2023 22:46:19] -> Run 1/8: Organizing Data from Run INFO: [16/03/2023 22:46:19] -> Run 1/8: Creating Calibration Search Space... INFO: [16/03/2023 22:46:20] -> Run 1/8: Creating Search Space... INFO: [16/03/2023 22:46:20] -> Size of search space [MB]: 0 INFO: [16/03/2023 22:46:20] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 22:46:20] -> Run 1/8: MS2 Index Generation INFO: [16/03/2023 22:46:21] -> MS2 Index Generation Time: 1.19s INFO: [16/03/2023 22:46:21] -> Run 1/8: Method-Specific Pre-Processing... INFO: [16/03/2023 22:46:21] -> Initializing... INFO: [16/03/2023 22:46:28] -> Finalizing HTRMS File... INFO: [16/03/2023 22:47:07] -> Processed in 45.8s INFO: [16/03/2023 22:47:08] -> Done INFO: [16/03/2023 22:47:08] -> Run 1/8: Process Raw File... WARNING: [16/03/2023 22:47:08] -> Hard drive space is low (<100 GB)! Please free some space or set the temporary folder of SpectroMine to a different drive. INFO: [16/03/2023 22:47:24] -> Run 1/8: Preparing Partitions... INFO: [16/03/2023 22:47:24] -> Part 1/1 - Run 1/8: Preparing Calibration Searches... INFO: [16/03/2023 22:47:26] -> Part 1/1 - Run 1/8: First Pass Calibration Search... INFO: [16/03/2023 22:47:31] -> Part 1/1 - Run 1/8: Calibration Search... INFO: [16/03/2023 22:47:40] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5146 [8.2s] INFO: [16/03/2023 22:47:43] -> Part 1/1 - Run 1/8: Preparing Main Search... INFO: [16/03/2023 22:47:44] -> Part 1/1 - Run 1/8: Main Search... INFO: [16/03/2023 22:50:22] -> Extracting 211072 MS1 XICs INFO: [16/03/2023 22:51:19] -> Run 1/8: Cleaning Up Run.. INFO: [16/03/2023 22:51:19] -> SuperRun 2/8: Initializing (H510_Dox_total_200ng_03.htrms) INFO: [16/03/2023 22:51:19] -> Run 2/8: Organizing Data from Run INFO: [16/03/2023 22:51:19] -> Run 2/8: Creating Calibration Search Space... INFO: [16/03/2023 22:51:19] -> Run 2/8: Creating Search Space... INFO: [16/03/2023 22:51:19] -> Size of search space [MB]: 0 INFO: [16/03/2023 22:51:19] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 22:51:19] -> Run 2/8: MS2 Index Generation INFO: [16/03/2023 22:51:21] -> MS2 Index Generation Time: 1.27s INFO: [16/03/2023 22:51:21] -> Run 2/8: Method-Specific Pre-Processing... INFO: [16/03/2023 22:51:21] -> Initializing... INFO: [16/03/2023 22:51:27] -> Finalizing HTRMS File... INFO: [16/03/2023 22:52:06] -> Processed in 45.4s INFO: [16/03/2023 22:52:07] -> Done INFO: [16/03/2023 22:52:07] -> Run 2/8: Process Raw File... INFO: [16/03/2023 22:52:20] -> Run 2/8: Preparing Partitions... INFO: [16/03/2023 22:52:20] -> Part 1/1 - Run 2/8: Preparing Calibration Searches... INFO: [16/03/2023 22:52:21] -> Part 1/1 - Run 2/8: First Pass Calibration Search... INFO: [16/03/2023 22:52:27] -> Part 1/1 - Run 2/8: Calibration Search... INFO: [16/03/2023 22:52:32] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4966 [5.2s] INFO: [16/03/2023 22:52:35] -> Part 1/1 - Run 2/8: Preparing Main Search... INFO: [16/03/2023 22:52:37] -> Part 1/1 - Run 2/8: Main Search... INFO: [16/03/2023 22:54:50] -> Extracting 194533 MS1 XICs INFO: [16/03/2023 22:55:43] -> Run 2/8: Cleaning Up Run.. INFO: [16/03/2023 22:55:43] -> SuperRun 3/8: Initializing (H510_Dox_total_200ng_02.htrms) INFO: [16/03/2023 22:55:43] -> Run 3/8: Organizing Data from Run INFO: [16/03/2023 22:55:43] -> Run 3/8: Creating Calibration Search Space... INFO: [16/03/2023 22:55:43] -> Run 3/8: Creating Search Space... INFO: [16/03/2023 22:55:43] -> Size of search space [MB]: 0 INFO: [16/03/2023 22:55:43] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 22:55:43] -> Run 3/8: MS2 Index Generation INFO: [16/03/2023 22:55:44] -> MS2 Index Generation Time: 1.38s INFO: [16/03/2023 22:55:44] -> Run 3/8: Method-Specific Pre-Processing... INFO: [16/03/2023 22:55:44] -> Initializing... INFO: [16/03/2023 22:55:51] -> Finalizing HTRMS File... INFO: [16/03/2023 22:56:24] -> Processed in 40.2s INFO: [16/03/2023 22:56:25] -> Done INFO: [16/03/2023 22:56:25] -> Run 3/8: Process Raw File... INFO: [16/03/2023 22:56:38] -> Run 3/8: Preparing Partitions... INFO: [16/03/2023 22:56:38] -> Part 1/1 - Run 3/8: Preparing Calibration Searches... INFO: [16/03/2023 22:56:40] -> Part 1/1 - Run 3/8: First Pass Calibration Search... INFO: [16/03/2023 22:56:45] -> Part 1/1 - Run 3/8: Calibration Search... INFO: [16/03/2023 22:56:50] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5083 [5.3s] INFO: [16/03/2023 22:56:53] -> Part 1/1 - Run 3/8: Preparing Main Search... INFO: [16/03/2023 22:56:55] -> Part 1/1 - Run 3/8: Main Search... INFO: [16/03/2023 22:59:05] -> Extracting 191941 MS1 XICs INFO: [16/03/2023 