public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
string testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
string peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
Run run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
ChromPeakIqTarget testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
ChromPeak testPeak = new ChromPeak(5184, 840963, 50, 0);
testTarget.SetWorkflow(new ChromPeakAnalyzerIqWorkflow(run, parameters));
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
testTarget.DoWorkflow();
IqResult result = testTarget.GetResult();
Console.WriteLine("Fit Score: " + result.FitScore + " Flagged: " + result.IsIsotopicProfileFlagged);
}
public void getPeakChromatogramTest1()
{
var run = RunUtilities.CreateAndLoadPeaks(FileRefs.RawDataMSFiles.OrbitrapStdFile1,
FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
var targetMZ = 759.4032;
var startScan = 5500;
var stopScan = 6500;
double toleranceInPPM = 20;
var chromGen = new PeakChromatogramGenerator();
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(toleranceInPPM);
peakChromGen.Execute(run.ResultCollection);
run.XYData.Display();
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
//make sure that the 0's are not trimmed off
Assert.AreEqual(0, run.XYData.Yvalues[1]);
}
public void JoshGenerateN15LabelledTheorProfileTest2()
{
var mt = TestDataCreationUtilities.CreateN14N15TestMassTagList().First(p => p.ID == 23085470);
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
Console.WriteLine("Total nitrogens = " + mt.GetAtomCountForElement("N"));
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
Console.WriteLine();
var n15theorGenerator = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
n15theorGenerator.GenerateTheorFeature(mt);
unlabelledTheorGenerator.GenerateTheorFeature(mt);
n15theorGenerator.GenerateTheorFeature(mt);
unlabelledTheorGenerator.GenerateTheorFeature(mt);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfileLabelled);
}
public void Test1()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var n14n15Util = new N14N15TestingUtilities();
//get MS
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
var mt23140708 = n14n15Util.CreateMT23140708_Z3();
var featureGen2 = new JoshTheorFeatureGenerator();
featureGen2.GenerateTheorFeature(mt23140708);
//get ms peaks
var peakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, false);
var msPeakList = peakDet.FindPeaks(massSpectrum, 0, 0);
var bff = new BasicTFF(featureFinderTol, featureFinderRequiresMonoPeak);
var n14Profile = bff.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var theorXYData = mt23140708.IsotopicProfile.GetTheoreticalIsotopicProfileXYData(n14Profile.GetFWHM());
var theorMaxY = theorXYData.Yvalues.Max();
double obsMaxY = n14Profile.getMostIntensePeak().Height;
for (var i = 0; i < theorXYData.Xvalues.Length; i++)
{
theorXYData.Yvalues[i] = theorXYData.Yvalues[i] * obsMaxY;
}
offsetDistribution(theorXYData, mt23140708.IsotopicProfile, n14Profile);
var subtracted = XYDataUtilities.SubtractXYData(massSpectrum, theorXYData, n14Profile.MonoPeakMZ - 1,
n14Profile.MonoPeakMZ + 3, 0.01);
var outputFileMS = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TextFile\massSpectrum1.txt";
var outputFileMSSubtracted = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TextFile\massSpectrum1_withDataSubtracted.txt";
TestUtilities.WriteToFile(massSpectrum, outputFileMS);
TestUtilities.WriteToFile(subtracted, outputFileMSSubtracted);
// XYDataUtilities.NormalizeXYData()
}
public void GenerateIsotopicProfileTest1()
{
var peptideUtils = new PeptideUtils();
var empiricalFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence("SAMPLERSAMPLER");
var featureGenerator = new JoshTheorFeatureGenerator();
}
public void ChromCorrelatorTest1()
{
var rawFilename = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
var run = new RunFactory().CreateRun(rawFilename);
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new IqExecutor(executorBaseParameters, run);
executor.LoadChromData(run);
var workflowAssigner = new IqWorkflowAssigner();
TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters();
IqWorkflow workflow = new O16O18IqWorkflow(run, workflowParameters);
IqTarget iqTarget = new IqChargeStateTarget();
iqTarget.EmpiricalFormula = "C58H100N18O20";
iqTarget.Code = "GAAQNIIPASTGAAK";
iqTarget.ID = 1093;
iqTarget.ChargeState = 0;
var iqTargetList = new List <IqTarget>();
iqTargetList.Add(iqTarget);
var utilities = new IqTargetUtilities();
utilities.CreateChildTargets(iqTargetList);
workflowAssigner.AssignWorkflowToParent(workflow, iqTargetList);
workflowAssigner.AssignWorkflowToChildren(workflow, iqTargetList);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
foreach (var target in iqTarget.ChildTargets())
{
utilities.UpdateTargetMissingInfo(target);
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
}
foreach (var childTarget in iqTarget.ChildTargets())
{
var result = childTarget.CreateResult();
var correlator = new O16O18ChromCorrelator(7, 0.1, 20, Globals.ToleranceUnit.PPM);
var corrData = correlator.CorrelateData(run, result, 5700, 6500);
var corrDataItem1 = corrData.CorrelationDataItems.First();
Console.WriteLine("z= \t" + childTarget.ChargeState + "\tCorrelationData (slope,intercept,rsquared)= \t" + corrDataItem1);
}
}
public void JoshGenerateTheorProfileTest1()
{
var mt = TestDataCreationUtilities.CreateN14N15TestMassTagList().First(p => p.ID == 23085473);
var theorGenerator = new JoshTheorFeatureGenerator();
theorGenerator.GenerateTheorFeature(mt);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
//TODO: add an Assert, with a manually confirmed number.
