MetaMorpheus: version 1.1.1
Time to run task: 00:24:42.2158777

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All target PSMs with q-value <= 0.01: 566491
All target peptides with q-value <= 0.01: 51699
All target protein groups with q-value <= 0.01 (1% FDR): 6820

LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01 - Target PSMs with q-value <= 0.01: 88048
LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01 - Target peptides with q-value <= 0.01: 36500
LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_01 - Target protein groups within 1 % FDR: 5381

LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02 - Target PSMs with q-value <= 0.01: 93319
LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02 - Target peptides with q-value <= 0.01: 37004
LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_02 - Target protein groups within 1 % FDR: 5569

LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03 - Target PSMs with q-value <= 0.01: 99170
LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03 - Target peptides with q-value <= 0.01: 38941
LFQ_Orbitrap_DDA_Condition_A_Sample_Alpha_03 - Target protein groups within 1 % FDR: 5823

LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01 - Target PSMs with q-value <= 0.01: 91761
LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01 - Target peptides with q-value <= 0.01: 37352
LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_01 - Target protein groups within 1 % FDR: 5543

LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02 - Target PSMs with q-value <= 0.01: 93761
LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02 - Target peptides with q-value <= 0.01: 36456
LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_02 - Target protein groups within 1 % FDR: 5488

LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03 - Target PSMs with q-value <= 0.01: 100465
LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03 - Target peptides with q-value <= 0.01: 39110
LFQ_Orbitrap_DDA_Condition_B_Sample_Alpha_03 - Target protein groups within 1 % FDR: 5665



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Engine Results:

Engine type: ClassicSearchEngine
Time to run engine: 00:00:58.6527075

Engine type: ClassicSearchEngine
Time to run engine: 00:01:11.2375688

Engine type: ClassicSearchEngine
Time to run engine: 00:01:09.3881692

Engine type: ClassicSearchEngine
Time to run engine: 00:01:05.1028368

Engine type: ClassicSearchEngine
Time to run engine: 00:01:08.7863024

Engine type: ClassicSearchEngine
Time to run engine: 00:01:06.6787281

Engine type: FdrAnalysisEngine
Time to run engine: 00:03:31.5525307
PSMs within 1% FDR: 573058
Delta Score Used for FDR Analysis: False

************************************************************
*       Metrics for Determination of PEP Using Binary Classification      
*-----------------------------------------------------------
*       Accuracy:  0.9864796752835339
*       Area Under Curve:  0.9978210273940555
*       Area under Precision recall Curve:  0.9944849785682738
*       F1Score:  0.9703655800935491
*       LogLoss:  0.05933045703067658
*       LogLossReduction:  0.9235982152824831
*       PositivePrecision:  0.9747688512806845
*       PositiveRecall:  0.9660040572720546
*       NegativePrecision:  0.9899212169587926
*       NegativeRecall:  0.9925664112609411
*       Count of Ambiguous Peptides Removed:  0
*       Q-Value Cutoff for Training Targets:  0.005
*       Targets Used for Training:  48949
*       Decoys Used for Training:  164655
************************************************************



Engine type: ModificationAnalysisEngine
Time to run engine: 00:00:01.0670508
Localized mods seen below q-value 0.01:
	Carbamidomethyl on C	10561
	Oxidation on M	3175
	Carbamidomethyl on U	1
(Approx) Additional localized but protein ambiguous mods seen below q-value 0.01:

(Approx) Additional unlocalized mods seen below q-value 0.01:

(Approx) Additional unlocalized modification formulas seen below q-value 0.01:


All mods in database limited to peptides observed in the results:



Engine type: ProteinParsimonyEngine
Time to run engine: 00:00:34.8736420


Engine type: ProteinScoringAndFdrEngine
Time to run engine: 00:00:09.2075109
Number of proteins within 1% FDR: 6888

Engine type: FdrAnalysisEngine
Time to run engine: 00:00:01.3300854
PSMs within 1% FDR: 89091
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:01.6216195
PSMs within 1% FDR: 92924
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:01.3622842
PSMs within 1% FDR: 100198
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:01.5090688
PSMs within 1% FDR: 101567
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:01.5447588
PSMs within 1% FDR: 94942
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:01.3313949
PSMs within 1% FDR: 94467
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:00.7807400
peptides within 1% FDR: 36977
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:00.8842029
peptides within 1% FDR: 37717
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:00.8755609
peptides within 1% FDR: 39357
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:00.9701162
peptides within 1% FDR: 39428
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:00.9904085
peptides within 1% FDR: 36922
Delta Score Used for FDR Analysis: False



Engine type: FdrAnalysisEngine
Time to run engine: 00:00:00.8729745
peptides within 1% FDR: 37451
Delta Score Used for FDR Analysis: False



Engine type: ProteinScoringAndFdrEngine
Time to run engine: 00:00:01.7194776
Number of proteins within 1% FDR: 5434

Engine type: ProteinScoringAndFdrEngine
Time to run engine: 00:00:03.6471405
Number of proteins within 1% FDR: 5598

Engine type: ProteinScoringAndFdrEngine
Time to run engine: 00:00:01.5796438
Number of proteins within 1% FDR: 5881

Engine type: ProteinScoringAndFdrEngine
Time to run engine: 00:00:09.8691098
Number of proteins within 1% FDR: 5721

Engine type: ProteinScoringAndFdrEngine
Time to run engine: 00:00:01.4626682
Number of proteins within 1% FDR: 5542

Engine type: ProteinScoringAndFdrEngine
Time to run engine: 00:00:01.4007934
Number of proteins within 1% FDR: 5624

