public static Run CreateResultsFromThreeScansOfStandardOrbitrapData() { Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1); run.ScanSetCollection.Create(run, 6000, 6020, 1, 1, false); Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); Task peakDetector = new DeconToolsPeakDetectorV2(); Task decon = new ThrashDeconvolutorV2(); Task msScanInfoCreator = new ScanResultUpdater(); Task flagger = new ResultValidatorTask(); foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); msScanInfoCreator.Execute(run.ResultCollection); flagger.Execute(run.ResultCollection); } return(run); }
public void deconWithRAPID_Then_ValidateTest1() { Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1); ScanSet scanSet = new ScanSet(6005); run.CurrentScanSet = scanSet; MSGenerator msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); DeconToolsPeakDetectorV2 peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true); RapidDeconvolutor decon = new RapidDeconvolutor(); ResultValidatorTask validator = new ResultValidatorTask(); msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); validator.Execute(run.ResultCollection); Assert.AreEqual(190, run.ResultCollection.ResultList.Count); IsosResult testResult = run.ResultCollection.ResultList[0]; Assert.AreEqual(0.0213668719893332m, (decimal)testResult.InterferenceScore); //TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList); }
protected virtual void InitializeProcessingTasks() { MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType); PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters); Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters); //the new iThrash imports the _peaks.txt file if (Deconvolutor is DeconTools.Backend.ProcessingTasks.Deconvoluters.InformedThrashDeconvolutor) { _deconvolutorRequiresPeaksFile = true; } //Will initialize these but whether or not they are used are determined elsewhere ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill); Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth, NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder); FitScoreCalculator = new DeconToolsFitScoreCalculator(); ScanResultUpdater = new ScanResultUpdater(NewDeconToolsParameters.ScanBasedWorkflowParameters.ProcessMS2); ResultValidator = new ResultValidatorTask(); IsosResultExporter = IsosExporterFactory.CreateIsosExporter(Run.ResultCollection.ResultType, ExporterType, IsosOutputFileName); ScanResultExporter = ScansExporterFactory.CreateScansExporter(Run.MSFileType, ExporterType, ScansOutputFileName); if (!_deconvolutorRequiresPeaksFile) { PeakListExporter = PeakListExporterFactory.Create(ExporterType, Run.MSFileType, PeakListExporterTriggerValue, PeakListOutputFileName); } PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator(); }
public SmartChromPeakSelector(SmartChromPeakSelectorParameters parameters) { this.Parameters = parameters; MSPeakDetector = new DeconToolsPeakDetectorV2(parameters.MSPeakDetectorPeakBR, parameters.MSPeakDetectorSigNoiseThresh, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true); var iterativeTFFParams = new IterativeTFFParameters(); iterativeTFFParams.ToleranceInPPM = parameters.MSToleranceInPPM; iterativeTFFParams.MinimumRelIntensityForForPeakInclusion = parameters.IterativeTffMinRelIntensityForPeakInclusion; if (parameters.MSFeatureFinderType == DeconTools.Backend.Globals.TargetedFeatureFinderType.BASIC) { throw new NotSupportedException("Currently the Basic TFF is not supported in the SmartChromPeakSelector"); //TargetedMSFeatureFinder = new TargetedFeatureFinders.BasicTFF(parameters.MSToleranceInPPM); } else { TargetedMSFeatureFinder = new IterativeTFF(iterativeTFFParams); } resultValidator = new ResultValidatorTask(); fitScoreCalc = new IsotopicProfileFitScoreCalculator(); InterferenceScorer = new InterferenceScorer(); }