}
public void ComparePeakFitterVsAreaFitter()
{
var massTagFile1 = Path.Combine(FileRefs.RawDataBasePath, "TargetedWorkflowStandards", "QCShew_peptidesWithObsCountGreaterThan1000.txt");
//load target
var masstagImporter = new MassTagFromTextFileImporter(massTagFile1);
var targets = masstagImporter.Import().TargetList;
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true);
var scanSet = new ScanSet(9575);
run.CurrentScanSet = scanSet;
msgen.Execute(run.ResultCollection);
peakDetector.Execute(run.ResultCollection);
var selectedTarget = targets.First(p => p.ID == 635428 && p.ChargeState == 3);
var theorFeatureGen = new JoshTheorFeatureGenerator(Backend.Globals.LabellingType.NONE, 0.005);
theorFeatureGen.GenerateTheorFeature(selectedTarget);
var peakForFWHM = run.PeakList.First(p => p.XValue > 768.38 && p.XValue < 768.39);
var theorXYdata =
TheorXYDataCalculationUtilities.GetTheoreticalIsotopicProfileXYData(selectedTarget.IsotopicProfile,
peakForFWHM.Width);
theorXYdata.NormalizeYData();
var areaFitter = new AreaFitter();
var areaFitScore = areaFitter.GetFit(theorXYdata, run.XYData, 0.1);
var peakLeastSquaresFitter = new PeakLeastSquaresFitter();
var peakBasedFitScore = peakLeastSquaresFitter.GetFit(new List <Peak>(selectedTarget.IsotopicProfile.Peaklist), run.PeakList, 0.1, 25);
Console.WriteLine("fit score based on XYData = " + areaFitScore);
Console.WriteLine("fit score based on Peaks= " + peakBasedFitScore);
Assert.IsTrue(peakBasedFitScore < 0.1);
}
public void ChromPeakAnalyzerWorkflowTest()
{
//Reference JIRA: https://jira.pnnl.gov/jira/browse/OMCS-884
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = UnitTesting2.FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500;
var run = new RunFactory().CreateRun(testFile);
TargetedWorkflowParameters parameters = new BasicTargetedWorkflowParameters();
var testTarget = new ChromPeakIqTarget();
ITheorFeatureGenerator TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
var testPeak = new ChromPeak(5184, 840963, 50, 0);
var executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new TopDownMSAlignExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
var workflow = new ChromPeakAnalyzerIqWorkflow(run, parameters);
testTarget.SetWorkflow(workflow);
testTarget.ID = 1;
testTarget.Code = "NGIIMMENR";
testTarget.EmpiricalFormula = "C43H76N14O14S2";
testTarget.MonoMassTheor = 1076.510631;
testTarget.ChromPeak = testPeak;
testTarget.ChargeState = 1;
testTarget.TheorIsotopicProfile = TheorFeatureGen.GenerateTheorProfile(testTarget.EmpiricalFormula, testTarget.ChargeState);
var testTargetList = new List <IqTarget>();
IqTarget testParent = new IqChargeStateTarget();
testParent.AddTarget(testTarget);
testTargetList.Add(testTarget);
executor.Execute(testTargetList);
var result = testTarget.GetResult();
Assert.NotNull(result.LCScanSetSelected);
Assert.AreNotEqual(1, result.FitScore);
Assert.AreEqual(true, result.IsotopicProfileFound);
}
public void CorrelationTest2_UsingExecutorMethod()
{
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
double chromToleranceInPPM = 10;
var startScan = 5460;
var stopScan = 5755;
var smoother = new SavitzkyGolaySmoother(3, 2);
var peakChromGen = new PeakChromatogramGenerator(chromToleranceInPPM);
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, mt.IsotopicProfile.Peaklist[0].XValue, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var result = run.ResultCollection.GetTargetedResult(mt);
ChromatogramCorrelatorBase correlator = new ChromatogramCorrelator(3);
var corrData = correlator.CorrelatePeaksWithinIsotopicProfile(run, mt.IsotopicProfile, startScan, stopScan);
Debug.Assert(corrData.CorrelationDataItems != null, "corrData.CorrelationDataItems != null");
Assert.AreEqual(0.98m, (decimal)Math.Round((double)corrData.CorrelationDataItems[1].CorrelationRSquaredVal, 2));
foreach (var item in corrData.CorrelationDataItems)
{
