public void effectOfFWHMOnFitTest()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1160, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
var result1 = results.ResultList[0];
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
var distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
var sb = new StringBuilder();
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(distcreator.Data, run.XYData, 10);
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
for (var fwhm = 0.001; fwhm < 0.050; fwhm = fwhm + 0.0005)
{
distcreator = new MercuryDistributionCreator();
resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / fwhm;
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
areafitter = new AreaFitter();
fitval = areafitter.GetFit(distcreator.Data, run.XYData, 10);
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
}
//Console.Write(sb.ToString());
}
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 fitterOnRapidDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
bool isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
msGen.Execute(results);
DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters();
detectorParams.PeakBackgroundRatio = 0.5;
detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC;
detectorParams.SignalToNoiseThreshold = 3;
detectorParams.ThresholdedData = false;
Task peakDetector = new DeconToolsPeakDetectorV2(detectorParams);
peakDetector.Execute(results);
Task decon = new RapidDeconvolutor();
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
// theorXYData.Display();
AreaFitter areafitter = new AreaFitter();
double fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0207350903681061m, (decimal)fitval);
}
public void fitterOnHornDataTest1()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(1154, 1158, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
var deconParameters = new DeconToolsParameters();
deconParameters.ThrashParameters.MinMSFeatureToBackgroundRatio = 2; // PeptideMinBackgroundRatio
Task decon = new HornDeconvolutor(deconParameters);
decon.Execute(results);
var result1 = results.ResultList[0];
var distcreator = new MercuryDistributionCreator();
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
var theorXYData = distcreator.Data;
//StringBuilder sb = new StringBuilder();
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
//Console.WriteLine(sb.ToString());
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0207350903681061m, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void fitterOnHornDataTest2()
{
Run run = new XCaliburRun2(xcaliburTestfile);
var results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
var isTicRequested = false;
Task msGen = new GenericMSGenerator(579, 582, isTicRequested);
msGen.Execute(results);
Task peakDetector = new DeconToolsPeakDetectorV2(0.5, 3, Globals.PeakFitType.QUADRATIC, false);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
var result1 = results.ResultList[1];
var resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
var distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
var sb = new StringBuilder();
var theorXYData = distcreator.Data;
//TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
distcreator.OffsetDistribution(result1.IsotopicProfile);
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
//Console.WriteLine(sb.ToString());
var areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, run.XYData, 10);
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0763818319332606m, (decimal)fitval);
}
private double getFitValue(XYData rawXYData, IsotopicProfile theorIso, IsotopicProfile isoN15)
{
var indexOfMostAbundantTheorPeak = theorIso.GetIndexOfMostIntensePeak();
var indexOfCorrespondingObservedPeak = PeakUtilities.getIndexOfClosestValue(isoN15.Peaklist,
theorIso.getMostIntensePeak().XValue, 0, isoN15.Peaklist.Count - 1, 0.1);
var mzOffset = isoN15.Peaklist[indexOfCorrespondingObservedPeak].XValue - theorIso.Peaklist[indexOfMostAbundantTheorPeak].XValue;
var fwhm = isoN15.GetFWHM();
var theorXYData = theorIso.GetTheoreticalIsotopicProfileXYData(isoN15.GetFWHM());
theorXYData.OffSetXValues(mzOffset); //May want to avoid this offset if the masses have been aligned using LCMS Warp
areafitter = new AreaFitter();
var fitval = areafitter.GetFit(theorXYData, rawXYData, 0.1);
if (fitval == double.NaN || fitval > 1)
{
fitval = 1;
}
return(fitval);
}
private void PerformIterativeFittingAndGetAlignedProfile(XYData xyData, XYData theorXYData, int chargeState, ref IsotopicProfile theorIso, ref double bestFitVal)
{
if (xyData == null || xyData.Xvalues.Length == 0)
{
bestFitVal = 1;
return;
}
double relIntensityUseForFitting = 0;
int ionCountUsed;
var fitval = _areafitter.GetFit(theorXYData, xyData, relIntensityUseForFitting, out ionCountUsed);
if (fitval < bestFitVal)
{
bestFitVal = fitval;
}
double bestOffsetForTheorProfile = 0;
// move fitting window to the left
