public void getTheorIsotopicProfileXYDataTest1()
{
MassTag mt = new MassTag();
mt.ID = 56488;
mt.MonoIsotopicMass = 2275.1694779;
mt.PeptideSequence = "TTPSIIAYTDDETIVGQPAKR";
mt.NETVal = 0.3520239f;
mt.CreatePeptideObject();
mt.ChargeState = 2;
Run run = new XCaliburRun();
ResultCollection rc = new ResultCollection(run);
rc.Run.CurrentMassTag = mt;
Task theorGen = new TomTheorFeatureGenerator();
theorGen.Execute(rc);
mt.CalculateMassesForIsotopicProfile(mt.ChargeState);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
XYData xydata = TheorXYDataCalculationUtilities.Get_Theoretical_IsotopicProfileXYData(mt.IsotopicProfile, 0.02);
TestUtilities.DisplayXYValues(xydata);
}
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);
}
private XYData GetTheoreticalIsotopicProfileXYData(IsotopicProfile iso, double fwhm, double minRelIntensity)
{
var xydata = new XYData();
var xvals = new List <double>();
var yvals = new List <double>();
var mspeaks = new List <MSPeak>(iso.Peaklist);
var zeroIntensityPeakToTheLeft = new MSPeak();
zeroIntensityPeakToTheLeft.XValue = iso.Peaklist[0].XValue - 1 * 1.00235 / iso.ChargeState;
zeroIntensityPeakToTheLeft.Height = 0;
mspeaks.Insert(0, zeroIntensityPeakToTheLeft);
//TheorXYDataCalculationUtilities.GetTheoreticalIsotopicProfileXYData()
for (var peakIndex = 0; peakIndex < mspeaks.Count; peakIndex++)
{
var msPeak = mspeaks[peakIndex];
var tempXYData = TheorXYDataCalculationUtilities.GetTheorPeakData(msPeak, fwhm, NumPointsPerTheorPeak);
for (var j = 0; j < tempXYData.Xvalues.Length; j++)
{
//First peak is a zero-intensity peak. We always want to add that one. For the others,
//add intensity points that are above a certain intensity
if (peakIndex > 0)
{
if (tempXYData.Yvalues[j] >= minRelIntensity)
{
xvals.Add(tempXYData.Xvalues[j]);
yvals.Add(tempXYData.Yvalues[j]);
}
}
else
{
xvals.Add(tempXYData.Xvalues[j]);
yvals.Add(tempXYData.Yvalues[j]);
}
}
}
xydata.Xvalues = xvals.ToArray();
xydata.Yvalues = yvals.ToArray();
return(xydata);
}
public XYData GetTheorPeakData(double fwhm, int numPointsPerPeak)
{
return(TheorXYDataCalculationUtilities.GetTheorPeakData(XValue, Height, fwhm, numPointsPerPeak));
}
