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 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 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 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 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);
}
}
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 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 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]);
}
}