22:59:57] -> Run 3/8: Cleaning Up Run.. INFO: [16/03/2023 22:59:57] -> SuperRun 4/8: Initializing (H510_Dox_total_200ng_01.htrms) INFO: [16/03/2023 22:59:57] -> Run 4/8: Organizing Data from Run INFO: [16/03/2023 22:59:57] -> Run 4/8: Creating Calibration Search Space... INFO: [16/03/2023 22:59:57] -> Run 4/8: Creating Search Space... INFO: [16/03/2023 22:59:57] -> Size of search space [MB]: 0 INFO: [16/03/2023 22:59:57] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 22:59:57] -> Run 4/8: MS2 Index Generation INFO: [16/03/2023 22:59:59] -> MS2 Index Generation Time: 1.26s INFO: [16/03/2023 22:59:59] -> Run 4/8: Method-Specific Pre-Processing... INFO: [16/03/2023 22:59:59] -> Initializing... INFO: [16/03/2023 23:00:05] -> Finalizing HTRMS File... INFO: [16/03/2023 23:00:38] -> Processed in 39s INFO: [16/03/2023 23:00:39] -> Done INFO: [16/03/2023 23:00:39] -> Run 4/8: Process Raw File... INFO: [16/03/2023 23:00:50] -> Run 4/8: Preparing Partitions... INFO: [16/03/2023 23:00:50] -> Part 1/1 - Run 4/8: Preparing Calibration Searches... INFO: [16/03/2023 23:00:52] -> Part 1/1 - Run 4/8: First Pass Calibration Search... INFO: [16/03/2023 23:00:57] -> Part 1/1 - Run 4/8: Calibration Search... INFO: [16/03/2023 23:01:02] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5152 [4.8s] INFO: [16/03/2023 23:01:05] -> Part 1/1 - Run 4/8: Preparing Main Search... INFO: [16/03/2023 23:01:07] -> Part 1/1 - Run 4/8: Main Search... INFO: [16/03/2023 23:03:03] -> Extracting 175241 MS1 XICs INFO: [16/03/2023 23:03:51] -> Run 4/8: Cleaning Up Run.. INFO: [16/03/2023 23:03:51] -> SuperRun 5/8: Initializing (H510_Control_total_200ng_04.htrms) INFO: [16/03/2023 23:03:51] -> Run 5/8: Organizing Data from Run INFO: [16/03/2023 23:03:51] -> Run 5/8: Creating Calibration Search Space... INFO: [16/03/2023 23:03:51] -> Run 5/8: Creating Search Space... INFO: [16/03/2023 23:03:51] -> Size of search space [MB]: 0 INFO: [16/03/2023 23:03:51] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 23:03:51] -> Run 5/8: MS2 Index Generation INFO: [16/03/2023 23:03:53] -> MS2 Index Generation Time: 1.27s INFO: [16/03/2023 23:03:53] -> Run 5/8: Method-Specific Pre-Processing... INFO: [16/03/2023 23:03:53] -> Initializing... INFO: [16/03/2023 23:03:59] -> Finalizing HTRMS File... INFO: [16/03/2023 23:04:38] -> Processed in 45.1s INFO: [16/03/2023 23:04:39] -> Done INFO: [16/03/2023 23:04:39] -> Run 5/8: Process Raw File... INFO: [16/03/2023 23:04:51] -> Run 5/8: Preparing Partitions... INFO: [16/03/2023 23:04:51] -> Part 1/1 - Run 5/8: Preparing Calibration Searches... INFO: [16/03/2023 23:04:52] -> Part 1/1 - Run 5/8: First Pass Calibration Search... INFO: [16/03/2023 23:04:57] -> Part 1/1 - Run 5/8: Calibration Search... INFO: [16/03/2023 23:05:03] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4908 [5.1s] INFO: [16/03/2023 23:05:05] -> Part 1/1 - Run 5/8: Preparing Main Search... INFO: [16/03/2023 23:05:07] -> Part 1/1 - Run 5/8: Main Search... INFO: [16/03/2023 23:06:47] -> Extracting 159518 MS1 XICs INFO: [16/03/2023 23:07:29] -> Run 5/8: Cleaning Up Run.. INFO: [16/03/2023 23:07:29] -> SuperRun 6/8: Initializing (H510_Control_total_200ng_03.htrms) INFO: [16/03/2023 23:07:29] -> Run 6/8: Organizing Data from Run INFO: [16/03/2023 23:07:29] -> Run 6/8: Creating Calibration Search Space... INFO: [16/03/2023 23:07:29] -> Run 6/8: Creating Search Space... INFO: [16/03/2023 23:07:29] -> Size of search space [MB]: 0 INFO: [16/03/2023 23:07:29] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 23:07:29] -> Run 6/8: MS2 Index Generation INFO: [16/03/2023 23:07:30] -> MS2 Index Generation Time: 1.23s INFO: [16/03/2023 23:07:30] -> Run 6/8: Method-Specific Pre-Processing... INFO: [16/03/2023 23:07:30] -> Initializing... INFO: [16/03/2023 23:07:36] -> Finalizing HTRMS File... INFO: [16/03/2023 23:08:12] -> Processed in 41.9s INFO: [16/03/2023 23:08:13] -> Done INFO: [16/03/2023 23:08:13] -> Run 6/8: Process Raw File... INFO: [16/03/2023 23:08:25] -> Run 6/8: Preparing Partitions... INFO: [16/03/2023 23:08:25] -> Part 1/1 - Run 6/8: Preparing Calibration Searches... INFO: [16/03/2023 23:08:27] -> Part 1/1 - Run 6/8: First Pass Calibration Search... INFO: [16/03/2023 23:08:32] -> Part 1/1 - Run 6/8: Calibration Search... INFO: [16/03/2023 23:08:38] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4798 [5.7s] INFO: [16/03/2023 23:08:41] -> Part 1/1 - Run 6/8: Preparing Main Search... INFO: [16/03/2023 23:08:42] -> Part 1/1 - Run 6/8: Main Search... INFO: [16/03/2023 23:10:47] -> Extracting 190086 MS1 XICs INFO: [16/03/2023 23:11:37] -> Run 