Console.WriteLine(item.CorrelationRSquaredVal);
}
}
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 static IqTarget GetIQTargetStandard(int standardNum)
{
//MassTagID MonoisotopicMass NET NETStDev Obs minMSGF mod_count mod_description pmt_quality_score peptide peptideex Multiple_Proteins
//86963986 1516.791851 0.227147 0.007416702 3 1 0 2.00000 AAKEGISCEIIDLR M.AAKEGISCEIIDLR.T 0
IqTarget target = new IqChargeStateTarget(null);
target.ID = 86963986;
target.MonoMassTheor = 1516.791851;
target.EmpiricalFormula = "C64H112N18O22S";
target.Code = "AAKEGISCEIIDLR";
target.ChargeState = 2;
target.ElutionTimeTheor = 0.227147;
target.MZTheor = target.MonoMassTheor / target.ChargeState + Globals.PROTON_MASS;
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
return(target);
}
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>();
}
public void TestScoring()
{
string formula = "C9H13ClN6";
string fileLocation = Cae;
MolecularTarget target = new MolecularTarget(formula, IonizationMethod.Protonated, "CAE");
Console.WriteLine("CompositionWithoutAdduct: " + target.CompositionWithoutAdduct);
Console.WriteLine("Monoisotopic ViperCompatibleMass: " + target.MonoisotopicMass);
CrossSectionSearchParameters parameters = new CrossSectionSearchParameters(driftTubeLength);
var smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
CrossSectionWorkfow workflow = new CrossSectionWorkfow(fileLocation, "output", parameters);
Console.WriteLine("Ionization method: " + target.Adduct);
Console.WriteLine("Targeting centerMz: " + target.MassWithAdduct);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.CompositionWithAdduct != null)
{
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
var theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
// Generate VoltageSeparatedAccumulatedXICs
var uimfReader = new DataReader(fileLocation);
Console.WriteLine("Input file: {0}", fileLocation);
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(uimfReader, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm, driftTubeLength);
Console.WriteLine();
// For each voltage, find 2D XIC features
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
Console.WriteLine("Voltage group: {0} V, Frame {1}-{2}, {3:F2}K, {4:F2}Torr",
voltageGroup.MeanVoltageInVolts,
voltageGroup.FirstFrameNumber,
voltageGroup.LastFrameNumber,
voltageGroup.MeanTemperatureInKelvin,
voltageGroup.MeanPressureInTorr);
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, smoother, parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, uimfReader, voltageGroup, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm)).ToList();
// feature scorings and Target selection.
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, uimfReader);
// Check each XIC Peak found
foreach (var featurePeak in standardPeaks)
{
// Evaluate feature scores.
double intensityScore = FeatureScoreUtilities.IntensityScore(featurePeak, globalMaxIntensity);
double isotopicScoreAngle = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Angle,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistance = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistance,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScorePerson = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.PearsonCorrelation,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreBhattacharyya = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Bhattacharyya,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistanceAlternative = FeatureScoreUtilities.IsotopicProfileScore(
featurePeak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistanceAlternative,
globalMaxIntensity,
workflow.NumberOfScans);
double peakShapeScore = FeatureScoreUtilities.PeakShapeScore(featurePeak, workflow.uimfReader, workflow.Parameters.MzWindowHalfWidthInPpm, workflow.Parameters.DriftTimeToleranceInMs, voltageGroup, globalMaxIntensity, workflow.NumberOfScans);
// Report all features.
