Spectronaut 20.0.250602.92449
Computer Name: WD25-1003
User Domain Name: WD25-1003
User Name: pinson
Analysis Mode: UI
Analysis Type: directDIA
Analysis Date: 13-June-2025 12:00:40 UTC +02:00 


[BEGIN-SETTINGS]
Settings Used: BGS Factory Settings
   ├─ DIA Analysis\Calibration
   │  ├─ MZ Extraction Strategy:	Maximum Intensity
   │  ├─ Allow source specific iRT Calibration:	True
   │  ├─ Precision iRT:	True
   │  │  ├─ Exclude De-amidated Peptides:	True
   │  │  └─ iRT <-> RT Regression Type:	Local (Non-Linear) Regression
   │  ├─ MS1 Mass Tolerance Strategy:	System Default
   │  └─ MS2 Mass Tolerance Strategy:	System Default
   ├─ DIA Analysis\Identification
   │  ├─ Precursor Qvalue Cutoff:	0.01
   │  ├─ Precursor Qvalue Cutoff (Experiment):	0.01
   │  ├─ Precursor PEP Cutoff:	0.2
   │  ├─ Protein Qvalue Cutoff (Experiment):	0.01
   │  ├─ Protein Qvalue Cutoff (Run):	0.05
   │  ├─ Protein PEP Cutoff:	0.75
   │  ├─ Single Hit Definition:	By Stripped Sequence
   │  ├─ Single Hit Protein Rule:	Stratified Single Hit Protein FDR
   │  ├─ Run-Level Protein Scoring:	All Observations
   │  ├─ Exclude Duplicate Assays:	True
   │  ├─ Exclude Predicted Fragment Scores:	False
   │  ├─ Generate Decoys:	True
   │  │  ├─ Decoy Generation Method:	Mutated
   │  │  │  └─ Preferred Fragment Source:	NN Predicted Fragments
   │  │  └─ Decoy Limit Strategy:	Dynamic
   │  │     └─ Library Size Fraction:	0.1
   │  └─ Pvalue Estimator:	Kernel Density Estimator
   ├─ DIA Analysis\Pipeline Mode
   │  ├─ Export All XICs:	False
   │  ├─ Generate SNE File:	True
   │  │  └─ Store Ion traces in SNE:	True
   │  ├─ Post Analysis Reports:	
   │  │  ├─ Binned CVs:	False
   │  │  ├─ Binned Identification:	False
   │  │  ├─ CV Density Line Chart:	False
   │  │  ├─ CVs Below X Bar Chart:	False
   │  │  ├─ Data Completeness Bar Chart:	False
   │  │  ├─ Run Identifications Bar Chart:	False
   │  │  ├─ Scoring Histograms:	False
   │  │  └─ TIC Overlay:	False
   │  ├─ PTM Report Schema:	
   │  ├─ Report Schema:	BGS Factory Report (Normal)
   │  └─ Reporting Unit:	Across Experiment
   ├─ DIA Analysis\Post Analysis
   │  ├─ Differential Abundance Testing:	Unpaired t-test
   │  │  ├─ Assume Equal Variance:	False
   │  │  ├─ Group-Wise Testing Correction:	False
   │  │  ├─ Log2 Ratio Candidate Filter:	0.58
   │  │  └─ Confidence Candidate Filter:	Qvalue
   │  │     └─ Confidence:	0.05
   │  ├─ Differential Abundance Grouping:	Major Group (Quantification Settings)
   │  │  └─ Smallest Quantitative Unit:	Major Group (Quantification Settings)
   │  │     └─ Use All MS-Level Quantities:	False
   │  ├─ Calculate Explained TIC:	None
   │  ├─ Calculate Sample Correlation Matrix:	False
   │  ├─ Gene Ontology:	C:\Users\pinson\AppData\Roaming\Spectronaut\geneOntology\Ontologies\bgs_default_go-basic.obo
   │  └─ Hierarchical Clustering:	True
   │     ├─ Distance Metric:	Manhattan Distance
   │     ├─ Linkage Strategy:	Ward's Method
   │     ├─ Order Runs by Clustering:	True
   │     └─ Z-score Transformation:	False
   ├─ DIA Analysis\Protein Inference
   │  └─ Protein Inference Workflow:	Automatic
   │     └─ Inference Algorithm:	IDPicker
   ├─ DIA Analysis\PTM Workflow
   │  ├─ Input Normalization Strategy:	None
   │  └─ PTM Localization:	False
   ├─ DIA Analysis\Quantification
   │  ├─ Precursor Filtering:	Identified (Qvalue)
   │  │  ├─ Imputation Strategy:	None
   │  │  └─ Multi Channel Qvalue Filter:	Group Qvalue
   │  ├─ Proteotypicity Filter:	None
   │  ├─ Protein LFQ Method:	Automatic
   │  ├─ Quantity MS Level:	MS2
   │  ├─ Quantity Type:	Area
   │  ├─ Cross-Run Normalization:	True
   │  │  ├─ Normalization Filter Type:	None
   │  │  ├─ Normalization Strategy:	Automatic
   │  │  └─ Row Selection:	Automatic
   │  ├─ Perform background noise removal:	True
   │  ├─ Quantification window:	Synchronized
   │  ├─ Interference Correction:	True
   │  │  ├─ Only Identified Peptides:	True
   │  │  ├─ Exclude All Multi-Channel Interferences:	True
   │  │  ├─ MS1 Min:	2
   │  │  └─ MS2 Min:	3
   │  ├─ Major Group Quantity:	Mean peptide quantity
   │  ├─ Minor (Peptide) Grouping:	by Stripped Sequence
   │  ├─ Major (Protein) Grouping:	by Protein Group Id
   │  ├─ Major Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Minor Group Quantity:	Mean precursor quantity
   │  ├─ Minor Group Top N:	True
   │  │  ├─ Max:	3
   │  │  └─ Min:	1
   │  ├─ Use Log2 Quantity Filter:	True
   │  │  └─ Minimum Log2 Precursor Quantity:	0
   │  └─ Perform IM Peak Picking for Quantification:	True
   ├─ DIA Analysis\Workflow
   │  ├─ Method Evaluation:	False
   │  ├─ MS2 DeMultiplexing:	Automatic
   │  ├─ Multi-Channel Workflow Definition:	From Library Annotation
   │  │  └─ Fallback Option:	Labeled
   │  ├─ Profiling Strategy:	None
   │  ├─ Run Limit for directDIA Library:	-1
   │  ├─ Hybrid (DDA + DIA) Library:	False
   │  └─ Unify Peptide Peaks Strategy:	None
   ├─ DIA Analysis\XIC Extraction
   │  ├─ XIC IM Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ XIC RT Extraction Window:	Dynamic
   │  │  └─ Correction Factor:	1
   │  ├─ MS1 Mass Tolerance Strategy:	Dynamic
   │  │  └─ Correction Factor:	1
   │  └─ MS2 Mass Tolerance Strategy:	Dynamic
   │     └─ Correction Factor:	1
   ├─ Pulsar Search\Identification
   │  ├─ PSM FDR:	0.01
   │  ├─ Peptide FDR:	0.01
   │  ├─ Protein Group FDR:	0.01
   │  ├─ directDIA Workflow:	directDIA+ (Deep)
   │  └─ PTM Localization Filter:	False
   ├─ Pulsar Search\iRT Calibration