public void deconWithTHRASH_Then_ValidateTest1() { Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1); var scanSet = new ScanSet(6005); run.CurrentScanSet = scanSet; var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true); var decon = new HornDeconvolutor(); var validator = new ResultValidatorTask(); msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); validator.Execute(run.ResultCollection); Assert.AreEqual(93, run.ResultCollection.ResultList.Count); var testResult = run.ResultCollection.ResultList[0]; Assert.AreEqual(0.0532199478712594m, (decimal)testResult.InterferenceScore); //TestUtilities.DisplayMSFeatures(run.ResultCollection.ResultList); }
protected virtual void DoMainInitialization() { ValidateParameters(); TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); ChromGen = new PeakChromatogramGenerator(WorkflowParameters.ChromGenTolerance, WorkflowParameters.ChromGeneratorMode, DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED, WorkflowParameters.ChromGenToleranceUnit) { TopNPeaksLowerCutOff = 0.333, ChromWindowWidthForAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2, ChromWindowWidthForNonAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2 }; //only var allowNegativeValues = false; ChromSmoother = new SavitzkyGolaySmoother(WorkflowParameters.ChromSmootherNumPointsInSmooth, 2, allowNegativeValues); ChromPeakDetector = new ChromPeakDetector(WorkflowParameters.ChromPeakDetectorPeakBR, WorkflowParameters.ChromPeakDetectorSigNoise); ChromPeakSelector = CreateChromPeakSelector(WorkflowParameters); ChromPeakAnalyzer = new ChromPeakAnalyzer(WorkflowParameters); IterativeTffParameters = new IterativeTFFParameters(); IterativeTffParameters.ToleranceInPPM = WorkflowParameters.MSToleranceInPPM; MsfeatureFinder = new IterativeTFF(IterativeTffParameters); FitScoreCalc = new IsotopicProfileFitScoreCalculator(); InterferenceScorer = new InterferenceScorer(); ResultValidator = new ResultValidatorTask(); ChromatogramCorrelator = new IqChromCorrelator(WorkflowParameters.ChromSmootherNumPointsInSmooth, 0.05, WorkflowParameters.ChromGenTolerance); }
public void outputToText_xcaliburData_Test1() { string testFile = xcalibur_text_IsosResultOutputFile1; List <Run> runcoll = new List <Run>(); Run run = new XCaliburRun(xcaliburFile1); runcoll.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6020, 1, 1, false); sscc.Create(); Task msgen = new GenericMSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new HornDeconvolutor(); Task flagger = new ResultValidatorTask(); Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.BasicIsosResultTextFileExporter(testFile); Task peakExporter = new DeconTools.Backend.ProcessingTasks.PeakListExporters.PeakListSQLiteExporter(100000, peakExporter1); Stopwatch sw; foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); flagger.Execute(run.ResultCollection); sw = new Stopwatch(); sw.Start(); isosExporter.Execute(run.ResultCollection); sw.Stop(); if (sw.ElapsedMilliseconds > 10) { Console.WriteLine("Exporter execution time = \t" + sw.ElapsedMilliseconds); } peakExporter.Execute(run.ResultCollection); } Assert.AreEqual(true, File.Exists(testFile)); FileInfo fi = new FileInfo(testFile); //Assert.AreEqual(25881, fi.Length); Console.Write(fi.Length); }
protected override void InitializeProcessingTasks() { MSGenerator = MSGeneratorFactory.CreateMSGenerator(Run.MSFileType); PeakDetector = PeakDetectorFactory.CreatePeakDetector(NewDeconToolsParameters); var moreSensitivePeakToBackgroundRatio = NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio / 2; var moreSensitiveSigNoiseThresh = NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold; _moreSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(moreSensitivePeakToBackgroundRatio, moreSensitiveSigNoiseThresh, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType, NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded); _superSensitiveMS1PeakDetector = new DeconToolsPeakDetectorV2(0, 0, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType, NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded); Deconvolutor = DeconvolutorFactory.CreateDeconvolutor(NewDeconToolsParameters); //Will initialize these but whether or not they are used are determined elsewhere ZeroFiller = new DeconToolsZeroFiller(NewDeconToolsParameters.MiscMSProcessingParameters.ZeroFillingNumZerosToFill); Smoother = new SavitzkyGolaySmoother(NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayNumPointsInSmooth, NewDeconToolsParameters.MiscMSProcessingParameters.SavitzkyGolayOrder); FitScoreCalculator = new DeconToolsFitScoreCalculator(); ResultValidator = new ResultValidatorTask(); PeakToMSFeatureAssociator = new PeakToMSFeatureAssociator(); _ms2PeakDetectorForCentroidData = new DeconToolsPeakDetectorV2(0, 0, Globals.PeakFitType.QUADRATIC, true) { RawDataType = Globals.RawDataType.Centroided }; _ms2PeakDetectorForProfileData = new DeconToolsPeakDetectorV2(NewDeconToolsParameters.PeakDetectorParameters.PeakToBackgroundRatio, NewDeconToolsParameters.PeakDetectorParameters.SignalToNoiseThreshold, NewDeconToolsParameters.PeakDetectorParameters.PeakFitType, NewDeconToolsParameters.PeakDetectorParameters.IsDataThresholded); Check.Ensure(Deconvolutor is ThrashDeconvolutorV2, "Error. Currently the DeconMSn workflow only works with the ThrashV2 deconvolutor. Selected deconvolutor= " + Deconvolutor); }
public void outputToText_xcaliburData_Test2() { string testFile = xcalibur_text_IsosResultOutputFile1; List <Run> runcoll = new List <Run>(); Run run = new XCaliburRun(xcaliburFile1); runcoll.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 6000, 6020, 1, 1, false); sscc.Create(); Task msgen = new GenericMSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new HornDeconvolutor(); Task flagger = new ResultValidatorTask(); BasicIsosResultTextFileExporter isosExporter = new BasicIsosResultTextFileExporter(testFile); Stopwatch sw; foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); flagger.Execute(run.ResultCollection); } isosExporter.ExportIsosResults(run.ResultCollection.ResultList); Assert.AreEqual(true, File.Exists(testFile)); FileInfo fi = new FileInfo(testFile); //Assert.AreEqual(25881, fi.Length); Console.Write(fi.Length); }
//public override WorkflowParameters WorkflowParameters //{ // get // { // throw new NotImplementedException(); // } // set // { // throw new NotImplementedException(); // } //} public void InitializeWorkflow() { this.ChromGenToleranceInPPM = 20; this.ChromGenerator = new ChromatogramGenerator(); this.ChromSmoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2); this.ChromPeakDetector = new ChromPeakDetector(0.5, 0.5); this.MSPeakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false); // To include support for Rapid, you must add a reference to DeconEngine.dll, which was compiled with Visual Studio 2003 and uses MSVCP71.dll // Note that DeconEngine.dll also depends on xerces-c_2_7.dll while DeconEngineV2.dll depends on xerces-c_2_8.dll #if INCLUDE_RAPID this.Deconvolutor = new RapidDeconvolutor(); Validator = new ResultValidatorTask(); isosExporter = new DeconTools.Backend.FileIO.MSFeatureToTextFileExporterBasic(m_isosResultFileName); #else throw new NotSupportedException("Support for Rapid is not included in this version of the DLL"); #endif }
protected virtual void DoMainInitialization() { ValidateParameters(); _theorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); _chromGen = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, _workflowParameters.ChromGeneratorMode, DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED, _workflowParameters.ChromGenToleranceUnit) { TopNPeaksLowerCutOff = 0.333, ChromWindowWidthForAlignedData = (float)_workflowParameters.ChromNETTolerance * 2, ChromWindowWidthForNonAlignedData = (float)_workflowParameters.ChromNETTolerance * 2 }; //only var allowNegativeValues = false; _chromSmoother = new SavitzkyGolaySmoother(_workflowParameters.ChromSmootherNumPointsInSmooth, 