Console.WriteLine(" feature found at scan number {0}", featurePeak.PeakApex.DriftTimeCenterInScanNumber);
Console.WriteLine(" IntensityScore: {0}", intensityScore);
Console.WriteLine(" peakShapeScore: {0}", peakShapeScore);
Console.WriteLine(" isotopicScore - Angle: {0}", isotopicScoreAngle);
Console.WriteLine(" isotopicScore - Distance: {0}", isotopicScoreDistance);
Console.WriteLine(" isotopicScore - Distance2:{0}", isotopicScoreDistanceAlternative);
Console.WriteLine(" isotopicScore - Pearson: {0}", isotopicScorePerson);
Console.WriteLine(" isotopicScore - Bhattacharyya: {0}", isotopicScoreBhattacharyya);
Console.WriteLine();
}
Console.WriteLine();
}
workflow.Dispose();
}
public void CalculateLabelingDistributionTest2()
{
//mass_tag_id monoisotopic_mass NET obs mod_count mod_description pmt peptide peptideex
//355176429 1538.8166126 0.42422 1 0 2.00000 LFLASACLYGAALAGV R.LFLASACLYGAALAGV.C
//------------------------load theor data ------------------------------------
var peptideUtils = new PeptideUtils();
var peptide = new PeptideTarget();
peptide.Code = "LFLASACLYGAALAGV";
peptide.EmpiricalFormula = new PeptideUtils().GetEmpiricalFormulaForPeptideSequence(peptide.Code);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
theorFeatureGenerator.GenerateTheorFeature(peptide);
var theorProfile = peptide.IsotopicProfile;
var theorIntensities = theorProfile.Peaklist.Select(p => (double)p.Height).ToList();
Console.WriteLine("Total carbons = " + peptideUtils.GetNumAtomsForElement("C", peptide.EmpiricalFormula));
var obsIntensities = new List <double>(new[]
{
1, 0.8335001, 0.4029815, 0.1846439, 0.1116047, 0.09458135, 0.07157851, 0.04972008,
0.03036686, 0.01545749, 0.008299164, 0.004003931, 0.001711554, 0.000766305,
0.000484514
});
var relexCorrectedIntensities = new List <double>(new[]
{
1, 0.84416, 0.4174013, 0.1843375, 0.1073706, 0.09557419, 0.07190877, 0.04823519,
0.02991197, 0.01456759, 0.008299164, 0.004003931, 0.001711554, 0.000766305,
0.000484514
});
/*
*
* Data for observed profile:
* LCMSFeature 8517 from Yellow_C13_070_23Mar10_Griffin_10-01-28
* *
* peak mz relIntens width sn
* 0 770.418569278349 1 0.008119391 285.256
* 1 770.919748892834 0.8335001 0.008161238 884.9909
* 2 771.421020812818 0.4029815 0.008248929 566.6187
* 3 771.922575912402 0.1846439 0.008058954 703.6938
* 4 772.424544684666 0.1116047 0.007997629 358.0133
* 5 772.926348484216 0.09458135 0.008128829 677.3434
* 6 773.428080290323 0.07157851 0.008151106 100
* 7 773.929769365137 0.04972008 0.008104968 100
* 8 774.431542463583 0.03036686 0.007982519 100
* 9 774.933237566856 0.01545749 0.008024476 100
* 10 775.434950373045 0.008299164 0.008166174 740.9502
* 11 775.936532837365 0.004003931 0.007899459 100
* 12 776.438361528879 0.001711554 0.00877683 44.79652
* 13 776.940072709136 0.0007663054 0.007601836 17.12788
* 14 777.441663634739 0.0004845143 0.007320933 100
*
*/
var labelDistCalc = new LabelingDistributionCalculator();
double[] solvedXVals;
double[] solvedYvals;
var d = 0.1;
labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, d, d, out solvedXVals, out solvedYvals);
var xydata = new XYData();
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
Console.WriteLine("threshold= " + d);
xydata.Display();
labelDistCalc.CalculateLabelingDistribution(theorIntensities, relexCorrectedIntensities, d, d, out solvedXVals, out solvedYvals);
xydata.Xvalues = solvedXVals;
xydata.Yvalues = solvedYvals;
Console.WriteLine();
Console.WriteLine("Relex-corrected isotopic profile= " + d);
xydata.Display();
double fractionUnlabelled, fractionLabelled, averageLabelsIncorporated;
labelDistCalc.OutputLabelingInfo(solvedYvals.ToList(), out fractionUnlabelled, out fractionLabelled,
out averageLabelsIncorporated);
Console.WriteLine();
Console.WriteLine("fractionUnlabelled= " + fractionUnlabelled);
Console.WriteLine("fractionLabelled= " + fractionLabelled);
Console.WriteLine("averageAmountLabelIncorp= " + averageLabelsIncorporated);
//for (double d = 0; d < 2.1; d+=0.1)
//{
// labelDistCalc.CalculateLabelingDistribution(theorIntensities, obsIntensities, d, d, out solvedXVals, out solvedYvals);
// XYData xydata = new XYData();
// xydata.Xvalues = solvedXVals;