   │  ├─ Calibrate from Empirical RT:	False
   │  ├─ Auto-assign iRT source:	True
   │  ├─ iRT Reference Strategy:	Deep Learning Assisted iRT Regression
   │  ├─ Use Source Specific iRT:	Auto
   │  └─ Minimum Rsquare:	0.8
   ├─ Pulsar Search\Labeling
   │  └─ Channels:	
   │     ├─ Channel 1:	False
   │     ├─ Channel 2:	False
   │     ├─ Channel 3:	False
   │     ├─ Channel 4:	False
   │     └─ Channel 5:	False
   ├─ Pulsar Search\Modifications
   │  └─ Search Mode:	Closed Search
   │     ├─ Max Variable Modifications:	1
   │     ├─ Fixed Modifications::	Carbamidomethyl (C)
   │     └─ Variable Modifications::	Acetyl (Protein N-term), Oxidation (M)
   ├─ Pulsar Search\Peptides
   │  ├─ Enzymes / Cleavage Rules:	Trypsin/P
   │  ├─ Digest Type:	Specific
   │  ├─ Decoy Generation Rule:	KR
   │  ├─ Max Peptide Length:	52
   │  ├─ Min Peptide Length:	6
   │  ├─ 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:	2000
   │  │  │  └─ Min:	50
   │  │  ├─ Overlapping between Channels:	False
   │  │  └─ Relative Intensity:	True
   │  │     └─ Min:	1
   │  └─ Precursors:	
   │     ├─ Amino Acids:	False
   │     ├─ Best N Fragments per Peptide:	True
   │     │  ├─ Max:	6
   │     │  └─ Min:	3
   │     ├─ Best N Peptides per Protein Group:	False
   │     ├─ Channel Count:	False
   │     ├─ FASTA Matched:	False
   │     ├─ Missed Cleavage:	False
   │     ├─ Modifications:	None
   │     ├─ Peptide Charge:	False
   │     └─ Proteotypicity:	False
   ├─ Pulsar Search\Speed-Up
   │  ├─ MS2 Index:	Automatic
   │  └─ diaPASEF Pre-Processing:	Automatic
   ├─ Pulsar Search\Tolerances
   │  └─ Tolerance Parameters:	
   │     ├─ Thermo IonTrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     ├─ Thermo Orbitrap:	
   │     │  ├─ Calibration Search:	Dynamic
   │     │  │  ├─ MS1 Correction Factor:	1
   │     │  │  └─ MS2 Correction Factor:	1
   │     │  └─ Main Search:	Dynamic
   │     │     ├─ MS1 Correction Factor:	1
   │     │     └─ MS2 Correction Factor:	1
   │     └─ TOF:	
   │        ├─ Calibration Search:	Dynamic
   │        │  ├─ MS1 Correction Factor:	1
   │        │  └─ MS2 Correction Factor:	1
   │        └─ Main Search:	Dynamic
   │           ├─ MS1 Correction Factor:	1
   │           └─ MS2 Correction Factor:	1
   └─ Pulsar Search\Workflow
      ├─ Fragment Ion Selection Strategy:	Intensity Based
      ├─ In-Silico Generate Missing Channels:	False
      └─ Use DNN Predicted Ion Mobility:	Auto
[END-SETTINGS]

[BEGIN-SETUP]
Run: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01
   ├─ Path: "F:\Spectronaut\Proteobench\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw"
   ├─ Condition: A
   ├─ Replicate: 1
   ├─ HTRMS Version: 20.0.250602.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 13-June-2025 09:44:51 UTC +02:00 
   │     ├─ Date Modified: 13-June-2025 11:43:07 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02
   ├─ Path: "F:\Spectronaut\Proteobench\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw"
   ├─ Condition: A
   ├─ Replicate: 2
   ├─ HTRMS Version: 20.0.250602.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 13-June-2025 09:44:51 UTC +02:00 
   │     ├─ Date Modified: 13-June-2025 11:43:07 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03
   ├─ Path: "F:\Spectronaut\Proteobench\LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw"
   ├─ Condition: A
   ├─ Replicate: 3
   ├─ HTRMS Version: 20.0.250602.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 13-June-2025 09:44:51 UTC +02:00 
   │     ├─ Date Modified: 13-June-2025 11:43:07 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01
   ├─ Path: "F:\Spectronaut\Proteobench\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw"
   ├─ Condition: B
   ├─ Replicate: 1
   ├─ HTRMS Version: 20.0.250602.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 13-June-2025 09:44:51 UTC +02:00 
   │     ├─ Date Modified: 13-June-2025 11:43:07 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02
   ├─ Path: "F:\Spectronaut\Proteobench\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw"
   ├─ Condition: B
   ├─ Replicate: 2
   ├─ HTRMS Version: 20.0.250602.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 13-June-2025 09:44:51 UTC +02:00 
   │     ├─ Date Modified: 13-June-2025 11:43:07 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

Run: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw
   ├─ Vendor: Thermo
   ├─ File: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03
   ├─ Path: "F:\Spectronaut\Proteobench\LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw"
   ├─ Condition: B
   ├─ Replicate: 3
   ├─ HTRMS Version: 20.0.250602.92449
   ├─ Protein Databases Used
   │  └─ ProteoBenchFASTA_MixedSpecies_HYE
   │     ├─ Protein Entries: 31,889
   │     ├─ Original File: ProteoBenchFASTA_MixedSpecies_HYE.fasta
   │     ├─ Date Created: 13-June-2025 09:44:51 UTC +02:00 
   │     ├─ Date Modified: 13-June-2025 11:43:07 UTC +02:00 
   │     └─ Parsing Rule: UniProt FASTA
   └─ MS2 Method
      ├─ [396.4 - 400.4]
      ├─ [400.4 - 404.4]
      ├─ [404.4 - 408.4]
      ├─ [408.4 - 412.4]
      ├─ [412.4 - 416.4]
      ├─ [416.4 - 420.4]
      ├─ [420.4 - 424.4]
      ├─ [424.4 - 428.4]
      ├─ [428.4 - 432.4]
      ├─ [432.4 - 436.4]
      ├─ [436.5 - 440.4]
      ├─ [440.5 - 444.5]
      ├─ [444.5 - 448.5]
      ├─ [448.5 - 452.5]
      ├─ [452.5 - 456.5]
      ├─ [456.5 - 460.5]
      ├─ [460.5 - 464.5]
      ├─ [464.5 - 468.5]
      ├─ [468.5 - 472.5]
