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 ChromPeakAnalyzerIqWorkflow(TargetedWorkflowParameters parameters) : base(parameters)
{
var iterativeTffParameters = new IterativeTFFParameters();
TargetedMSFeatureFinder = new IterativeTFF(iterativeTffParameters);
PeakFitter = new PeakLeastSquaresFitter();
}
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();
}
protected override void DoPostInitialization()
{
base.DoPostInitialization();
_iterativeTFFParameters = new IterativeTFFParameters
{
ToleranceInPPM = _workflowParameters.MSToleranceInPPM
};
_iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.4; //TODO: add comment why we need this
_msfeatureFinder = new IterativeTFF(_iterativeTFFParameters);
}
public ChromPeakAnalyzer(TargetedWorkflowParameters parameters)
{
Parameters = parameters;
var iterativeTffParameters = new IterativeTFFParameters();
TargetedMSFeatureFinder = new IterativeTFF(iterativeTffParameters);
InterferenceScorer = new InterferenceScorer();
MSPeakDetector = new DeconToolsPeakDetectorV2();
FitScoreCalc = new IsotopicProfileFitScoreCalculator();
ResultValidator = new ResultValidatorTask();
}
public void getVeryLowN15ProfileWithIterativeTFFTest1()
{
var n14n15Util = new N14N15TestingUtilities();
//get sample MS from Test Data
var rf = new RunFactory();
var run = rf.CreateRun(N14N15TestingUtilities.MS_AMTTag23085904_z2_sum1_lowN15);
run.XYData = N14N15TestingUtilities.GetTestSpectrum(N14N15TestingUtilities.MS_AMTTag23085904_z2_sum1_lowN15);
var mt23140708 = n14n15Util.CreateMT23085904_Z2();
run.CurrentMassTag = mt23140708;
run.ResultCollection.ResultType = Globals.ResultType.N14N15_TARGETED_RESULT;
var theorN14FeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
theorN14FeatureGen.GenerateTheorFeature(mt23140708);
var theorN15FeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
theorN15FeatureGen.GenerateTheorFeature(mt23140708);
var parameters = new IterativeTFFParameters();
parameters.IsotopicProfileType = Globals.IsotopicProfileType.LABELLED;
parameters.ToleranceInPPM = 30;
var itff = new IterativeTFF(parameters);
itff.Execute(run.ResultCollection);
// IsotopicProfile iso = itff.iterativelyFindMSFeature(run, mt23140708.IsotopicProfileLabelled);
var result = (N14N15_TResult)run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.IsNotNull(result.IsotopicProfileLabeled);
Assert.AreEqual(82280, (int)result.IntensityAggregate);
Assert.AreEqual(3, result.IsotopicProfileLabeled.MonoIsotopicPeakIndex);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfileLabeled);
}
protected override void DoPostInitialization()
{
base.DoPostInitialization();
//we want the theorFeature generator to generate even very low peaks
_theorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.00000001);
//we want the MSFeature finder to dig way down low for any peaks
_iterativeTFFParameters = new IterativeTFFParameters();
_iterativeTFFParameters.ToleranceInPPM = _workflowParameters.MSToleranceInPPM;
_iterativeTFFParameters.PeakDetectorPeakBR = 2.1;
_iterativeTFFParameters.PeakBRStep = 0.2;
_iterativeTFFParameters.PeakDetectorMinimumPeakBR = 0.1;
_msfeatureFinder = new SipperIterativeMSFeatureFinder(_iterativeTFFParameters);
_quantifier = new SipperQuantifier();
//always do ChromCorrelation whether you want it or not!
_workflowParameters.ChromatogramCorrelationIsPerformed = true;
}
public PartialLabelingQuantifier(string element, int lightIsotope, int heavyIsotope, int numLeftZeroPads = 1, int numRightZeroPads = 1, bool isTheorProfileTrimmed = false)
{
MinLabelAmount = 0;
MaxLabelAmount = 100;
StepAmountForIterator = 1;
_elementLabeled = element;
_lightIsotope = lightIsotope;
_heavyIsotope = heavyIsotope;
_theorLabeledProfiles = new List <IsotopicProfile>();
var tffParameters = new IterativeTFFParameters();
tffParameters.ToleranceInPPM = 30;
_iterativeTff = new IterativeTFF(tffParameters);
NumLeftZeroPads = numLeftZeroPads;
NumRightZeroPads = numRightZeroPads;
IsTheoreticalTrimmedDownToObserved = isTheorProfileTrimmed;
}
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 SaturationDetector(string uimfFileLocation)
{
_uimfReader = new DataReader(uimfFileLocation);
_smoother = new SavitzkyGolaySmoother(9, 2);
_peakDetector = new ChromPeakDetector(0.0001, 0.0001);
_theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
if (!_uimfReader.DoesContainBinCentricData())
{
DataWriter dataWriter = new DataWriter(uimfFileLocation);
dataWriter.CreateBinCentricTables();
}
IterativeTFFParameters msFeatureFinderParameters = new IterativeTFFParameters
{
MinimumRelIntensityForForPeakInclusion = 0.0000000001,
PeakDetectorMinimumPeakBR = 0,
PeakDetectorPeakBR = 5.00000000000002,
PeakBRStep = 0.25,
PeakDetectorSigNoiseRatioThreshold = 0.00000000001,
ToleranceInPPM = 50
};
_msFeatureFinder = new IterativeTFF(msFeatureFinderParameters);
}
/// <summary>
/// Initializes a new instance of the <see cref="LcImsPeptideSearchWorkfow"/> class.
/// </summary>
/// <param name="uimfFileLocation">
/// The uimf file location.
/// </param>
/// <param name="parameters">
/// The parameters.
/// </param>
public LcImsPeptideSearchWorkfow(string uimfFileLocation, LcImsPeptideSearchParameters parameters)
{
this._buildWatershedStopWatch = new Stopwatch();
this._smoothStopwatch = new Stopwatch();
this._featureFindStopWatch = new Stopwatch();
this._featureFindCount = 0;
this._pointCount = 0;
this._uimfFileLocation = uimfFileLocation;
this._uimfReader = new DataReader(uimfFileLocation);
// Append bin-centric table to the uimf if not present.
if (!this._uimfReader.DoesContainBinCentricData())
{
DataWriter dataWriter = new DataWriter(uimfFileLocation);
dataWriter.CreateBinCentricTables();
}
this._parameters = parameters;
this._smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
this._theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
this._leftOfMonoPeakLooker = new LeftOfMonoPeakLooker();
this._peakDetector = new ChromPeakDetector(0.0001, 0.0001);
this._isotopicPeakFitScoreCalculator = new PeakLeastSquaresFitter();
IterativeTFFParameters msFeatureFinderParameters = new IterativeTFFParameters
{
MinimumRelIntensityForForPeakInclusion = 0.0001,
PeakDetectorMinimumPeakBR = 0.0001,
PeakDetectorPeakBR = 5.0002,
PeakBRStep = 0.25,
PeakDetectorSigNoiseRatioThreshold = 0.0001,
ToleranceInPPM = parameters.MassToleranceInPpm
};
this._msFeatureFinder = new IterativeTFF(msFeatureFinderParameters);
this.NumberOfFrames = this._uimfReader.GetGlobalParams().NumFrames;
this.NumberOfScans = this._uimfReader.GetFrameParams(1).Scans;
}
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>();
}