// xydata.Yvalues = solvedYvals;
// Console.WriteLine();
// Console.WriteLine("threshold= " + d);
// xydata.Display();
//}
}
public void CorrelationTest1()
{
//TODO: test something
var run = new RunFactory().CreateRun(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
var mt = TestUtilities.GetMassTagStandard(1);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new JoshTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
double chromToleranceInPPM = 10;
var startScan = 5460;
var stopScan = 5755;
var smoother = new SavitzkyGolaySmoother(3, 2);
var peakChromGen = new PeakChromatogramGenerator(chromToleranceInPPM);
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, mt.IsotopicProfile.Peaklist[0].XValue, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var chromdata1 = run.XYData.TrimData(startScan, stopScan);
run.XYData = peakChromGen.GenerateChromatogram(run, startScan, stopScan, mt.IsotopicProfile.Peaklist[3].XValue, chromToleranceInPPM);
run.XYData = smoother.Smooth(run.XYData);
var chromdata2 = run.XYData.TrimData(startScan, stopScan);
//chromdata1.Display();
//Console.WriteLine();
//chromdata2.Display();
ChromatogramCorrelatorBase correlator = new ChromatogramCorrelator(3);
double slope = 0;
double intercept = 0;
double rsquaredVal = 0;
correlator.GetElutionCorrelationData(chromdata1, chromdata2, out slope, out intercept, out rsquaredVal);
Console.WriteLine(mt);
Console.WriteLine("slope = \t" + slope);
Console.WriteLine("intercept = \t" + intercept);
Console.WriteLine("rsquared = \t" + rsquaredVal);
for (var i = 0; i < chromdata1.Xvalues.Length; i++)
{
Console.WriteLine(chromdata1.Xvalues[i].ToString("0") + "\t" + chromdata1.Yvalues[i].ToString("0") + "\t" + chromdata2.Yvalues[i]);
}
}
public void test01_mt230140708_z3()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var numPeaksUsedInQuant = 3;
var n14n15Util = new N14N15TestingUtilities();
//get MS
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
var smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(3, 2);
massSpectrum = smoother.Smooth(massSpectrum);
//get target MT
var mt23140708 = n14n15Util.CreateMT23140708_Z3();
//get ms peaks
var peakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, false);
var msPeakList = peakDet.FindPeaks(massSpectrum, 0, 0);
//TestUtilities.DisplayPeaks(msPeakList);
var featureGen = new TomTheorFeatureGenerator();
featureGen.GenerateTheorFeature(mt23140708);
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var featureGen2 = new JoshTheorFeatureGenerator();
featureGen2.GenerateTheorFeature(mt23140708);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
var gen = new N15IsotopeProfileGenerator();
var theorN15Profile = gen.GetN15IsotopicProfile(mt23140708, 0.005);
var bff = new BasicTFF(featureFinderTol, featureFinderRequiresMonoPeak);
var n14Profile = bff.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var n15Profile = bff.FindMSFeature(msPeakList, theorN15Profile);
Console.WriteLine(mt23140708.GetEmpiricalFormulaFromTargetCode());
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(theorN15Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n14Profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n15Profile);
var quant = new BasicN14N15Quantifier(featureFinderTol);
double ratioContribIso1;
double ratioContribIso2;
double ratio;
quant.GetRatioBasedOnTopPeaks(n14Profile, n15Profile, mt23140708.IsotopicProfile, theorN15Profile, peakDet.BackgroundIntensity,
numPeaksUsedInQuant, out ratio, out ratioContribIso1, out ratioContribIso2);
Console.WriteLine("--------------------------------");
Console.WriteLine("Background intensity = " + peakDet.BackgroundIntensity);
Console.WriteLine("--------------------------------");
Console.WriteLine("Ratio = " + ratio);
Console.WriteLine("Ratio contrib Iso1 = " + ratioContribIso1);
Console.WriteLine("Ratio contrib Iso2 = " + ratioContribIso2);
Console.WriteLine("--------------------------------");
Assert.AreEqual(1.458267m, (decimal)Math.Round(ratio, 6)); //see 'N14N15Quantification_manualValidation_of_algorithm.xls' for manual validation
}
public void TestFormulaPerturbance()
{
List<Tuple<string, string>> formulas = new List<Tuple<string, string>>();