      ├─ [472.5 - 476.5]
      ├─ [476.5 - 480.5]
      ├─ [480.5 - 484.5]
      ├─ [484.5 - 488.5]
      ├─ [488.5 - 492.5]
      ├─ [492.5 - 496.5]
      ├─ [496.5 - 500.5]
      ├─ [500.5 - 504.5]
      ├─ [504.5 - 508.5]
      ├─ [508.5 - 512.5]
      ├─ [512.5 - 516.5]
      ├─ [516.5 - 520.5]
      ├─ [520.5 - 524.5]
      ├─ [524.5 - 528.5]
      ├─ [528.5 - 532.5]
      ├─ [532.5 - 536.5]
      ├─ [536.5 - 540.5]
      ├─ [540.5 - 544.5]
      ├─ [544.5 - 548.5]
      ├─ [548.5 - 552.5]
      ├─ [552.5 - 556.5]
      ├─ [556.5 - 560.5]
      ├─ [560.5 - 564.5]
      ├─ [564.5 - 568.5]
      ├─ [568.5 - 572.5]
      ├─ [572.5 - 576.5]
      ├─ [576.5 - 580.5]
      ├─ [580.5 - 584.5]
      ├─ [584.5 - 588.5]
      ├─ [588.5 - 592.5]
      ├─ [592.5 - 596.5]
      ├─ [596.5 - 600.5]
      ├─ [600.5 - 604.5]
      ├─ [604.5 - 608.5]
      ├─ [608.5 - 612.5]
      ├─ [612.5 - 616.5]
      ├─ [616.5 - 620.5]
      ├─ [620.5 - 624.5]
      ├─ [624.5 - 628.5]
      ├─ [628.5 - 632.5]
      ├─ [632.5 - 636.5]
      ├─ [636.5 - 640.5]
      ├─ [640.5 - 644.5]
      ├─ [644.5 - 648.5]
      ├─ [648.5 - 652.5]
      ├─ [652.5 - 656.5]
      ├─ [656.6 - 660.5]
      ├─ [660.6 - 664.6]
      ├─ [664.6 - 668.6]
      ├─ [668.6 - 672.6]
      ├─ [672.6 - 676.6]
      ├─ [676.6 - 680.6]
      ├─ [680.6 - 684.6]
      ├─ [684.6 - 688.6]
      ├─ [688.6 - 692.6]
      ├─ [692.6 - 696.6]
      ├─ [696.6 - 700.6]
      ├─ [700.6 - 704.6]
      ├─ [704.6 - 708.6]
      ├─ [708.6 - 712.6]
      ├─ [712.6 - 716.6]
      ├─ [716.6 - 720.6]
      ├─ [720.6 - 724.6]
      ├─ [724.6 - 728.6]
      ├─ [728.6 - 732.6]
      ├─ [732.6 - 736.6]
      ├─ [736.6 - 740.6]
      ├─ [740.6 - 744.6]
      ├─ [744.6 - 748.6]
      ├─ [748.6 - 752.6]
      ├─ [752.6 - 756.6]
      ├─ [756.6 - 760.6]
      ├─ [760.6 - 764.6]
      ├─ [764.6 - 768.6]
      ├─ [768.6 - 772.6]
      ├─ [772.6 - 776.6]
      ├─ [776.6 - 780.6]
      ├─ [780.6 - 784.6]
      ├─ [784.6 - 788.6]
      ├─ [788.6 - 792.6]
      ├─ [792.6 - 796.6]
      ├─ [796.6 - 800.6]
      ├─ [800.6 - 804.6]
      ├─ [804.6 - 808.6]
      ├─ [808.6 - 812.6]
      ├─ [812.6 - 816.6]
      ├─ [816.6 - 820.6]
      ├─ [820.6 - 824.6]
      ├─ [824.6 - 828.6]
      ├─ [828.6 - 832.6]
      ├─ [832.6 - 836.6]
      ├─ [836.6 - 840.6]
      ├─ [840.6 - 844.6]
      ├─ [844.6 - 848.6]
      ├─ [848.6 - 852.6]
      ├─ [852.6 - 856.6]
      ├─ [856.6 - 860.6]
      ├─ [860.6 - 864.6]
      ├─ [864.6 - 868.6]
      ├─ [868.6 - 872.6]
      ├─ [872.6 - 876.6]
      ├─ [876.7 - 880.6]
      ├─ [880.7 - 884.7]
      ├─ [884.7 - 888.7]
      ├─ [888.7 - 892.7]
      ├─ [892.7 - 896.7]
      ├─ [896.7 - 900.7]
      ├─ [900.7 - 904.7]
      ├─ [904.7 - 908.7]
      ├─ [908.7 - 912.7]
      ├─ [912.7 - 916.7]
      ├─ [916.7 - 920.7]
      ├─ [920.7 - 924.7]
      ├─ [924.7 - 928.7]
      ├─ [928.7 - 932.7]
      ├─ [932.7 - 936.7]
      ├─ [936.7 - 940.7]
      ├─ [940.7 - 944.7]
      ├─ [944.7 - 948.7]
      ├─ [948.7 - 952.7]
      ├─ [952.7 - 956.7]
      ├─ [956.7 - 960.7]
      ├─ [960.7 - 964.7]
      ├─ [964.7 - 968.7]
      ├─ [968.7 - 972.7]
      ├─ [972.7 - 976.7]
      ├─ [976.7 - 980.7]
      ├─ [980.7 - 984.7]
      ├─ [984.7 - 988.7]
      ├─ [988.7 - 992.7]
      ├─ [992.7 - 996.7]
      ├─ [996.7 - 1000.7]
      └─ [1000.7 - 1004.7]

[END-SETUP]

[BEGIN-LOG]
INFO:    [13/06/2025 09:58:03] -> Initializing Pipeline...
INFO:    [13/06/2025 09:58:03] -> Preprocessing Run #1 of 6...
INFO:    [13/06/2025 09:58:05] -> Searching DIA with Pulsar...
INFO:    [13/06/2025 09:58:06] -> Initialize Pipeline...
INFO:    [13/06/2025 09:58:06] -> Initialize Pipeline
INFO:    [13/06/2025 09:58:17] -> Initialize Pipeline...
INFO:    [13/06/2025 09:58:17] -> Creating Experiment Environment
INFO:    [13/06/2025 09:58:17] -> SuperRun 1/6: Initializing (LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw)
INFO:    [13/06/2025 09:58:17] -> Run 1/6: Organizing Data from Run
INFO:    [13/06/2025 09:58:17] -> Run 1/6: Creating Calibration Search Space...
INFO:    [13/06/2025 09:58:20] -> Collecting Search Space Parameters...
INFO:    [13/06/2025 09:58:24] -> Creating the Search Space...
INFO:    [13/06/2025 09:58:24] -> Run 1/6: Creating Search Space...
INFO:    [13/06/2025 09:58:24] -> Collecting Search Space Parameters...
INFO:    [13/06/2025 09:58:47] -> Creating the Search Space...
INFO:    [13/06/2025 09:58:47] -> Size of search space [MB]: 0
INFO:    [13/06/2025 09:58:47] -> Number of IMPGs in search space: 0
INFO:    [13/06/2025 09:58:47] -> Run 1/6: MS2 Index Generation
INFO:    [13/06/2025 10:00:31] -> MS2 Index Generation Time: 1.74m
INFO:    [13/06/2025 10:00:31] -> Run 1/6: Method-Specific Pre-Processing...
INFO:    [13/06/2025 10:00:33] -> Initializing...
INFO:    [13/06/2025 10:00:57] -> Finalizing HTRMS File...
INFO:    [13/06/2025 10:01:43] -> Processed in 1.2m
INFO:    [13/06/2025 10:01:43] -> Done
INFO:    [13/06/2025 10:01:43] -> Run 1/6: Process Raw File...
INFO:    [13/06/2025 10:01:56] -> Run 1/6: Preparing Partitions...
INFO:    [13/06/2025 10:01:56] -> Part 1/1 - Run 1/6: Preparing Calibration Searches...
INFO:    [13/06/2025 10:01:59] -> Part 1/1 - Run 1/6: First Pass Calibration Search...
INFO:    [13/06/2025 10:02:04] -> Part 1/1 - Run 1/6: Calibration Search...
INFO:    [13/06/2025 10:02:11] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5275 [7.3s]
INFO:    [13/06/2025 10:02:19] -> Part 1/1 - Run 1/6: Preparing Main Search...