2, allowNegativeValues); _chromPeakDetector = new ChromPeakDetectorMedianBased(_workflowParameters.ChromPeakDetectorPeakBR, _workflowParameters.ChromPeakDetectorSigNoise); _chromPeakSelector = CreateChromPeakSelector(_workflowParameters); _iterativeTFFParameters = new IterativeTFFParameters(); _iterativeTFFParameters.ToleranceInPPM = _workflowParameters.MSToleranceInPPM; _msfeatureFinder = new IterativeTFF(_iterativeTFFParameters); _fitScoreCalc = new IsotopicProfileFitScoreCalculator(); _resultValidator = new ResultValidatorTask(); _chromatogramCorrelator = new ChromatogramCorrelator(_workflowParameters.ChromSmootherNumPointsInSmooth, 0.01, _workflowParameters.ChromGenTolerance); ChromatogramXYData = new XYData(); MassSpectrumXYData = new XYData(); ChromPeaksDetected = new List <ChromPeak>(); }
public static Run CreateResultsFromTwoFramesOfStandardUIMFData() { var run = new UIMFRun(FileRefs.RawDataMSFiles.UIMFStdFile1); run.ResultCollection.ResultType = Globals.ResultType.UIMF_TRADITIONAL_RESULT; run.ScanSetCollection.Create(run, 500, 501, 3, 1); run.IMSScanSetCollection.Create(run, 250, 270, 9, 1); Task msgen = new UIMF_MSGenerator(); Task peakDetector = new DeconToolsPeakDetectorV2(); Task decon = new ThrashDeconvolutorV2(); Task msScanInfoCreator = new ScanResultUpdater(); Task flagger = new ResultValidatorTask(); Task ticExtractor = new DeconTools.Backend.ProcessingTasks.UIMF_TICExtractor(); Task driftTimeextractor = new UIMFDriftTimeExtractor(); foreach (var frame in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = frame; foreach (IMSScanSet scan in run.IMSScanSetCollection.ScanSetList) { run.CurrentIMSScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); flagger.Execute(run.ResultCollection); driftTimeextractor.Execute(run.ResultCollection); msScanInfoCreator.Execute(run.ResultCollection); ticExtractor.Execute(run.ResultCollection); } } return(run); }
public static Run CreatePeakDataFromStandardOrbitrapData() { Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1); run.ScanSetCollection.Create(run, 6000, 6050, 1, 1, false); Task msgen = new GenericMSGenerator(); var peakDetector = new DeconToolsPeakDetectorV2(); peakDetector.PeaksAreStored = true; Task decon = new ThrashDeconvolutorV2(); Task msScanInfoCreator = new ScanResultUpdater(); Task flagger = new ResultValidatorTask(); foreach (var scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); } return(run); }
public void outputToText_uimf_test1() { if (File.Exists(uimf_text_IsosResultOutputFile1)) { File.Delete(uimf_text_IsosResultOutputFile1); } List <Run> runcoll = new List <Run>(); Run run = new UIMFRun(uimfFile1); runcoll.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 200, 240, 9, 1, false); sscc.Create(); FrameSetCollectionCreator fsc = new FrameSetCollectionCreator(run, 800, 801, 3, 1); fsc.Create(); Task msgen = new UIMF_MSGenerator(); Task peakDetector = new DeconToolsPeakDetector(); Task decon = new HornDeconvolutor(); Task driftTimeExtractor = new DeconTools.Backend.ProcessingTasks.UIMFDriftTimeExtractor(); Task origIntensExtr = new DeconTools.Backend.ProcessingTasks.OriginalIntensitiesExtractor(); Task isosExporter = new DeconTools.Backend.ProcessingTasks.ResultExporters.IsosResultExporters.UIMFIsosResultTextFileExporter(uimf_text_IsosResultOutputFile1, 1000000); Task flagger = new ResultValidatorTask(); Stopwatch sw; foreach (FrameSet frame in ((UIMFRun)run).FrameSetCollection.FrameSetList) { ((UIMFRun)run).CurrentFrameSet = frame; foreach (ScanSet scan in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scan; msgen.Execute(run.ResultCollection); peakDetector.Execute(run.ResultCollection); decon.Execute(run.ResultCollection); flagger.Execute(run.ResultCollection); driftTimeExtractor.Execute(run.ResultCollection); origIntensExtr.Execute(run.ResultCollection); sw = new Stopwatch(); sw.Start(); isosExporter.Execute(run.ResultCollection); sw.Stop(); if (sw.ElapsedMilliseconds > 10) { Console.WriteLine("execution time = \t" + sw.ElapsedMilliseconds); } } } Assert.AreEqual(true, File.Exists(uimf_text_IsosResultOutputFile1)); FileInfo fi = new FileInfo(uimf_text_IsosResultOutputFile1); Assert.AreEqual(99743, fi.Length); Console.Write(fi.Length); }