// truth
formulas.Add(new Tuple<string, string>("True formula", "C12H10O4S"));
formulas.Add(new Tuple<string, string>("1 extra H", "C12H11O4S"));
formulas.Add(new Tuple<string, string>("2 extra H", "C12H12O4S"));
formulas.Add(new Tuple<string, string>("3 extra H", "C12H13O4S"));
formulas.Add(new Tuple<string, string>("3 extra H", "C12H14O4S"));
formulas.Add(new Tuple<string, string>("4 extra H", "C12H15O4S"));
formulas.Add(new Tuple<string, string>("5 extra H", "C12H16O4S"));
formulas.Add(new Tuple<string, string>("1 less H", "C12H9O4S"));
formulas.Add(new Tuple<string, string>("2 less H", "C12H8O4S"));
formulas.Add(new Tuple<string, string>("3 less H", "C12H7O4S"));
formulas.Add(new Tuple<string, string>("4 less H", "C12H6O4S"));
Console.WriteLine("[Intensity], [Distance1], [Distance2], [Angle], [Pearson], [Bucha]");
string fileLocation = BPSNegative;
CrossSectionSearchParameters parameters = new CrossSectionSearchParameters(driftTubeLength);
CrossSectionWorkfow workflow = new CrossSectionWorkfow(fileLocation, "output", parameters);
foreach (var form in formulas)
{
bool found = false;
MolecularTarget target = new MolecularTarget(form.Item2, new IonizationAdduct(IonizationMethod.Deprotonated), form.Item1);
Console.Write(form.Item1 + ": ");
var smoother = new SavitzkyGolaySmoother(parameters.NumPointForSmoothing, 2);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
if (target.CompositionWithAdduct != null)
{
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
var theoreticalFeatureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = theoreticalFeatureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
}
// Generate VoltageSeparatedAccumulatedXICs
var uimfReader = new DataReader(fileLocation);
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(uimfReader, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm, parameters.DriftTubeLengthInCm);
var voltageGroup = accumulatedXiCs.Keys.First();
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, smoother, parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, uimfReader, voltageGroup, target.MassWithAdduct, parameters.MzWindowHalfWidthInPpm)).ToList();
// feature scorings and Target selection.
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, uimfReader);
// Check each XIC Peak found
foreach (var peak in standardPeaks)
{
// Evaluate feature scores.
double intensityScore = FeatureScoreUtilities.IntensityScore(peak, globalMaxIntensity);
double isotopicScoreAngle = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Angle,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistance = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistance,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScorePerson = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.PearsonCorrelation,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreBhattacharyya = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.Bhattacharyya,
globalMaxIntensity,
workflow.NumberOfScans);
double isotopicScoreDistanceAlternative = FeatureScoreUtilities.IsotopicProfileScore(
peak,
workflow.uimfReader,
target,
theoreticalIsotopicProfilePeakList,
voltageGroup,
IsotopicScoreMethod.EuclideanDistanceAlternative,
globalMaxIntensity,
workflow.NumberOfScans);
double peakShapeScore = FeatureScoreUtilities.PeakShapeScore(peak, workflow.uimfReader, workflow.Parameters.MzWindowHalfWidthInPpm, workflow.Parameters.DriftTimeToleranceInMs, voltageGroup, globalMaxIntensity, workflow.NumberOfScans);
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", intensityScore);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreDistance);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreDistanceAlternative);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreAngle);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScorePerson);
found = true;
}
// Report all features.
if (peak.PeakApex.DriftTimeCenterInScanNumber == 115)
{
Console.Write("{0:F4} ", isotopicScoreBhattacharyya);
found = true;
}
}
if (!found)
{
Console.Write("No features");
}
Console.WriteLine();
}
// Manually dispose so it doesn't interfere with other tests.
workflow.Dispose();
}
/// <summary>
/// The run libray match workflow.