INFO:    [13/06/2025 10:02:21] -> Part 1/1 - Run 1/6: Main Search...
INFO:    [13/06/2025 10:04:43] -> Extracting 163420 MS1 XICs
INFO:    [13/06/2025 10:05:42] -> Run 1/6: Cleaning Up Run...
INFO:    [13/06/2025 10:05:42] -> SuperRun 2/6: Initializing (LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw)
INFO:    [13/06/2025 10:05:42] -> Run 2/6: Organizing Data from Run
INFO:    [13/06/2025 10:05:42] -> Run 2/6: Creating Calibration Search Space...
INFO:    [13/06/2025 10:05:42] -> Run 2/6: Creating Search Space...
INFO:    [13/06/2025 10:05:42] -> Size of search space [MB]: 0
INFO:    [13/06/2025 10:05:42] -> Number of IMPGs in search space: 0
INFO:    [13/06/2025 10:05:42] -> Run 2/6: MS2 Index Generation
INFO:    [13/06/2025 10:05:44] -> MS2 Index Generation Time: 2.11s
INFO:    [13/06/2025 10:05:44] -> Run 2/6: Method-Specific Pre-Processing...
INFO:    [13/06/2025 10:05:46] -> Initializing...
INFO:    [13/06/2025 10:06:05] -> Finalizing HTRMS File...
INFO:    [13/06/2025 10:06:51] -> Processed in 1.1m
INFO:    [13/06/2025 10:06:52] -> Done
INFO:    [13/06/2025 10:06:52] -> Run 2/6: Process Raw File...
INFO:    [13/06/2025 10:07:05] -> Run 2/6: Preparing Partitions...
INFO:    [13/06/2025 10:07:05] -> Part 1/1 - Run 2/6: Preparing Calibration Searches...
INFO:    [13/06/2025 10:07:07] -> Part 1/1 - Run 2/6: First Pass Calibration Search...
INFO:    [13/06/2025 10:07:12] -> Part 1/1 - Run 2/6: Calibration Search...
INFO:    [13/06/2025 10:07:19] -> The number of PSMs identified during calibration with FDR <= 0.01 is 5017 [7.3s]
INFO:    [13/06/2025 10:07:26] -> Part 1/1 - Run 2/6: Preparing Main Search...
INFO:    [13/06/2025 10:07:29] -> Part 1/1 - Run 2/6: Main Search...
INFO:    [13/06/2025 10:10:01] -> Extracting 156412 MS1 XICs
INFO:    [13/06/2025 10:10:55] -> Run 2/6: Cleaning Up Run...
INFO:    [13/06/2025 10:10:55] -> SuperRun 3/6: Initializing (LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw)
INFO:    [13/06/2025 10:10:55] -> Run 3/6: Organizing Data from Run
INFO:    [13/06/2025 10:10:55] -> Run 3/6: Creating Calibration Search Space...
INFO:    [13/06/2025 10:10:55] -> Run 3/6: Creating Search Space...
INFO:    [13/06/2025 10:10:55] -> Size of search space [MB]: 0
INFO:    [13/06/2025 10:10:55] -> Number of IMPGs in search space: 0
INFO:    [13/06/2025 10:10:55] -> Run 3/6: MS2 Index Generation
INFO:    [13/06/2025 10:10:57] -> MS2 Index Generation Time: 1.86s
INFO:    [13/06/2025 10:10:57] -> Run 3/6: Method-Specific Pre-Processing...
INFO:    [13/06/2025 10:10:58] -> Initializing...
INFO:    [13/06/2025 10:11:19] -> Finalizing HTRMS File...
INFO:    [13/06/2025 10:12:04] -> Processed in 1.1m
INFO:    [13/06/2025 10:12:04] -> Done
INFO:    [13/06/2025 10:12:04] -> Run 3/6: Process Raw File...
INFO:    [13/06/2025 10:12:16] -> Run 3/6: Preparing Partitions...
INFO:    [13/06/2025 10:12:16] -> Part 1/1 - Run 3/6: Preparing Calibration Searches...
INFO:    [13/06/2025 10:12:18] -> Part 1/1 - Run 3/6: First Pass Calibration Search...
INFO:    [13/06/2025 10:12:23] -> Part 1/1 - Run 3/6: Calibration Search...
INFO:    [13/06/2025 10:12:29] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4944 [6.1s]
INFO:    [13/06/2025 10:12:37] -> Part 1/1 - Run 3/6: Preparing Main Search...
INFO:    [13/06/2025 10:12:39] -> Part 1/1 - Run 3/6: Main Search...
INFO:    [13/06/2025 10:15:03] -> Extracting 160109 MS1 XICs
INFO:    [13/06/2025 10:15:59] -> Run 3/6: Cleaning Up Run...
INFO:    [13/06/2025 10:15:59] -> SuperRun 4/6: Initializing (LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw)
INFO:    [13/06/2025 10:15:59] -> Run 4/6: Organizing Data from Run
INFO:    [13/06/2025 10:15:59] -> Run 4/6: Creating Calibration Search Space...
INFO:    [13/06/2025 10:16:00] -> Run 4/6: Creating Search Space...
INFO:    [13/06/2025 10:16:00] -> Size of search space [MB]: 0
INFO:    [13/06/2025 10:16:00] -> Number of IMPGs in search space: 0
INFO:    [13/06/2025 10:16:00] -> Run 4/6: MS2 Index Generation
INFO:    [13/06/2025 10:16:02] -> MS2 Index Generation Time: 2.03s
INFO:    [13/06/2025 10:16:02] -> Run 4/6: Method-Specific Pre-Processing...
INFO:    [13/06/2025 10:16:03] -> Initializing...
INFO:    [13/06/2025 10:16:23] -> Finalizing HTRMS File...
INFO:    [13/06/2025 10:17:06] -> Processed in 1m
INFO:    [13/06/2025 10:17:06] -> Done
INFO:    [13/06/2025 10:17:06] -> Run 4/6: Process Raw File...
INFO:    [13/06/2025 10:17:19] -> Run 4/6: Preparing Partitions...
INFO:    [13/06/2025 10:17:19] -> Part 1/1 - Run 4/6: Preparing Calibration Searches...
INFO:    [13/06/2025 10:17:21] -> Part 1/1 - Run 4/6: First Pass Calibration Search...
INFO:    [13/06/2025 10:17:26] -> Part 1/1 - Run 4/6: Calibration Search...
INFO:    [13/06/2025 10:17:31] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4416 [5.8s]
INFO:    [13/06/2025 10:17:38] -> Part 1/1 - Run 4/6: Preparing Main Search...
INFO:    [13/06/2025 10:17:40] -> Part 1/1 - Run 4/6: Main Search...
INFO:    [13/06/2025 10:19:50] -> Extracting 162614 MS1 XICs
INFO:    [13/06/2025 10:20:46] -> Run 4/6: Cleaning Up Run...
INFO:    [13/06/2025 10:20:46] -> SuperRun 5/6: Initializing (LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw)
INFO:    [13/06/2025 10:20:46] -> Run 5/6: Organizing Data from Run
INFO:    [13/06/2025 10:20:46] -> Run 5/6: Creating Calibration Search Space...
INFO:    [13/06/2025 10:20:46] -> Run 5/6: Creating Search Space...