protected override void DoPostInitialization() { base.DoPostInitialization(); ValidateParameters(); theorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); theorN15FeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005); chromGenN14 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, _workflowParameters.ChromGeneratorMode); chromGenN14.TopNPeaksLowerCutOff = 0.333; chromGenN15 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, DeconTools.Backend.Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK, DeconTools.Backend.Globals.IsotopicProfileType.LABELLED); chromGenN15.TopNPeaksLowerCutOff = 0.333; var pointsToSmooth = (_workflowParameters.ChromSmootherNumPointsInSmooth + 1) / 2; chromSmoother = new SavitzkyGolaySmoother(_workflowParameters.ChromSmootherNumPointsInSmooth, 2); chromPeakDetector = new ChromPeakDetector(_workflowParameters.ChromPeakDetectorPeakBR, _workflowParameters.ChromPeakDetectorSigNoise); var smartchrompeakSelectorParams = new SmartChromPeakSelectorParameters(); smartchrompeakSelectorParams.MSFeatureFinderType = DeconTools.Backend.Globals.TargetedFeatureFinderType.ITERATIVE; smartchrompeakSelectorParams.MSPeakDetectorPeakBR = _workflowParameters.MSPeakDetectorPeakBR; smartchrompeakSelectorParams.MSPeakDetectorSigNoiseThresh = _workflowParameters.MSPeakDetectorSigNoise; smartchrompeakSelectorParams.MSToleranceInPPM = _workflowParameters.MSToleranceInPPM; smartchrompeakSelectorParams.NETTolerance = (float)_workflowParameters.ChromNETTolerance; smartchrompeakSelectorParams.NumScansToSum = _workflowParameters.NumMSScansToSum; smartchrompeakSelectorParams.NumChromPeaksAllowed = 10; smartchrompeakSelectorParams.IterativeTffMinRelIntensityForPeakInclusion = 0.5; chromPeakSelectorN14 = new SmartChromPeakSelector(smartchrompeakSelectorParams); var chromPeakSelectorParameters = new ChromPeakSelectorParameters(); chromPeakSelectorParameters.NumScansToSum = _workflowParameters.NumMSScansToSum; chromPeakSelectorParameters.NETTolerance = (float)_workflowParameters.ChromNETTolerance; chromPeakSelectorParameters.PeakSelectorMode = DeconTools.Backend.Globals.PeakSelectorMode.N15IntelligentMode; chromPeakSelectorN15 = new BasicChromPeakSelector(chromPeakSelectorParameters); chromPeakSelectorN15.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED; msPeakDetector = new DeconToolsPeakDetectorV2(_workflowParameters.MSPeakDetectorPeakBR, _workflowParameters.MSPeakDetectorSigNoise, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false); var iterativeTFFParameters = new IterativeTFFParameters(); iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM; iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33; iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED; unlabelledProfilefinder = new IterativeTFF(iterativeTFFParameters); iterativeTFFParameters = new IterativeTFFParameters(); iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM; iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33; iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED; labelledProfileFinder = new IterativeTFF(iterativeTFFParameters); quantifier = new N14N15QuantifierTask(_n14N15Workflow2Parameters.NumPeaksUsedInQuant, _workflowParameters.MSToleranceInPPM); fitScoreCalc = new IsotopicProfileFitScoreCalculator(); var minRelativeIntensityForScore = 0.2; resultValidatorN14 = new ResultValidatorTask(minRelativeIntensityForScore, true); resultValidatorN15 = new LabelledIsotopicProfileScorer(minRelativeIntensityForScore); ChromatogramXYData = new XYData(); MassSpectrumXYData = new XYData(); ChromPeaksDetected = new List <ChromPeak>(); }