/// </summary>
/// <param name="target">
/// The Target.
/// </param>
/// <returns>
/// The <see cref="LibraryMatchResult"/>.
/// </returns>
private LibraryMatchResult RunLibrayMatchWorkflow(DriftTimeTarget target)
{
Trace.WriteLine(" Target: " + target.CorrespondingChemical);
Trace.WriteLine(" Target Info: " + target.TargetDescriptor);
// Generate Theoretical Isotopic Profile
List<Peak> theoreticalIsotopicProfilePeakList = null;
string empiricalFormula = target.CompositionWithAdduct.ToPlainString();
ITheorFeatureGenerator featureGenerator = new JoshTheorFeatureGenerator();
IsotopicProfile theoreticalIsotopicProfile = featureGenerator.GenerateTheorProfile(empiricalFormula, 1);
theoreticalIsotopicProfilePeakList = theoreticalIsotopicProfile.Peaklist.Cast<Peak>().ToList();
// Voltage grouping
VoltageSeparatedAccumulatedXiCs accumulatedXiCs = new VoltageSeparatedAccumulatedXiCs(this.uimfReader, target.MassWithAdduct, this.Parameters.InitialSearchMassToleranceInPpm, target.NormalizedDriftTimeInMs, this.Parameters.DriftTimeToleranceInMs, this.Parameters.DriftTubeLengthInCm);
foreach (VoltageGroup voltageGroup in accumulatedXiCs.Keys)
{
// TODO Verify the temperature, pressure and drift tube voltage of the voltage group
// Because we don't record TVP info in the AMT library. we can't verify it yet, so stick with last voltage group.
if (IMSUtil.IsLastVoltageGroup(voltageGroup, this.NumberOfFrames))
{
double globalMaxIntensity = IMSUtil.MaxIntensityAfterFrameAccumulation(voltageGroup, this.uimfReader);
Trace.WriteLine(string.Format(" Temperature/Pressure/Voltage Adjusted Drift time: {0:F4} ms", IMSUtil.DeNormalizeDriftTime(target.NormalizedDriftTimeInMs, voltageGroup)));
// Find peaks using multidimensional peak finder.
List<IntensityPoint> intensityPoints = accumulatedXiCs[voltageGroup].IntensityPoints;
List<FeatureBlob> featureBlobs = PeakFinding.FindPeakUsingWatershed(intensityPoints, this.smoother, this.Parameters.FeatureFilterLevel);
List<StandardImsPeak> standardPeaks = featureBlobs.Select(featureBlob => new StandardImsPeak(featureBlob, this.uimfReader, voltageGroup, target.MassWithAdduct, this.Parameters.InitialSearchMassToleranceInPpm)).ToList();
// Score features
IDictionary<StandardImsPeak, PeakScores> scoresTable = new Dictionary<StandardImsPeak, PeakScores>();
Trace.WriteLine(string.Format(" Voltage Group: {0:F4} V, [{1}-{2}]", voltageGroup.MeanVoltageInVolts, voltageGroup.FirstFrameNumber, voltageGroup.LastFrameNumber));
foreach (StandardImsPeak peak in standardPeaks)
{
PeakScores currentStatistics = FeatureScoreUtilities.ScoreFeature(
peak,
globalMaxIntensity,
this.uimfReader,
this.Parameters.InitialSearchMassToleranceInPpm,
this.Parameters.DriftTimeToleranceInMs,
voltageGroup,
this.NumberOfScans,
target,
IsotopicScoreMethod.Angle,
theoreticalIsotopicProfilePeakList);
scoresTable.Add(peak, currentStatistics);
}
// filter out features with Ims scans at 1% left or right.