INFO:    [13/06/2025 10:20:46] -> Size of search space [MB]: 0
INFO:    [13/06/2025 10:20:46] -> Number of IMPGs in search space: 0
INFO:    [13/06/2025 10:20:46] -> Run 5/6: MS2 Index Generation
INFO:    [13/06/2025 10:20:48] -> MS2 Index Generation Time: 1.98s
INFO:    [13/06/2025 10:20:48] -> Run 5/6: Method-Specific Pre-Processing...
INFO:    [13/06/2025 10:20:50] -> Initializing...
INFO:    [13/06/2025 10:21:09] -> Finalizing HTRMS File...
INFO:    [13/06/2025 10:21:57] -> Processed in 1.1m
INFO:    [13/06/2025 10:21:57] -> Done
INFO:    [13/06/2025 10:21:57] -> Run 5/6: Process Raw File...
INFO:    [13/06/2025 10:22:09] -> Run 5/6: Preparing Partitions...
INFO:    [13/06/2025 10:22:09] -> Part 1/1 - Run 5/6: Preparing Calibration Searches...
INFO:    [13/06/2025 10:22:12] -> Part 1/1 - Run 5/6: First Pass Calibration Search...
INFO:    [13/06/2025 10:22:16] -> Part 1/1 - Run 5/6: Calibration Search...
INFO:    [13/06/2025 10:22:23] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4089 [7.5s]
INFO:    [13/06/2025 10:22:29] -> Part 1/1 - Run 5/6: Preparing Main Search...
INFO:    [13/06/2025 10:22:32] -> Part 1/1 - Run 5/6: Main Search...
INFO:    [13/06/2025 10:24:48] -> Extracting 153061 MS1 XICs
INFO:    [13/06/2025 10:25:40] -> Run 5/6: Cleaning Up Run...
INFO:    [13/06/2025 10:25:40] -> SuperRun 6/6: Initializing (LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw)
INFO:    [13/06/2025 10:25:40] -> Run 6/6: Organizing Data from Run
INFO:    [13/06/2025 10:25:40] -> Run 6/6: Creating Calibration Search Space...
INFO:    [13/06/2025 10:25:40] -> Run 6/6: Creating Search Space...
INFO:    [13/06/2025 10:25:40] -> Size of search space [MB]: 0
INFO:    [13/06/2025 10:25:40] -> Number of IMPGs in search space: 0
INFO:    [13/06/2025 10:25:40] -> Run 6/6: MS2 Index Generation
INFO:    [13/06/2025 10:25:42] -> MS2 Index Generation Time: 1.95s
INFO:    [13/06/2025 10:25:42] -> Run 6/6: Method-Specific Pre-Processing...
INFO:    [13/06/2025 10:25:43] -> Initializing...
INFO:    [13/06/2025 10:26:01] -> Finalizing HTRMS File...
INFO:    [13/06/2025 10:26:41] -> Processed in 57.7s
INFO:    [13/06/2025 10:26:41] -> Done
INFO:    [13/06/2025 10:26:41] -> Run 6/6: Process Raw File...
INFO:    [13/06/2025 10:26:53] -> Run 6/6: Preparing Partitions...
INFO:    [13/06/2025 10:26:53] -> Part 1/1 - Run 6/6: Preparing Calibration Searches...
INFO:    [13/06/2025 10:26:55] -> Part 1/1 - Run 6/6: First Pass Calibration Search...
INFO:    [13/06/2025 10:27:00] -> Part 1/1 - Run 6/6: Calibration Search...
INFO:    [13/06/2025 10:27:06] -> The number of PSMs identified during calibration with FDR <= 0.01 is 4072 [6.1s]
INFO:    [13/06/2025 10:27:13] -> Part 1/1 - Run 6/6: Preparing Main Search...
INFO:    [13/06/2025 10:27:15] -> Part 1/1 - Run 6/6: Main Search...
INFO:    [13/06/2025 10:29:35] -> Extracting 159317 MS1 XICs
INFO:    [13/06/2025 10:30:29] -> Run 6/6: Cleaning Up Run...
INFO:    [13/06/2025 10:30:35] -> Remove Aborted Runs (if any) from the Experiment...
INFO:    [13/06/2025 10:30:35] -> Score Post-Processing
INFO:    [13/06/2025 10:32:04] -> Score Post-Processing: 1.49m
INFO:    [13/06/2025 10:32:04] -> PSM FDR...
INFO:    [13/06/2025 10:32:34] -> PSM FDR: 29.34s
INFO:    [13/06/2025 10:32:34] -> Converting to non-redundant data structure...
INFO:    [13/06/2025 10:32:53] -> Performing Peptide FDR...
INFO:    [13/06/2025 10:32:58] -> Performing Protein Inference...
INFO:    [13/06/2025 10:33:00] -> Performing Protein FDR...
INFO:    [13/06/2025 10:33:01] -> Calculating Result Values at Run and Experiment Level...
INFO:    [13/06/2025 10:33:10] -> Pulsar identified 221052 PSMs, 50832 stripped sequences, 62230 peptide precursors, 6692 protein groups.
INFO:    [13/06/2025 10:33:10] -> Calculating Summary...
INFO:    [13/06/2025 10:33:15] -> Identifying Calibration Peptides...
INFO:    [13/06/2025 10:33:17] -> iRT Calibration...
INFO:    [13/06/2025 10:33:23] -> Performing directDIA+ search...
INFO:    [13/06/2025 10:34:57] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw
INFO:    [13/06/2025 10:39:55] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw
INFO:    [13/06/2025 10:42:24] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw
INFO:    [13/06/2025 10:44:32] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw
INFO:    [13/06/2025 10:46:34] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw
INFO:    [13/06/2025 10:48:50] -> directDIA+ search: LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw
INFO:    [13/06/2025 10:50:52] -> Total nr of Searched Peptides: 1,744,571 of 2,903,000
INFO:    [13/06/2025 10:50:52] -> Performing directDIA+ Post Processing...
INFO:    [13/06/2025 10:51:01] -> Writing experiment store..
INFO:    [13/06/2025 10:51:13] -> Assigning iRT Source...
INFO:    [13/06/2025 10:51:13] -> Calculating iRT...
INFO:    [13/06/2025 10:51:14] -> Cleaning Up Experiment...
INFO:    [13/06/2025 10:51:14] -> Summarizing Identifications
INFO:    [13/06/2025 10:53:16] -> Identifiying Significant Precursors...
INFO:    [13/06/2025 10:53:45] -> Predicting Ion Mobility
INFO:    [13/06/2025 10:54:04] -> Calculating Median iRT
INFO:    [13/06/2025 10:54:06] -> Building BGS Protein Grouping...
INFO:    [13/06/2025 10:54:06] -> Digesting Fasta...
INFO:    [13/06/2025 10:54:08] -> Annotating Proteins...
INFO:    [13/06/2025 10:54:08] -> Grouping Proteins...
INFO:    [13/06/2025 10:54:10] -> Calculating Run Summary Statistics...
INFO:    [13/06/2025 10:54:56] -> Building Consensus Fragment Spectra...
INFO:    [13/06/2025 10:56:09] -> Selecting best fragment ions
INFO:    [13/06/2025 11:01:17] -> Initializing Experiment...
INFO:    [13/06/2025 11:01:17] -> Loading Spectral Libraries...
INFO:    [13/06/2025 11:02:57] -> Initialize Scoring...
INFO:    [13/06/2025 11:02:57] -> Generating Scan Map...