for (var numPeaksToTheLeft = 1; numPeaksToTheLeft < 10; numPeaksToTheLeft++)
{
var offsetForTheorProfile = -1 * numPeaksToTheLeft * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / chargeState;
//negative offset
fitval = _areafitter.GetFit(theorXYData, xyData, relIntensityUseForFitting, out ionCountUsed, offsetForTheorProfile);
if (fitval > bestFitVal || fitval >= 1 || double.IsNaN(fitval))
{
break;
}
bestFitVal = fitval;
bestOffsetForTheorProfile = offsetForTheorProfile;
}
//move fitting window to the right
for (var numPeaksToTheRight = 1; numPeaksToTheRight < 10; numPeaksToTheRight++)
{
var offsetForTheorProfile = numPeaksToTheRight * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS / chargeState;
fitval = _areafitter.GetFit(theorXYData, xyData, relIntensityUseForFitting, out ionCountUsed, offsetForTheorProfile);
if (fitval >= bestFitVal || fitval >= 1 || double.IsNaN(fitval))
{
break;
}
bestFitVal = fitval;
bestOffsetForTheorProfile = offsetForTheorProfile;
}
foreach (var theorMSPeak in theorIso.Peaklist)
{
theorMSPeak.XValue = theorMSPeak.XValue + bestOffsetForTheorProfile;
}
theorIso.MonoPeakMZ = theorIso.getMonoPeak().XValue;
theorIso.MonoIsotopicMass = (theorIso.MonoPeakMZ - Globals.PROTON_MASS) * chargeState;
theorIso.MostAbundantIsotopeMass = (theorIso.getMostIntensePeak().XValue - Globals.PROTON_MASS) * chargeState;
}
public override void Deconvolute(ResultCollection resultList)
{
float[] xvals = new float[1];
float[] yvals = new float[1];
resultList.Run.XYData.GetXYValuesAsSingles(ref xvals, ref yvals);
int sizeOfRapidArray = 10000;
int[] chargeResults = new int[sizeOfRapidArray];
double[] intensityResults = new double[sizeOfRapidArray];
double[] mzResults = new double[sizeOfRapidArray];
double[] scoreResults = new double[sizeOfRapidArray];
double[] avgmassResults = new double[sizeOfRapidArray];
double[] massResults = new double[sizeOfRapidArray];
double[] mostAbundantMassResults = new double[sizeOfRapidArray];
if (resultList.Run.PeakList == null || resultList.Run.PeakList.Count == 0)
{
return;
}
rapidPeakList = ConvertPeakListToRapidPeakList(resultList.Run.PeakList);
if (rapidPeakList == null || rapidPeakList.Length == 0)
{
return;
}
double rapidsBackgroundIntensityParameter = (resultList.Run.CurrentBackgroundIntensity * minPeptideToBackgroundRatio);
Transformer.PerformTransform_cluster(Convert.ToSingle(rapidsBackgroundIntensityParameter),
ref xvals, ref yvals, ref rapidPeakList, ref chargeResults,
ref intensityResults, ref mzResults, ref scoreResults, ref avgmassResults,
ref massResults, ref mostAbundantMassResults);
GenerateResults(resultList, ref chargeResults, ref intensityResults,
ref mzResults, ref scoreResults,
ref avgmassResults, ref massResults,
ref mostAbundantMassResults, this.resultCombiningMode);
if (this.IsNewFitCalculationPerformed)
{
//HACK: RAPID doesn't return the peaks of the isotopic profile. And it's score is meaningless. So will iterate over
//the results and 1) get the peaks of the isotopic profile and 2) get a least-squares fit of the isotopic profile.
foreach (IsosResult result in resultList.IsosResultBin)
{
//create a temporary mass tag, as a data object for storing relevent info, and using the CalculateMassesForIsotopicProfile() method.
PeptideTarget mt = new PeptideTarget();
mt.ChargeState = (short)result.IsotopicProfile.ChargeState;
mt.MonoIsotopicMass = result.IsotopicProfile.MonoIsotopicMass;
mt.MZ = (mt.MonoIsotopicMass / mt.ChargeState) + Globals.PROTON_MASS;
mt.EmpiricalFormula = _TomIsotopicPatternCreator.GetClosestAvnFormula(result.IsotopicProfile.MonoIsotopicMass, false);
mt.IsotopicProfile = _TomIsotopicPatternCreator.GetIsotopePattern(mt.EmpiricalFormula, _TomIsotopicPatternCreator.aafIsos);
mt.CalculateMassesForIsotopicProfile(mt.ChargeState);
double toleranceInPPM = calcToleranceInPPMFromIsotopicProfile(result.IsotopicProfile);
//this finds the isotopic profile based on the theor. isotopic profile.
BasicTFF bff = new BasicTFF(toleranceInPPM, false);
IsotopicProfile iso = bff.FindMSFeature(resultList.Run.PeakList, mt.IsotopicProfile);
if (iso != null && iso.Peaklist != null && iso.Peaklist.Count > 1)
{
//start at the second peak... and add the newly found peaks
for (int i = 1; i < iso.Peaklist.Count; i++)
{
result.IsotopicProfile.Peaklist.Add(iso.Peaklist[i]);
}
//now that we have the peaks, we can get info for MonoPlusTwoAbundance
result.IsotopicProfile.MonoPlusTwoAbundance = result.IsotopicProfile.GetMonoPlusTwoAbundance();
}
XYData theorXYData = mt.IsotopicProfile.GetTheoreticalIsotopicProfileXYData(result.IsotopicProfile.GetFWHM());
//offset the theor isotopic profile
offsetDistribution(theorXYData, mt.IsotopicProfile, result.IsotopicProfile);
AreaFitter areafitter = new AreaFitter();
int ionCountUsed;
double fitval = areafitter.GetFit(theorXYData, result.Run.XYData, 0.1, out ionCountUsed);
if (fitval == double.NaN || fitval > 1)
{
fitval = 1;
}
result.IsotopicProfile.Score = fitval;
}
}
}