public void GetDistributionTest1()
{
//I got the data below from file: QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW
// scan = 6067
//can use this as a means of overlaying the mercury data on the actual data
double mz = 1154.98841279744; //mono MZ
int chargestate = 2;
double fwhm = 0.0290254950523376; //from second peak of isotopic profile
double monoMass = 1154.98841279744 * chargestate - chargestate * 1.00727649;
double resolution = mz / fwhm;
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(monoMass, chargestate, resolution);
Assert.AreEqual(3778, distcreator.Data.Xvalues.Length);
Assert.AreEqual("C103H151N28O31S1", distcreator.MolecularFormula.ToFormulaString());
//MolecularFormula.Phosphorus.
StringBuilder sb = new StringBuilder();
TestUtilities.GetXYValuesToStringBuilder(sb, distcreator.Data.Xvalues, distcreator.Data.Yvalues);
Console.Write(sb.ToString());
}
public void compareTomIsotopicDist_with_Mercury()
{
double mz = 1154.98841279744; //mono MZ
int chargestate = 2;
double fwhm = 0.0290254950523376; //from second peak of isotopic profile
double monoMass = 1154.98841279744 * chargestate - chargestate * 1.00727649;
double resolution = mz / fwhm;
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(monoMass, chargestate, resolution);
distcreator.getIsotopicProfile();
Assert.AreEqual(8, distcreator.IsotopicProfile.GetNumOfIsotopesInProfile());
StringBuilder sb = new StringBuilder();
TestUtilities.ReportIsotopicProfileData(sb, distcreator.IsotopicProfile);
IsotopicProfile cluster = TomIsotopicPattern.GetAvnPattern(monoMass, false);
sb.Append(Environment.NewLine);
TestUtilities.ReportIsotopicProfileData(sb, cluster);
Console.Write(sb.ToString());
}
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 fitterOnHornDataTest1()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6067);
Task msGen = new GenericMSGenerator(1154, 1158);
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 DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
DeconToolsV2.HornTransform.clsHornTransformParameters hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters();
hornParameters.PeptideMinBackgroundRatio = 2;
Task decon = new HornDeconvolutor(hornParameters);
decon.Execute(results);
IsosResult result1 = results.ResultList[0];
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
distcreator.OffsetDistribution(result1.IsotopicProfile);
XYData theorXYData = distcreator.Data;
StringBuilder sb = new StringBuilder();
TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues);
Console.WriteLine(sb.ToString());
AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10);
double fitval = areafitter.getFit();
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score);
Assert.AreEqual(0.0209385414928986, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m
}
public void fitterOnHornDataTest2()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
Task msGen = new GenericMSGenerator(579, 582);
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 DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
decon.Execute(results);
IsosResult result1 = results.ResultList[1];
double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM();
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution);
StringBuilder sb = new StringBuilder();
XYData 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());
AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10);
double fitval = areafitter.getFit();
Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval);
Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score * 100);
Assert.AreEqual(0.0704215577242672, (decimal)fitval);
}
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);
}
public void getFormulasTest1()
{
MercuryDistributionCreator merc = new MercuryDistributionCreator();
int chargeState = 3;
MolecularFormula formula;
for (double mz = 100; mz < 3000; mz++)
{
formula = merc.GetAveragineFormula(mz, chargeState);
StringBuilder sb = new StringBuilder();
sb.Append(mz);
sb.Append("\t");
reportFormula(sb, formula);
Console.Write(sb.ToString());
}
}
public MercuryDistCollection CreateMercuryDistCollection(double startMass, double stopMass, double stepSize, double fwhm)
{
var mercDistCollection = new MercuryDistCollection();
mercDistCreator = new MercuryDistributionCreator();
Check.Require(stepSize > 0, "Step size must be greater than 0");
Check.Require(stopMass >= startMass, "Stop MZ must be greater than Start MZ");
Check.Require(startMass > 0, "Starting MZ must be greater than 0");
for (var mass = startMass; mass <= stopMass; mass = mass + stepSize)
{
var mercdist = new MercuryDist();
mercDistCreator.CreateDistribution(mass, 1, fwhm);
mercdist.Xydata = mercDistCreator.Data;
mercDistCollection.mercDistList.Add(mercdist);
}
return(mercDistCollection);
}
public void getpeaksFromDistributionTest1()
{
double mz = 1154.98841279744; //mono MZ
int chargestate = 2;
double fwhm = 0.0290254950523376; //from second peak of isotopic profile
double monoMass = 1154.98841279744 * chargestate - chargestate * 1.00727649;
double resolution = mz / fwhm;
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(monoMass, chargestate, resolution);
distcreator.getIsotopicProfile();
Assert.AreEqual(8, distcreator.IsotopicProfile.GetNumOfIsotopesInProfile());
StringBuilder sb = new StringBuilder();
TestUtilities.ReportIsotopicProfileData(sb, distcreator.IsotopicProfile);
Console.Write(sb.ToString());
}
public void test1()
{
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);
MercuryDistributionCreator distcreator = new MercuryDistributionCreator();
distcreator.CreateDistribution(mt.MonoIsotopicMass, mt.ChargeState, 40000);
distcreator.getIsotopicProfile();
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
//TestUtilities.DisplayIsotopicProfileData(distcreator.IsotopicProfile);
Assert.AreEqual(7, mt.IsotopicProfile.Peaklist.Count);
Assert.AreEqual(1138.59201544m, (decimal)mt.IsotopicProfile.Peaklist[0].XValue);
Assert.AreEqual((1138.59201544m + 1.00235m / 2m), (decimal)mt.IsotopicProfile.Peaklist[1].XValue);
}
public void effectOfFWHMOnFitTest()
{
Run run = new XCaliburRun(xcaliburTestfile);
ResultCollection results = new ResultCollection(run);
run.CurrentScanSet = new ScanSet(6005);
Task msGen = new GenericMSGenerator(1154, 1160);
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 DeconToolsPeakDetector(detectorParams);
peakDetector.Execute(results);
Task decon = new HornDeconvolutor();
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);
StringBuilder sb = new StringBuilder();
AreaFitter areafitter = new AreaFitter(distcreator.Data, run.XYData, 10);
double fitval = areafitter.getFit();
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
for (double 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(distcreator.Data, run.XYData, 10);
fitval = areafitter.getFit();
sb.Append(resolution);
sb.Append("\t");
sb.Append(fitval);
sb.Append("\n");
}
//Console.Write(sb.ToString());
}