INFO:    [13/06/2025 11:02:57] -> Initializing Workpackages...
INFO:    [13/06/2025 11:02:57] -> Performing Basic Calibration...
INFO:    [13/06/2025 11:03:02] -> Identifying Calibration Peptides...
INFO:    [13/06/2025 11:03:02] -> Correcting Gradient Fine Structure...
INFO:    [13/06/2025 11:03:11] -> Initializing Pipeline...
INFO:    [13/06/2025 11:03:11] -> Preprocessing Run #1 of 6...
INFO:    [13/06/2025 11:03:11] -> Initialize Scoring...
INFO:    [13/06/2025 11:03:11] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:03:40] -> Machine Learning...
INFO:    [13/06/2025 11:05:34] -> Pipeline executed in 2.39m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:05:44] -> Initializing Pipeline...
INFO:    [13/06/2025 11:05:44] -> Preprocessing Run #1 of 6...
INFO:    [13/06/2025 11:05:44] -> Initialize Scoring...
INFO:    [13/06/2025 11:05:44] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:06:18] -> Machine Learning...
INFO:    [13/06/2025 11:06:26] -> Pipeline executed in 41.9s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:06:39] -> Initialize Scoring...
INFO:    [13/06/2025 11:06:39] -> Preprocessing Run #2 of 6...
INFO:    [13/06/2025 11:06:39] -> Searching DIA with Pulsar...
INFO:    [13/06/2025 11:06:39] -> Initializing Experiment...
INFO:    [13/06/2025 11:06:39] -> Loading Spectral Libraries...
INFO:    [13/06/2025 11:06:39] -> Initialize Scoring...
INFO:    [13/06/2025 11:06:39] -> Generating Scan Map...
INFO:    [13/06/2025 11:06:39] -> Initializing Workpackages...
INFO:    [13/06/2025 11:06:39] -> Performing Basic Calibration...
INFO:    [13/06/2025 11:06:43] -> Identifying Calibration Peptides...
INFO:    [13/06/2025 11:06:43] -> Correcting Gradient Fine Structure...
INFO:    [13/06/2025 11:06:50] -> Initializing Pipeline...
INFO:    [13/06/2025 11:06:50] -> Preprocessing Run #2 of 6...
INFO:    [13/06/2025 11:06:50] -> Initialize Scoring...
INFO:    [13/06/2025 11:06:50] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:07:20] -> Machine Learning...
INFO:    [13/06/2025 11:09:14] -> Pipeline executed in 2.4m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:09:24] -> Initializing Pipeline...
INFO:    [13/06/2025 11:09:24] -> Preprocessing Run #2 of 6...
INFO:    [13/06/2025 11:09:24] -> Initialize Scoring...
INFO:    [13/06/2025 11:09:24] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:09:59] -> Machine Learning...
INFO:    [13/06/2025 11:10:07] -> Pipeline executed in 42.57s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:10:19] -> Initialize Scoring...
INFO:    [13/06/2025 11:10:19] -> Preprocessing Run #3 of 6...
INFO:    [13/06/2025 11:10:19] -> Searching DIA with Pulsar...
INFO:    [13/06/2025 11:10:19] -> Initializing Experiment...
INFO:    [13/06/2025 11:10:19] -> Loading Spectral Libraries...
INFO:    [13/06/2025 11:10:19] -> Initialize Scoring...
INFO:    [13/06/2025 11:10:19] -> Generating Scan Map...
INFO:    [13/06/2025 11:10:19] -> Initializing Workpackages...
INFO:    [13/06/2025 11:10:19] -> Performing Basic Calibration...
INFO:    [13/06/2025 11:10:23] -> Identifying Calibration Peptides...
INFO:    [13/06/2025 11:10:23] -> Correcting Gradient Fine Structure...
INFO:    [13/06/2025 11:10:30] -> Initializing Pipeline...
INFO:    [13/06/2025 11:10:30] -> Preprocessing Run #3 of 6...
INFO:    [13/06/2025 11:10:30] -> Initialize Scoring...
INFO:    [13/06/2025 11:10:30] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:10:59] -> Machine Learning...
INFO:    [13/06/2025 11:12:54] -> Pipeline executed in 2.39m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:13:04] -> Initializing Pipeline...
INFO:    [13/06/2025 11:13:04] -> Preprocessing Run #3 of 6...
INFO:    [13/06/2025 11:13:04] -> Initialize Scoring...
INFO:    [13/06/2025 11:13:04] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:13:39] -> Machine Learning...
INFO:    [13/06/2025 11:13:47] -> Pipeline executed in 43.83s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:14:00] -> Initialize Scoring...
INFO:    [13/06/2025 11:14:00] -> Preprocessing Run #4 of 6...
INFO:    [13/06/2025 11:14:00] -> Searching DIA with Pulsar...
INFO:    [13/06/2025 11:14:00] -> Initializing Experiment...
INFO:    [13/06/2025 11:14:00] -> Loading Spectral Libraries...
INFO:    [13/06/2025 11:14:00] -> Initialize Scoring...
INFO:    [13/06/2025 11:14:00] -> Generating Scan Map...
INFO:    [13/06/2025 11:14:00] -> Initializing Workpackages...
INFO:    [13/06/2025 11:14:00] -> Performing Basic Calibration...
INFO:    [13/06/2025 11:14:04] -> Identifying Calibration Peptides...
INFO:    [13/06/2025 11:14:04] -> Correcting Gradient Fine Structure...
INFO:    [13/06/2025 11:14:11] -> Initializing Pipeline...
INFO:    [13/06/2025 11:14:11] -> Preprocessing Run #4 of 6...
INFO:    [13/06/2025 11:14:11] -> Initialize Scoring...
INFO:    [13/06/2025 11:14:11] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:14:41] -> Machine Learning...
INFO:    [13/06/2025 11:16:35] -> Pipeline executed in 2.4m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:16:45] -> Initializing Pipeline...
INFO:    [13/06/2025 11:16:45] -> Preprocessing Run #4 of 6...
INFO:    [13/06/2025 11:16:45] -> Initialize Scoring...
INFO:    [13/06/2025 11:16:45] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:17:21] -> Machine Learning...
INFO:    [13/06/2025 11:17:29] -> Pipeline executed in 44.06s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:17:41] -> Initialize Scoring...
INFO:    [13/06/2025 11:17:41] -> Preprocessing Run #5 of 6...
INFO:    [13/06/2025 11:17:41] -> Searching DIA with Pulsar...
INFO:    [13/06/2025 11:17:41] -> Initializing Experiment...
INFO:    [13/06/2025 11:17:41] -> Loading Spectral Libraries...
INFO:    [13/06/2025 11:17:41] -> Initialize Scoring...
INFO:    [13/06/2025 11:17:41] -> Generating Scan Map...
INFO:    [13/06/2025 11:17:41] -> Initializing Workpackages...
INFO:    [13/06/2025 11:17:41] -> Performing Basic Calibration...
INFO:    [13/06/2025 11:17:45] -> Identifying Calibration Peptides...
INFO:    [13/06/2025 11:17:45] -> Correcting Gradient Fine Structure...
INFO:    [13/06/2025 11:17:52] -> Initializing Pipeline...
INFO:    [13/06/2025 11:17:52] -> Preprocessing Run #5 of 6...
INFO:    [13/06/2025 11:17:52] -> Initialize Scoring...