6/8: Cleaning Up Run.. INFO: [16/03/2023 23:11:37] -> SuperRun 7/8: Initializing (H510_Control_total_200ng_02.htrms) INFO: [16/03/2023 23:11:37] -> Run 7/8: Organizing Data from Run INFO: [16/03/2023 23:11:37] -> Run 7/8: Creating Calibration Search Space... INFO: [16/03/2023 23:11:37] -> Run 7/8: Creating Search Space... INFO: [16/03/2023 23:11:37] -> Size of search space [MB]: 0 INFO: [16/03/2023 23:11:37] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 23:11:37] -> Run 7/8: MS2 Index Generation INFO: [16/03/2023 23:11:38] -> MS2 Index Generation Time: 1.43s INFO: [16/03/2023 23:11:38] -> Run 7/8: Method-Specific Pre-Processing... INFO: [16/03/2023 23:11:38] -> Initializing... INFO: [16/03/2023 23:11:43] -> Finalizing HTRMS File... INFO: [16/03/2023 23:12:16] -> Processed in 37.9s INFO: [16/03/2023 23:12:17] -> Done INFO: [16/03/2023 23:12:17] -> Run 7/8: Process Raw File... INFO: [16/03/2023 23:12:28] -> Run 7/8: Preparing Partitions... INFO: [16/03/2023 23:12:28] -> Part 1/1 - Run 7/8: Preparing Calibration Searches... INFO: [16/03/2023 23:12:30] -> Part 1/1 - Run 7/8: First Pass Calibration Search... INFO: [16/03/2023 23:12:35] -> Part 1/1 - Run 7/8: Calibration Search... INFO: [16/03/2023 23:12:40] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5227 [5s] INFO: [16/03/2023 23:12:43] -> Part 1/1 - Run 7/8: Preparing Main Search... INFO: [16/03/2023 23:12:45] -> Part 1/1 - Run 7/8: Main Search... INFO: [16/03/2023 23:14:32] -> Extracting 167162 MS1 XICs INFO: [16/03/2023 23:15:16] -> Run 7/8: Cleaning Up Run.. INFO: [16/03/2023 23:15:16] -> SuperRun 8/8: Initializing (H510_Control_total_200ng_01.htrms) INFO: [16/03/2023 23:15:16] -> Run 8/8: Organizing Data from Run INFO: [16/03/2023 23:15:16] -> Run 8/8: Creating Calibration Search Space... INFO: [16/03/2023 23:15:16] -> Run 8/8: Creating Search Space... INFO: [16/03/2023 23:15:16] -> Size of search space [MB]: 0 INFO: [16/03/2023 23:15:16] -> Number of IMPGs in search space: 0 INFO: [16/03/2023 23:15:16] -> Run 8/8: MS2 Index Generation INFO: [16/03/2023 23:15:17] -> MS2 Index Generation Time: 1.64s INFO: [16/03/2023 23:15:17] -> Run 8/8: Method-Specific Pre-Processing... INFO: [16/03/2023 23:15:17] -> Initializing... INFO: [16/03/2023 23:15:23] -> Finalizing HTRMS File... INFO: [16/03/2023 23:15:54] -> Processed in 36.2s INFO: [16/03/2023 23:15:55] -> Done INFO: [16/03/2023 23:15:55] -> Run 8/8: Process Raw File... INFO: [16/03/2023 23:16:07] -> Run 8/8: Preparing Partitions... INFO: [16/03/2023 23:16:07] -> Part 1/1 - Run 8/8: Preparing Calibration Searches... INFO: [16/03/2023 23:16:08] -> Part 1/1 - Run 8/8: First Pass Calibration Search... INFO: [16/03/2023 23:16:13] -> Part 1/1 - Run 8/8: Calibration Search... INFO: [16/03/2023 23:16:18] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5058 [5.2s] INFO: [16/03/2023 23:16:21] -> Part 1/1 - Run 8/8: Preparing Main Search... INFO: [16/03/2023 23:16:23] -> Part 1/1 - Run 8/8: Main Search... INFO: [16/03/2023 23:18:19] -> Extracting 180551 MS1 XICs INFO: [16/03/2023 23:19:06] -> Run 8/8: Cleaning Up Run.. INFO: [16/03/2023 23:19:10] -> Remove Aborted Runs (if any) from the Experiment... INFO: [16/03/2023 23:19:10] -> Score Post-Processing INFO: [16/03/2023 23:20:25] -> Score Post-Processing: 1.25m INFO: [16/03/2023 23:20:25] -> PSM FDR... INFO: [16/03/2023 23:20:59] -> PSM FDR: 33.89s INFO: [16/03/2023 23:20:59] -> Converting to non-redundant data structure... INFO: [16/03/2023 23:21:16] -> Performing Peptide FDR... INFO: [16/03/2023 23:21:21] -> Performing Protein Inference... INFO: [16/03/2023 23:21:23] -> Performing Protein FDR... INFO: [16/03/2023 23:21:25] -> Calculating Result Values at Run and Experiment Level... INFO: [16/03/2023 23:21:37] -> Pulsar identified 484343 PSMs, 38483 stripped sequences, 47630 peptide precursors, 4460 protein groups. INFO: [16/03/2023 23:21:37] -> Writing experiment store.. INFO: [16/03/2023 23:21:40] -> Selecting Data For Quantification... INFO: [16/03/2023 23:21:40] -> Calculating Quantities... INFO: [16/03/2023 23:21:51] -> Calculating Protein Group Quantities using MaxLFQ Algorithm... INFO: [16/03/2023 23:21:51] -> Collapsing PTM-Locations... INFO: [16/03/2023 23:21:51] -> Summarizing Fractions... INFO: [16/03/2023 23:21:52] -> Gathering Protein Information of all Matching Proteins INFO: [16/03/2023 23:21:52] -> Running Post Analysis Processes... INFO: [16/03/2023 23:21:52] -> Identifying Calibration Peptides... INFO: [16/03/2023 23:21:53] -> iRT Calibration... INFO: [16/03/2023 23:21:56] -> Assigning iRT Source... INFO: [16/03/2023 