Predicate<StandardImsPeak> scanPredicate = blob => FeatureFilters.FilterExtremeDriftTime(blob, (int)this.NumberOfScans);
Predicate<StandardImsPeak> shapeThreshold = blob => FeatureFilters.FilterBadPeakShape(blob, scoresTable[blob].PeakShapeScore, this.Parameters.PeakShapeThreshold);
Predicate<StandardImsPeak> isotopeThreshold = blob => FeatureFilters.FilterBadIsotopicProfile(blob, scoresTable[blob].IsotopicScore, this.Parameters.IsotopicThreshold);
Predicate<StandardImsPeak> massDistanceThreshold = blob => FeatureFilters.FilterHighMzDistance(blob, target, this.Parameters.MatchingMassToleranceInPpm);
// Print out candidate features that pass the intensity threshold.
foreach (StandardImsPeak peak in standardPeaks)
{
DriftTimeFeatureDistance distance = new DriftTimeFeatureDistance(target, peak, voltageGroup);
bool badScanRange = scanPredicate(peak);
bool badPeakShape = shapeThreshold(peak);
bool lowIsotopicAffinity = isotopeThreshold(peak);
bool lowMzAffinity = massDistanceThreshold(peak);
PeakScores currentStatistics = scoresTable[peak];
Trace.WriteLine(string.Empty);
Trace.WriteLine(string.Format(" Candidate feature found at drift time {0:F2} ms (scan number {1})",
peak.PeakApex.DriftTimeCenterInMs,
peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(
string.Format(
" M/Z: {0:F2} Dalton", peak.PeakApex.MzCenterInDalton));
Trace.WriteLine(
string.Format(
" Drift time: {0:F2} ms (scan number {1})",
peak.PeakApex.DriftTimeCenterInMs,
peak.PeakApex.DriftTimeCenterInScanNumber));
Trace.WriteLine(
string.Format(" MzInDalton difference: {0:F2} ppm", distance.MassDifferenceInPpm));
Trace.WriteLine(
string.Format(" Drift time difference: {0:F4} ms", distance.DriftTimeDifferenceInMs));
Trace.WriteLine(string.Format(" Intensity Score: {0:F4}", currentStatistics.IntensityScore));
Trace.WriteLine(string.Format(" Peak Shape Score: {0:F4}", currentStatistics.PeakShapeScore));
Trace.WriteLine(string.Format(" Isotopic Score: {0:F4}", currentStatistics.IsotopicScore));
Trace.WriteLine(string.Format(" AveragedPeakIntensities: {0:F4}", peak.SummedIntensities));
string rejectionReason = badScanRange ? " [Bad scan range] " : " ";
rejectionReason += badPeakShape ? "[Bad Peak Shape] " : string.Empty;
rejectionReason += lowMzAffinity ? "[Inaccurate Mass] " : string.Empty;
rejectionReason += lowIsotopicAffinity ? "[Different Isotopic Profile] " : string.Empty;
if (badScanRange || lowIsotopicAffinity || badPeakShape)
{
Trace.WriteLine(rejectionReason);
}
else
{
Trace.WriteLine(" [Pass]");
}
}
standardPeaks.RemoveAll(scanPredicate);
standardPeaks.RemoveAll(massDistanceThreshold);
standardPeaks.RemoveAll(shapeThreshold);
standardPeaks.RemoveAll(isotopeThreshold);
if (standardPeaks.Count == 0)
{
Trace.WriteLine(string.Format(" [No Match]"));
Trace.WriteLine(string.Empty);
return new LibraryMatchResult(null, AnalysisStatus.Negative, null);
}
StandardImsPeak closestPeak = standardPeaks.First();
DriftTimeFeatureDistance shortestDistance = new DriftTimeFeatureDistance(target, standardPeaks.First(), voltageGroup);
foreach (var peak in standardPeaks)
{
DriftTimeFeatureDistance distance = new DriftTimeFeatureDistance(target, peak, voltageGroup);
if (distance.CompareTo(shortestDistance) < 0)
{
closestPeak = peak;
}
}
Trace.WriteLine(string.Format(" [Match]"));
Trace.WriteLine(string.Empty);
return new LibraryMatchResult(closestPeak, AnalysisStatus.Positive, shortestDistance);
}
}
throw new Exception("No voltage groups in the Dataset match temerature, pressure, or drift tube voltage setting from the library. Matching failed.");
}