INFO:    [13/06/2025 11:17:52] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:18:21] -> Machine Learning...
INFO:    [13/06/2025 11:20:15] -> Pipeline executed in 2.39m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:20:25] -> Initializing Pipeline...
INFO:    [13/06/2025 11:20:25] -> Preprocessing Run #5 of 6...
INFO:    [13/06/2025 11:20:25] -> Initialize Scoring...
INFO:    [13/06/2025 11:20:25] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:21:02] -> Machine Learning...
INFO:    [13/06/2025 11:21:10] -> Pipeline executed in 44.84s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:21:21] -> Initialize Scoring...
INFO:    [13/06/2025 11:21:21] -> Preprocessing Run #6 of 6...
INFO:    [13/06/2025 11:21:21] -> Searching DIA with Pulsar...
INFO:    [13/06/2025 11:21:21] -> Initializing Experiment...
INFO:    [13/06/2025 11:21:21] -> Loading Spectral Libraries...
INFO:    [13/06/2025 11:21:21] -> Initialize Scoring...
INFO:    [13/06/2025 11:21:21] -> Generating Scan Map...
INFO:    [13/06/2025 11:21:21] -> Initializing Workpackages...
INFO:    [13/06/2025 11:21:21] -> Performing Basic Calibration...
INFO:    [13/06/2025 11:21:25] -> Identifying Calibration Peptides...
INFO:    [13/06/2025 11:21:25] -> Correcting Gradient Fine Structure...
INFO:    [13/06/2025 11:21:32] -> Initializing Pipeline...
INFO:    [13/06/2025 11:21:32] -> Preprocessing Run #6 of 6...
INFO:    [13/06/2025 11:21:32] -> Initialize Scoring...
INFO:    [13/06/2025 11:21:32] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:22:02] -> Machine Learning...
INFO:    [13/06/2025 11:23:56] -> Pipeline executed in 2.39m - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:24:05] -> Initializing Pipeline...
INFO:    [13/06/2025 11:24:05] -> Preprocessing Run #6 of 6...
INFO:    [13/06/2025 11:24:05] -> Initialize Scoring...
INFO:    [13/06/2025 11:24:05] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:24:41] -> Machine Learning...
INFO:    [13/06/2025 11:24:49] -> Pipeline executed in 43.97s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:25:01] -> Initialize Scoring...
INFO:    [13/06/2025 11:25:01] -> Initializing QC...
INFO:    [13/06/2025 11:25:01] -> Determining Calibration Parameter...
INFO:    [13/06/2025 11:25:02] -> Assigning ML Features...
INFO:    [13/06/2025 11:25:02] -> Generating Decoys...
INFO:    [13/06/2025 11:25:15] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:27:02] -> Releasing Raw Files...
INFO:    [13/06/2025 11:27:02] -> Machine Learning...
INFO:    [13/06/2025 11:27:43] -> Initializing HTRMS...
INFO:    [13/06/2025 11:27:43] -> Releasing Run Resources...
INFO:    [13/06/2025 11:27:44] -> Reducing Score Cache...
INFO:    [13/06/2025 11:27:49] -> Calculating Qvalues...
INFO:    [13/06/2025 11:27:51] -> Unique precursors: 99,303 of 108,514 | modified peptides: 87,476 of 94,618 | peptides: 79,809 of 85,641 |  protein groups: 8,750 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw]
INFO:    [13/06/2025 11:27:51] -> Collapsing Search Tree...
INFO:    [13/06/2025 11:27:51] -> Processed in 2.83m
INFO:    [13/06/2025 11:27:51] -> Initializing QC...
INFO:    [13/06/2025 11:27:51] -> Determining Calibration Parameter...
INFO:    [13/06/2025 11:27:51] -> Assigning ML Features...
INFO:    [13/06/2025 11:27:51] -> Generating Decoys...
INFO:    [13/06/2025 11:27:52] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:29:41] -> Releasing Raw Files...
INFO:    [13/06/2025 11:29:41] -> Machine Learning...
INFO:    [13/06/2025 11:30:21] -> Initializing HTRMS...
INFO:    [13/06/2025 11:30:21] -> Releasing Run Resources...
INFO:    [13/06/2025 11:30:22] -> Reducing Score Cache...
INFO:    [13/06/2025 11:30:26] -> Calculating Qvalues...
INFO:    [13/06/2025 11:30:28] -> Unique precursors: 101,120 of 108,514 | modified peptides: 88,386 of 94,618 | peptides: 80,587 of 85,641 |  protein groups: 8,775 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw]
INFO:    [13/06/2025 11:30:28] -> Collapsing Search Tree...
INFO:    [13/06/2025 11:30:28] -> Processed in 2.62m
INFO:    [13/06/2025 11:30:28] -> Initializing QC...
INFO:    [13/06/2025 11:30:28] -> Determining Calibration Parameter...
INFO:    [13/06/2025 11:30:29] -> Assigning ML Features...
INFO:    [13/06/2025 11:30:29] -> Generating Decoys...
INFO:    [13/06/2025 11:30:29] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:32:16] -> Releasing Raw Files...
INFO:    [13/06/2025 11:32:16] -> Machine Learning...
INFO:    [13/06/2025 11:32:57] -> Initializing HTRMS...
INFO:    [13/06/2025 11:32:57] -> Releasing Run Resources...
INFO:    [13/06/2025 11:32:57] -> Reducing Score Cache...
INFO:    [13/06/2025 11:33:02] -> Calculating Qvalues...
INFO:    [13/06/2025 11:33:04] -> Unique precursors: 95,855 of 108,514 | modified peptides: 84,652 of 94,618 | peptides: 77,432 of 85,641 |  protein groups: 8,636 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw]
INFO:    [13/06/2025 11:33:04] -> Collapsing Search Tree...
INFO:    [13/06/2025 11:33:04] -> Processed in 2.59m
INFO:    [13/06/2025 11:33:04] -> Initializing QC...
INFO:    [13/06/2025 11:33:04] -> Determining Calibration Parameter...
INFO:    [13/06/2025 11:33:04] -> Assigning ML Features...
INFO:    [13/06/2025 11:33:05] -> Generating Decoys...
INFO:    [13/06/2025 11:33:05] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:34:52] -> Releasing Raw Files...
INFO:    [13/06/2025 11:34:52] -> Machine Learning...
INFO:    [13/06/2025 11:35:33] -> Initializing HTRMS...
INFO:    [13/06/2025 11:35:33] -> Releasing Run Resources...
INFO:    [13/06/2025 11:35:34] -> Reducing Score Cache...
INFO:    [13/06/2025 11:35:38] -> Calculating Qvalues...
INFO:    [13/06/2025 11:35:40] -> Unique precursors: 83,740 of 108,514 | modified peptides: 73,588 of 94,618 | peptides: 72,185 of 85,641 |  protein groups: 8,539 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw]
INFO:    [13/06/2025 11:35:40] -> Collapsing Search Tree...
INFO:    [13/06/2025 11:35:40] -> Processed in 2.6m
INFO:    [13/06/2025 11:35:40] -> Initializing QC...
INFO:    [13/06/2025 11:35:40] -> Determining Calibration Parameter...
INFO:    [13/06/2025 11:35:41] -> Assigning ML Features...
INFO:    [13/06/2025 11:35:41] -> Generating Decoys...
INFO:    [13/06/2025 11:35:41] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:37:29] -> Releasing Raw Files...