23:21:56] -> Calculating iRT... INFO: [16/03/2023 23:21:57] -> Summarizing Identifications INFO: [16/03/2023 23:22:39] -> Generating directDIA+ search space INFO: [16/03/2023 23:27:06] -> directDIA+ search: H510_Dox_total_200ng_04.htrms INFO: [16/03/2023 23:30:44] -> directDIA+ search: H510_Dox_total_200ng_03.htrms INFO: [16/03/2023 23:34:18] -> directDIA+ search: H510_Dox_total_200ng_02.htrms INFO: [16/03/2023 23:37:35] -> directDIA+ search: H510_Dox_total_200ng_01.htrms INFO: [16/03/2023 23:40:37] -> directDIA+ search: H510_Control_total_200ng_04.htrms INFO: [16/03/2023 23:43:48] -> directDIA+ search: H510_Control_total_200ng_03.htrms INFO: [16/03/2023 23:47:08] -> directDIA+ search: H510_Control_total_200ng_02.htrms INFO: [16/03/2023 23:50:08] -> directDIA+ search: H510_Control_total_200ng_01.htrms INFO: [16/03/2023 23:54:41] -> Identifiying Significant Precurors... INFO: [16/03/2023 23:54:54] -> Predicting Ion Mobility INFO: [16/03/2023 23:54:56] -> Calculating Median iRT INFO: [16/03/2023 23:54:57] -> Building BGS Protein Grouping... INFO: [16/03/2023 23:54:57] -> Digesting Fasta... INFO: [16/03/2023 23:54:57] -> Annotating Proteins... INFO: [16/03/2023 23:54:58] -> Grouping Proteins... INFO: [16/03/2023 23:54:59] -> Calculating Run Summary Statistics... INFO: [16/03/2023 23:55:19] -> Building Consensus Fragment Spectra... INFO: [16/03/2023 23:56:03] -> Selecting best fragment ions INFO: [16/03/2023 23:57:38] -> Cleaning Up Experiment... INFO: [16/03/2023 23:57:39] -> Initializing Experiment... INFO: [16/03/2023 23:57:39] -> Loading Spectral Libraries... INFO: [16/03/2023 23:57:52] -> Initialize Scoring... INFO: [16/03/2023 23:57:52] -> Generating Scan Map... INFO: [16/03/2023 23:57:52] -> Initializing Workpackages... INFO: [16/03/2023 23:57:52] -> Performing Basic Calibration... INFO: [16/03/2023 23:57:54] -> Identifying Calibration Peptides... INFO: [16/03/2023 23:57:54] -> Correcting Gradient Fine Structure... INFO: [16/03/2023 23:57:56] -> Initializing Pipeline... INFO: [16/03/2023 23:57:56] -> Preprocessing Run #1 of 8... INFO: [16/03/2023 23:57:56] -> Initialize Scoring... INFO: [16/03/2023 23:57:56] -> Extracting Ion Currents... INFO: [16/03/2023 23:58:16] -> Machine Learning... INFO: [16/03/2023 23:58:17] -> Pipeline executed in 20.36s INFO: [16/03/2023 23:58:21] -> Initializing Pipeline... INFO: [16/03/2023 23:58:21] -> Preprocessing Run #1 of 8... INFO: [16/03/2023 23:58:21] -> Initialize Scoring... INFO: [16/03/2023 23:58:21] -> Extracting Ion Currents... INFO: [16/03/2023 23:58:36] -> Machine Learning... INFO: [16/03/2023 23:58:38] -> Pipeline executed in 17.46s INFO: [16/03/2023 23:58:44] -> Initialize Scoring... INFO: [16/03/2023 23:58:44] -> Preprocessing Run #2 of 8... INFO: [16/03/2023 23:58:44] -> Searching DIA with Pulsar... INFO: [16/03/2023 23:58:44] -> Initializing Experiment... INFO: [16/03/2023 23:58:44] -> Loading Spectral Libraries... INFO: [16/03/2023 23:58:44] -> Initialize Scoring... INFO: [16/03/2023 23:58:44] -> Generating Scan Map... INFO: [16/03/2023 23:58:44] -> Initializing Workpackages... INFO: [16/03/2023 23:58:44] -> Performing Basic Calibration... INFO: [16/03/2023 23:58:45] -> Identifying Calibration Peptides... INFO: [16/03/2023 23:58:45] -> Correcting Gradient Fine Structure... INFO: [16/03/2023 23:58:47] -> Initializing Pipeline... INFO: [16/03/2023 23:58:47] -> Preprocessing Run #2 of 8... INFO: [16/03/2023 23:58:47] -> Initialize Scoring... INFO: [16/03/2023 23:58:47] -> Extracting Ion Currents... INFO: [16/03/2023 23:59:07] -> Machine Learning... INFO: [16/03/2023 23:59:08] -> Pipeline executed in 20.21s INFO: [16/03/2023 23:59:11] -> Initializing Pipeline... INFO: [16/03/2023 23:59:11] -> Preprocessing Run #2 of 8... INFO: [16/03/2023 23:59:11] -> Initialize Scoring... INFO: [16/03/2023 23:59:11] -> Extracting Ion Currents... INFO: [16/03/2023 23:59:26] -> Machine Learning... INFO: [16/03/2023 23:59:28] -> Pipeline executed in 16.68s INFO: [16/03/2023 23:59:34] -> Initialize Scoring... INFO: [16/03/2023 23:59:34] -> Preprocessing Run #3 of 8... INFO: [16/03/2023 23:59:34] -> Searching DIA with Pulsar... INFO: [16/03/2023 23:59:34] -> Initializing Experiment... INFO: [16/03/2023 23:59:34] -> Loading Spectral Libraries... INFO: [16/03/2023 23:59:34] -> Initialize Scoring... INFO: [16/03/2023 23:59:34] -> Generating Scan Map... INFO: [16/03/2023 23:59:34] -> Initializing Workpackages... INFO: [16/03/2023 23:59:34] -> Performing Basic Calibration... INFO: [16/03/2023 23:59:35] -> Identifying Calibration Peptides... INFO: [16/03/2023 23:59:35] -> Correcting