INFO:    [13/06/2025 11:37:29] -> Machine Learning...
INFO:    [13/06/2025 11:38:11] -> Initializing HTRMS...
INFO:    [13/06/2025 11:38:11] -> Releasing Run Resources...
INFO:    [13/06/2025 11:38:12] -> Reducing Score Cache...
INFO:    [13/06/2025 11:38:16] -> Calculating Qvalues...
INFO:    [13/06/2025 11:38:19] -> Unique precursors: 86,746 of 108,514 | modified peptides: 75,587 of 94,618 | peptides: 73,036 of 85,641 |  protein groups: 8,587 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw]
INFO:    [13/06/2025 11:38:19] -> Collapsing Search Tree...
INFO:    [13/06/2025 11:38:19] -> Processed in 2.64m
INFO:    [13/06/2025 11:38:19] -> Initializing QC...
INFO:    [13/06/2025 11:38:19] -> Determining Calibration Parameter...
INFO:    [13/06/2025 11:38:19] -> Assigning ML Features...
INFO:    [13/06/2025 11:38:19] -> Generating Decoys...
INFO:    [13/06/2025 11:38:19] -> Extracting Ion Currents...
INFO:    [13/06/2025 11:40:05] -> Releasing Raw Files...
INFO:    [13/06/2025 11:40:05] -> Machine Learning...
INFO:    [13/06/2025 11:40:47] -> Initializing HTRMS...
INFO:    [13/06/2025 11:40:47] -> Releasing Run Resources...
INFO:    [13/06/2025 11:40:47] -> Reducing Score Cache...
INFO:    [13/06/2025 11:40:51] -> Calculating Qvalues...
INFO:    [13/06/2025 11:40:53] -> Unique precursors: 81,642 of 108,514 | modified peptides: 71,976 of 94,618 | peptides: 70,111 of 85,641 |  protein groups: 8,399 (Qvalue <= 0.01) [LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw]
INFO:    [13/06/2025 11:40:53] -> Collapsing Search Tree...
INFO:    [13/06/2025 11:40:53] -> Processed in 2.58m
INFO:    [13/06/2025 11:40:54] -> Normalizing Cscores...
INFO:    [13/06/2025 11:40:54] -> Calculating Global CVs
INFO:    [13/06/2025 11:40:55] -> Calculating Profile Qvalues...
INFO:    [13/06/2025 11:40:56] -> Initializing Protein Groups...
INFO:    [13/06/2025 11:41:12] -> Correcting Interferences...
INFO:    [13/06/2025 11:41:47] -> Calculating Global CVs
INFO:    [13/06/2025 11:41:48] -> Calculating Precursor Quantities...
INFO:    [13/06/2025 11:41:48] -> Normalizing Quantification...
INFO:    [13/06/2025 11:41:49] -> Performing Local Normalization...
INFO:    [13/06/2025 11:41:52] -> Calculating Global CVs
INFO:    [13/06/2025 11:41:53] -> Calculating Condition CVs
INFO:    [13/06/2025 11:41:56] -> Excluding Library Duplicates...
INFO:    [13/06/2025 11:41:57] -> Calculating Global CVs
INFO:    [13/06/2025 11:41:57] -> Building Protein Groups...
INFO:    [13/06/2025 11:42:10] -> Calculating Run-Wise Protein Group FDR...
INFO:    [13/06/2025 11:42:17] -> Annotating Protein Single Hits...
INFO:    [13/06/2025 11:42:18] -> Calculating Global CVs
INFO:    [13/06/2025 11:42:19] -> Updating Identification Counts...
INFO:    [13/06/2025 11:42:21] -> Subtracting background noise...
INFO:    [13/06/2025 11:42:21] -> Resetting existing imputation...
INFO:    [13/06/2025 11:42:23] -> Calculating Protein Quantities...
INFO:    [13/06/2025 11:42:24] -> Calculating Protein Quantities...
INFO:    [13/06/2025 11:42:24] -> Calculating MaxLFQ Protein Quantities...
INFO:    [13/06/2025 11:42:32] -> Collapsing PTM-Locations...
INFO:    [13/06/2025 11:42:32] -> PTM Stoichiometry calculation...
INFO:    [13/06/2025 11:42:32] -> Creating Protein Map...
INFO:    [13/06/2025 11:42:32] -> Compiling Run Summary Information...
INFO:    [13/06/2025 11:42:33] -> Running Post Analysis Processes...
INFO:    [13/06/2025 11:42:59] -> Saving Qc Data...
INFO:    [13/06/2025 11:43:07] -> Writing Summary Information...
INFO:    [13/06/2025 11:43:07] -> Unique precursors: 96,631 of 108,514 | modified peptides: 85,028 of 94,618 | peptides: 77,510 of 85,641 |  protein groups: 8,054 (Qvalue <= 0.01) for run #1 "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_01.raw"
INFO:    [13/06/2025 11:43:07] -> Unique precursors: 97,949 of 108,514 | modified peptides: 85,578 of 94,618 | peptides: 77,967 of 85,641 |  protein groups: 8,067 (Qvalue <= 0.01) for run #2 "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_02.raw"
INFO:    [13/06/2025 11:43:07] -> Unique precursors: 93,451 of 108,514 | modified peptides: 82,476 of 94,618 | peptides: 75,368 of 85,641 |  protein groups: 8,014 (Qvalue <= 0.01) for run #3 "LFQ_Orbitrap_AIF_Condition_A_Sample_Alpha_03.raw"
INFO:    [13/06/2025 11:43:07] -> Unique precursors: 81,799 of 108,514 | modified peptides: 71,797 of 94,618 | peptides: 70,413 of 85,641 |  protein groups: 7,996 (Qvalue <= 0.01) for run #4 "LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_01.raw"
INFO:    [13/06/2025 11:43:07] -> Unique precursors: 84,537 of 108,514 | modified peptides: 73,637 of 94,618 | peptides: 71,109 of 85,641 |  protein groups: 7,993 (Qvalue <= 0.01) for run #5 "LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_02.raw"
INFO:    [13/06/2025 11:43:07] -> Unique precursors: 79,970 of 108,514 | modified peptides: 70,452 of 94,618 | peptides: 68,604 of 85,641 |  protein groups: 7,919 (Qvalue <= 0.01) for run #6 "LFQ_Orbitrap_AIF_Condition_B_Sample_Alpha_03.raw"
INFO:    [13/06/2025 11:43:07] -> Unique precursors: 103,747 of 108,514 | modified peptides: 90,429 of 94,618 | peptides: 81,804 of 85,641 |  protein groups: 8,140 (Qvalue <= 0.01) for whole experiment "Condition"

INFO:    [13/06/2025 11:43:07] -> Saving SNE File...
INFO:    [13/06/2025 11:43:07] -> Storing SNE File: F:\Spectronaut\Spectronaut automatic SNE storage\20250613_095759_Condition.sne
INFO:    [13/06/2025 11:43:07] -> Initializing Pipeline...
INFO:    [13/06/2025 11:43:07] -> Calculating Qvalues...
INFO:    [13/06/2025 11:43:07] -> Saving...
INFO:    [13/06/2025 11:43:28] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:43:29] -> Pipeline executed in 21.3s - Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:43:31] -> Current Experiment had 0 Warnings and 0 Errors.
INFO:    [13/06/2025 11:43:31] -> Pipeline executed in 1.76h - Current Experiment had 0 Warnings and 0 Errors.
[END-LOG]