Gradient Fine Structure... INFO: [16/03/2023 23:59:37] -> Initializing Pipeline... INFO: [16/03/2023 23:59:37] -> Preprocessing Run #3 of 8... INFO: [16/03/2023 23:59:37] -> Initialize Scoring... INFO: [16/03/2023 23:59:37] -> Extracting Ion Currents... INFO: [16/03/2023 23:59:55] -> Machine Learning... INFO: [16/03/2023 23:59:56] -> Pipeline executed in 19.43s INFO: [17/03/2023 00:00:00] -> Initializing Pipeline... INFO: [17/03/2023 00:00:00] -> Preprocessing Run #3 of 8... INFO: [17/03/2023 00:00:00] -> Initialize Scoring... INFO: [17/03/2023 00:00:00] -> Extracting Ion Currents... INFO: [17/03/2023 00:00:14] -> Machine Learning... INFO: [17/03/2023 00:00:16] -> Pipeline executed in 16.12s INFO: [17/03/2023 00:00:21] -> Initialize Scoring... INFO: [17/03/2023 00:00:21] -> Preprocessing Run #4 of 8... INFO: [17/03/2023 00:00:21] -> Searching DIA with Pulsar... INFO: [17/03/2023 00:00:21] -> Initializing Experiment... INFO: [17/03/2023 00:00:21] -> Loading Spectral Libraries... INFO: [17/03/2023 00:00:21] -> Initialize Scoring... INFO: [17/03/2023 00:00:21] -> Generating Scan Map... INFO: [17/03/2023 00:00:21] -> Initializing Workpackages... INFO: [17/03/2023 00:00:21] -> Performing Basic Calibration... INFO: [17/03/2023 00:00:23] -> Identifying Calibration Peptides... INFO: [17/03/2023 00:00:23] -> Correcting Gradient Fine Structure... INFO: [17/03/2023 00:00:25] -> Initializing Pipeline... INFO: [17/03/2023 00:00:25] -> Preprocessing Run #4 of 8... INFO: [17/03/2023 00:00:25] -> Initialize Scoring... INFO: [17/03/2023 00:00:25] -> Extracting Ion Currents... INFO: [17/03/2023 00:00:44] -> Machine Learning... INFO: [17/03/2023 00:00:45] -> Pipeline executed in 20.23s INFO: [17/03/2023 00:00:49] -> Initializing Pipeline... INFO: [17/03/2023 00:00:49] -> Preprocessing Run #4 of 8... INFO: [17/03/2023 00:00:49] -> Initialize Scoring... INFO: [17/03/2023 00:00:49] -> Extracting Ion Currents... INFO: [17/03/2023 00:01:04] -> Machine Learning... INFO: [17/03/2023 00:01:06] -> Pipeline executed in 17.43s INFO: [17/03/2023 00:01:11] -> Initialize Scoring... INFO: [17/03/2023 00:01:11] -> Preprocessing Run #5 of 8... INFO: [17/03/2023 00:01:11] -> Searching DIA with Pulsar... INFO: [17/03/2023 00:01:11] -> Initializing Experiment... INFO: [17/03/2023 00:01:11] -> Loading Spectral Libraries... INFO: [17/03/2023 00:01:11] -> Initialize Scoring... INFO: [17/03/2023 00:01:11] -> Generating Scan Map... INFO: [17/03/2023 00:01:11] -> Initializing Workpackages... INFO: [17/03/2023 00:01:11] -> Performing Basic Calibration... INFO: [17/03/2023 00:01:12] -> Identifying Calibration Peptides... INFO: [17/03/2023 00:01:12] -> Correcting Gradient Fine Structure... INFO: [17/03/2023 00:01:14] -> Initializing Pipeline... INFO: [17/03/2023 00:01:14] -> Preprocessing Run #5 of 8... INFO: [17/03/2023 00:01:14] -> Initialize Scoring... INFO: [17/03/2023 00:01:14] -> Extracting Ion Currents... INFO: [17/03/2023 00:01:34] -> Machine Learning... INFO: [17/03/2023 00:01:35] -> Pipeline executed in 20.31s INFO: [17/03/2023 00:01:38] -> Initializing Pipeline... INFO: [17/03/2023 00:01:38] -> Preprocessing Run #5 of 8... INFO: [17/03/2023 00:01:38] -> Initialize Scoring... INFO: [17/03/2023 00:01:38] -> Extracting Ion Currents... INFO: [17/03/2023 00:01:52] -> Machine Learning... INFO: [17/03/2023 00:01:55] -> Pipeline executed in 16.47s INFO: [17/03/2023 00:02:00] -> Initialize Scoring... INFO: [17/03/2023 00:02:00] -> Preprocessing Run #6 of 8... INFO: [17/03/2023 00:02:00] -> Searching DIA with Pulsar... INFO: [17/03/2023 00:02:00] -> Initializing Experiment... INFO: [17/03/2023 00:02:00] -> Loading Spectral Libraries... INFO: [17/03/2023 00:02:00] -> Initialize Scoring... INFO: [17/03/2023 00:02:00] -> Generating Scan Map... INFO: [17/03/2023 00:02:00] -> Initializing Workpackages... INFO: [17/03/2023 00:02:00] -> Performing Basic Calibration... INFO: [17/03/2023 00:02:01] -> Identifying Calibration Peptides... INFO: [17/03/2023 00:02:01] -> Correcting Gradient Fine Structure... INFO: [17/03/2023 00:02:03] -> Initializing Pipeline... INFO: [17/03/2023 00:02:03] -> Preprocessing Run #6 of 8... INFO: [17/03/2023 00:02:03] -> Initialize Scoring... INFO: [17/03/2023 00:02:03] -> Extracting Ion Currents... INFO: [17/03/2023 00:02:22] -> Machine Learning... INFO: [17/03/2023 00:02:23] -> Pipeline executed in 20.36s INFO: [17/03/2023 00:02:27] -> Initializing Pipeline... INFO: [17/03/2023 00:02:27] -> Preprocessing Run #6 of 8... INFO: [17/03/2023 00:02:27] -> Initialize Scoring... INFO: [17/03/2023 00:02:27] -> Extracting Ion Currents... INFO: [17/03/2023 00:02:41] -> Machine Learning... INFO: [17/03/2023 00:02:44] -> Pipeline executed in 16.44s INFO: [17/03/2023 00:02:49] -> Initialize Scoring... INFO: [17/03/2023 00:02:49] -> Preprocessing Run #7 of 8... INFO: [17/03/2023 00:02:49] -> Searching DIA with Pulsar... INFO: [17/03/2023 00:02:49] -> Initializing Experiment... INFO: [17/03/2023 00:02:49] -> Loading Spectral Libraries... INFO: [17/03/2023 00:02:49] -> Initialize Scoring... INFO: [17/03/2023 00:02:49] -> Generating Scan Map... INFO: [17/03/2023 00:02:49] -> Initializing Workpackages... INFO: [17/03/2023 00:02:49] -> Performing Basic Calibration... INFO: [17/03/2023 00:02:50] -> Identifying Calibration Peptides... INFO: [17/03/2023 00:02:50] -> Correcting Gradient Fine Structure... INFO: [17/03/2023 00:02:52] -> Initializing Pipeline... INFO: [17/03/2023 00:02:52] -> Preprocessing Run #7 of 8... INFO: [17/03/2023 00:02:52] -> Initialize Scoring... INFO: [17/03/2023 00:02:52] -> Extracting Ion Currents... INFO: [17/03/2023 00:03:12] -> Machine Learning... INFO: [17/03/2023 00:03:13] -> Pipeline executed in 21.26s INFO: [17/03/2023 00:03:17] -> Initializing Pipeline... INFO: [17/03/2023 00:03:17] -> Preprocessing Run #7 of 8... INFO: [17/03/2023 00:03:17] -> Initialize Scoring... INFO: [17/03/2023 00:03:17] -> Extracting Ion Currents... INFO: [17/03/2023 00:03:31] -> Machine Learning... INFO: [17/03/2023 00:03:34] -> Pipeline executed in 16.85s INFO: [17/03/2023 00:03:38] -> Initialize Scoring... INFO: [17/03/2023 00:03:38] -> Preprocessing Run #8 of 8... INFO: [17/03/2023 00:03:38] -> Searching DIA with Pulsar... INFO: [17/03/2023 00:03:38] -> Initializing Experiment... INFO: [17/03/2023 00:03:38] -> Loading Spectral Libraries... INFO: [17/03/2023 00:03:38] -> Initialize Scoring... INFO: [17/03/2023 00:03:38] -> Generating Scan Map... INFO: [17/03/2023 00:03:38] -> Initializing Workpackages... INFO: [17/03/2023 00:03:38] -> Performing Basic Calibration... INFO: [17/03/2023 00:03:40] -> Identifying Calibration Peptides... INFO: [17/03/2023 00:03:40] -> Correcting Gradient Fine Structure... INFO: [17/03/2023 00:03:42] -> Initializing Pipeline... INFO: [17/03/2023 00:03:42] -> Preprocessing Run #8 of 8... INFO: [17/03/2023 00:03:42] -> Initialize Scoring... INFO: [17/03/2023 00:03:42] -> Extracting Ion Currents... INFO: [17/03/2023 00:04:02] -> Machine Learning... INFO: [17/03/2023 00:04:03] -> Pipeline executed in 21.2s INFO: [17/03/2023 00:04:07] -> Initializing Pipeline... INFO: [17/03/2023 00:04:07] -> Preprocessing Run #8 of 8... INFO: [17/03/2023 00:04:07] -> Initialize Scoring... INFO: [17/03/2023 00:04:07] -> Extracting Ion Currents... INFO: [17/03/2023 00:04:21] -> Machine Learning... INFO: [17/03/2023 00:04:23] -> Pipeline executed in 16.3s INFO: [17/03/2023 00:04:28] -> Initialize Scoring... INFO: [17/03/2023 00:04:28] -> Initializing QC... INFO: [17/03/2023 00:04:28] -> Determining Calibration Parameter... INFO: [17/03/2023 00:04:28] -> Assigning ML Features... INFO: [17/03/2023 00:04:28] -> Generating Decoys... INFO: [17/03/2023 00:04:31] -> Extracting Ion Currents... INFO: [17/03/2023 00:05:03] -> Releasing Raw Files... INFO: [17/03/2023 00:05:03] -> Machine Learning... INFO: [17/03/2023 00:05:21] -> Initializing HTRMS... INFO: [17/03/2023 00:05:21] -> Releasing Run Resources... INFO: [17/03/2023 00:05:23] -> Calculating Qvalues... INFO: [17/03/2023 00:05:23] -> Unique precursors: 63,293 of 64,467 | modified peptides: 56,185 of 57,135 | peptides: 49,677 of 50,479 | protein groups: 5,265 (Qvalue <= 0.01) [H510_Dox_total_200ng_04.htrms] INFO: [17/03/2023 00:05:23] -> Collapsing Search Tree... INFO: [17/03/2023 00:05:23] -> Processed in 55.62s INFO: [17/03/2023 00:05:24] -> Initializing QC... INFO: [17/03/2023 00:05:24] -> Determining Calibration Parameter... INFO: [17/03/2023 00:05:24] -> Assigning ML Features... INFO: [17/03/2023 00:05:24] -> Generating Decoys... INFO: [17/03/2023 00:05:24] -> Extracting Ion Currents... INFO: [17/03/2023 00:05:54] -> Releasing Raw Files... INFO: [17/03/2023 00:05:54] -> Machine Learning... INFO: [17/03/2023 00:06:11] -> Initializing HTRMS... INFO: [17/03/2023 00:06:11] -> Releasing Run Resources... INFO: [17/03/2023 00:06:13] -> Calculating Qvalues... INFO: [17/03/2023 00:06:14] -> Unique precursors: 62,385 of 64,467 | modified peptides: 55,384 of 57,135 | peptides: 48,988 of 50,479 | protein groups: 5,255 (Qvalue <= 0.01) [H510_Dox_total_200ng_03.htrms] INFO: [17/03/2023 00:06:14] -> Collapsing Search Tree... INFO: [17/03/2023 00:06:14] -> Processed in 50.15s INFO: [17/03/2023 00:06:14] -> Initializing QC... INFO: [17/03/2023 00:06:14] -> Determining Calibration Parameter... INFO: [17/03/2023 00:06:14] -> Assigning ML Features... INFO: [17/03/2023 00:06:14] -> Generating Decoys... INFO: [17/03/2023 00:06:14] -> Extracting Ion Currents... INFO: [17/03/2023 00:06:44] -> Releasing Raw Files... INFO: [17/03/2023 00:06:44] -> Machine Learning... INFO: [17/03/2023 00:07:05] -> Initializing HTRMS... INFO: [17/03/2023 00:07:05] -> Releasing Run Resources... INFO: [17/03/2023 00:07:07] -> Calculating Qvalues... INFO: [17/03/2023 00:07:08] -> Unique precursors: 61,239 of 64,467 | modified peptides: 54,487 of 57,135 | peptides: 48,191 of 50,479 | protein groups: 5,244 (Qvalue <= 0.01) [H510_Dox_total_200ng_02.htrms] INFO: [17/03/2023 00:07:08] -> Collapsing Search Tree... INFO: [17/03/2023 00:07:08] -> Processed in 54.23s INFO: [17/03/2023 00:07:08] -> Initializing QC... INFO: [17/03/2023 00:07:08] -> Determining Calibration Parameter... INFO: [17/03/2023 00:07:08] -> Assigning ML Features... INFO: [17/03/2023 00:07:08] -> Generating Decoys... INFO: [17/03/2023 00:07:08] -> Extracting Ion Currents... INFO: [17/03/2023 00:07:38] -> Releasing Raw Files... INFO: [17/03/2023 00:07:38] -> Machine Learning... INFO: [17/03/2023 00:07:58] -> Initializing HTRMS... INFO: [17/03/2023 00:07:58] -> Releasing Run Resources... INFO: [17/03/2023 00:08:00] -> Calculating Qvalues... INFO: [17/03/2023 00:08:00] -> Unique precursors: 60,371 of 64,467 | modified peptides: 53,861 of 57,135 | peptides: 47,632 of 50,479 | protein groups: 5,234 (Qvalue <= 0.01) [H510_Dox_total_200ng_01.htrms] INFO: [17/03/2023 00:08:00] -> Collapsing Search Tree... INFO: [17/03/2023 00:08:00] -> Processed in 52.09s INFO: [17/03/2023 00:08:00] -> Initializing QC... INFO: [17/03/2023 00:08:00] -> Determining Calibration Parameter... INFO: [17/03/2023 00:08:00] -> Assigning ML Features... INFO: [17/03/2023 00:08:00] -> Generating Decoys... INFO: [17/03/2023 00:08:00] -> Extracting Ion Currents... INFO: [17/03/2023 00:08:30] -> Releasing Raw Files... INFO: [17/03/2023 00:08:30] -> Machine Learning... INFO: [17/03/2023 00:08:52] -> Initializing HTRMS... INFO: [17/03/2023 00:08:52] -> Releasing Run Resources... INFO: [17/03/2023 00:08:54] -> Calculating Qvalues... INFO: [17/03/2023 00:08:54] -> Unique precursors: 60,328 of 64,467 | modified peptides: 53,736 of 57,135 | peptides: 47,525 of 50,479 | protein groups: 5,183 (Qvalue <= 0.01) [H510_Control_total_200ng_04.htrms] INFO: [17/03/2023 00:08:54] -> Collapsing Search Tree... INFO: [17/03/2023 00:08:54] -> Processed in 54.49s INFO: [17/03/2023 00:08:54] -> Initializing QC... INFO: [17/03/2023 00:08:55] -> Determining Calibration Parameter... INFO: [17/03/2023 00:08:55] -> Assigning ML Features... INFO: [17/03/2023 00:08:55] -> Generating Decoys... INFO: [17/03/2023 00:08:55] -> Extracting Ion Currents... INFO: [17/03/2023 00:09:25] -> Releasing Raw Files... INFO: [17/03/2023 00:09:25] -> Machine Learning... INFO: [17/03/2023 00:09:45] -> Initializing HTRMS... INFO: [17/03/2023 00:09:45] -> Releasing Run Resources... INFO: [17/03/2023 00:09:47] -> Calculating Qvalues... INFO: [17/03/2023 00:09:47] -> Unique precursors: 62,082 of 64,467 | modified peptides: 55,118 of 57,135 | peptides: 48,711 of 50,479 | protein groups: 5,239 (Qvalue <= 0.01) [H510_Control_total_200ng_03.htrms] INFO: [17/03/2023 00:09:47] -> Collapsing Search Tree... INFO: [17/03/2023 00:09:47] -> Processed in 52.62s INFO: [17/03/2023 00:09:47] -> Initializing QC... INFO: [17/03/2023 00:09:47] -> Determining Calibration Parameter... INFO: [17/03/2023 00:09:47] -> Assigning ML Features... INFO: [17/03/2023 00:09:47] -> Generating Decoys... INFO: [17/03/2023 00:09:47] -> Extracting Ion Currents... INFO: [17/03/2023 00:10:17] -> Releasing Raw Files... INFO: [17/03/2023 00:10:17] -> Machine Learning... INFO: [17/03/2023 00:10:39] -> Initializing HTRMS... INFO: [17/03/2023 00:10:39] -> Releasing Run Resources... INFO: [17/03/2023 00:10:41] -> Calculating Qvalues... INFO: [17/03/2023 00:10:41] -> Unique precursors: 58,377 of 64,467 | modified peptides: 52,228 of 57,135 | peptides: 46,225 of 50,479 | protein groups: 5,168 (Qvalue <= 0.01) [H510_Control_total_200ng_02.htrms] INFO: [17/03/2023 00:10:41] -> Collapsing Search Tree... INFO: [17/03/2023 00:10:41] -> Processed in 54.24s INFO: [17/03/2023 00:10:41] -> Initializing QC... INFO: [17/03/2023 00:10:41] -> Determining Calibration Parameter... INFO: [17/03/2023 00:10:41] -> Assigning ML Features... INFO: [17/03/2023 00:10:42] -> Generating Decoys... INFO: [17/03/2023 00:10:42] -> Extracting Ion Currents... INFO: [17/03/2023 00:11:12] -> Releasing Raw Files... INFO: [17/03/2023 00:11:12] -> Machine Learning... INFO: [17/03/2023 00:11:31] -> Initializing HTRMS... INFO: [17/03/2023 00:11:31] -> Releasing Run Resources... INFO: [17/03/2023 00:11:33] -> Calculating Qvalues... INFO: [17/03/2023 00:11:34] -> Unique precursors: 58,480 of 64,467 | modified peptides: 52,291 of 57,135 | peptides: 46,261 of 50,479 | protein groups: 5,171 (Qvalue <= 0.01) [H510_Control_total_200ng_01.htrms] INFO: [17/03/2023 00:11:34] -> Collapsing Search Tree... INFO: [17/03/2023 00:11:34] -> Processed in 52.47s INFO: [17/03/2023 00:11:34] -> Normalizing Cscores... INFO: [17/03/2023 00:11:34] -> Initializing Protein Groups... INFO: [17/03/2023 00:11:51] -> Correcting Interferences... INFO: [17/03/2023 00:12:16] -> Calculating Global CVs INFO: [17/03/2023 00:12:16] -> Calculating Precursor Quantities... INFO: [17/03/2023 00:12:16] -> Normalizing Quantification... INFO: [17/03/2023 00:12:16] -> Cross-run normalization disabled! INFO: [17/03/2023 00:12:16] -> Calculating Global CVs INFO: [17/03/2023 00:12:17] -> Calculating Condition CVs INFO: [17/03/2023 00:12:18] -> Excluding Library Duplicates... INFO: [17/03/2023 00:12:19] -> Calculating Global CVs INFO: [17/03/2023 00:12:19] -> Building Protein Groups... INFO: [17/03/2023 00:12:34] -> Calculating Run-Wise Protein Group FDR... INFO: [17/03/2023 00:12:36] -> Annotating Protein Single Hits... INFO: [17/03/2023 00:12:37] -> Calculating Global CVs INFO: [17/03/2023 00:12:38] -> Updating Identification Counts... INFO: [17/03/2023 00:12:39] -> Resetting existing imputation... INFO: [17/03/2023 00:12:39] -> Calculating Protein Quantities... INFO: [17/03/2023 00:12:40] -> Calculating Protein Quantities... INFO: [17/03/2023 00:12:40] -> Calculating MaxLFQ Protein Quantities... INFO: [17/03/2023 00:12:46] -> Collapsing PTM-Locations... INFO: [17/03/2023 00:12:46] -> Creating Protein Map... INFO: [17/03/2023 00:12:46] -> Compiling Run Summary Information... INFO: [17/03/2023 00:12:46] -> Running Post Analysis Processes... INFO: [17/03/2023 00:23:52] -> Saving Qc Data... INFO: [17/03/2023 00:23:56] -> Writing Summary Information... INFO: [17/03/2023 00:23:56] -> Unique precursors: 63,092 of 64,467 | modified peptides: 55,984 of 57,135 | peptides: 49,479 of 50,479 | protein groups: 5,079 (Qvalue <= 0.01) for run #1 "H510_Dox_total_200ng_04.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 62,215 of 64,467 | modified peptides: 55,214 of 57,135 | peptides: 48,820 of 50,479 | protein groups: 5,096 (Qvalue <= 0.01) for run #2 "H510_Dox_total_200ng_03.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 61,054 of 64,467 | modified peptides: 54,302 of 57,135 | peptides: 48,009 of 50,479 | protein groups: 5,072 (Qvalue <= 0.01) for run #3 "H510_Dox_total_200ng_02.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 60,196 of 64,467 | modified peptides: 53,686 of 57,135 | peptides: 47,458 of 50,479 | protein groups: 5,069 (Qvalue <= 0.01) for run #4 "H510_Dox_total_200ng_01.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 60,133 of 64,467 | modified peptides: 53,542 of 57,135 | peptides: 47,332 of 50,479 | protein groups: 4,997 (Qvalue <= 0.01) for run #5 "H510_Control_total_200ng_04.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 61,880 of 64,467 | modified peptides: 54,916 of 57,135 | peptides: 48,510 of 50,479 | protein groups: 5,052 (Qvalue <= 0.01) for run #6 "H510_Control_total_200ng_03.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 58,202 of 64,467 | modified peptides: 52,053 of 57,135 | peptides: 46,051 of 50,479 | protein groups: 5,004 (Qvalue <= 0.01) for run #7 "H510_Control_total_200ng_02.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 58,300 of 64,467 | modified peptides: 52,112 of 57,135 | peptides: 46,082 of 50,479 | protein groups: 4,996 (Qvalue <= 0.01) for run #8 "H510_Control_total_200ng_01.htrms" INFO: [17/03/2023 00:23:56] -> Unique precursors: 64,239 of 64,467 | modified peptides: 56,931 of 57,135 | peptides: 50,279 of 50,479 | protein groups: 5,116 (Qvalue <= 0.01) for whole experiment "278-Mirja_Total" INFO: [17/03/2023 00:23:56] -> Saving SNE File... INFO: [17/03/2023 00:23:56] -> Storing SNE File: D:\Proyectos\20230317_002356_278-Mirja_Total.sne INFO: [17/03/2023 00:23:56] -> Initializing Pipeline... INFO: [17/03/2023 00:23:56] -> Calculating Qvalues... INFO: [17/03/2023 00:23:56] -> Saving... INFO: [17/03/2023 00:24:12] -> Pipeline executed in 16.37s INFO: [17/03/2023 00:24:14] -> Pipeline executed in 1.63h [END-LOG]