public void DetectPeaksTest1()
{
var peakBR = 1.3;
double sigNoise = 2;
var isThresholded = true;
var peakfitType = DeconTools.Backend.Globals.PeakFitType.QUADRATIC;
var testFile = FileRefs.RawDataMSFiles.OrbitrapStdFile1;
Run run = new XCaliburRun2(testFile);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
run.CurrentScanSet = new ScanSet(6005);
msgen.Execute(run.ResultCollection);
var peakDet = new DeconToolsPeakDetectorV2(peakBR, sigNoise, peakfitType, isThresholded);
peakDet.PeaksAreStored = true;
var peakList = peakDet.FindPeaks(run.XYData, 0, 50000);
TestUtilities.DisplayPeaks(peakList);
}
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 n14N15LabelledData_TFFTest1()
{
double featureFinderTol = 15;
var featureFinderRequiresMonoPeak = false;
var n14n15Util = new N14N15TestingUtilities();
//get sample MS from Test Data
var massSpectrum = n14n15Util.GetSpectrumAMTTag23140708_Z3_Sum3(); //this is the diff b/w previous test and this one
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);
//generate theor unlabelled profile
var unlabelledfeatureGen = new TomTheorFeatureGenerator();
unlabelledfeatureGen.GenerateTheorFeature(mt23140708);
//generate theor N15-labelled profile
var n15featureGen = new TomTheorFeatureGenerator(Globals.LabellingType.N15, 0.005);
n15featureGen.GenerateTheorFeature(mt23140708);
//find features in experimental data, using the theoretical profiles
var msfeatureFinder = new BasicTFF();
msfeatureFinder.ToleranceInPPM = featureFinderTol;
msfeatureFinder.NeedMonoIsotopicPeak = featureFinderRequiresMonoPeak;
var n14profile = msfeatureFinder.FindMSFeature(msPeakList, mt23140708.IsotopicProfile);
var n15profile = msfeatureFinder.FindMSFeature(msPeakList, mt23140708.IsotopicProfileLabelled);
Console.WriteLine(mt23140708.GetEmpiricalFormulaFromTargetCode());
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(mt23140708.IsotopicProfileLabelled);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n14profile);
Console.WriteLine();
TestUtilities.DisplayIsotopicProfileData(n15profile);
}
public void OldPeakDetectorTest1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6005);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
var peaks = peakDetector.FindPeaks(run.XYData, 481.1, 481.4);
TestUtilities.DisplayPeaks(peaks);
}
public void CalcOfFwhmByOldPeakdetector_Test1()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6005);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 1.3;
peakDetector.SignalToNoiseThreshold = 2;
peakDetector.PeakFitType = Globals.PeakFitType.QUADRATIC;
peakDetector.IsDataThresholded = true;
var oldPeakDetector = new DeconToolsPeakDetectorV2(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
var mzStart = 692.8;
var mzStop = 693.2;
var peaks = peakDetector.FindPeaks(run.XYData.Xvalues, run.XYData.Yvalues, mzStart, mzStop);
var oldPeaks = oldPeakDetector.FindPeaks(run.XYData, mzStart, mzStop);
TestUtilities.DisplayPeaks(peaks);
TestUtilities.DisplayPeaks(oldPeaks);
}
public void NewPeakDetectorTest2()
{
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var scan = new ScanSet(6005);
var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType);
var peakDetector = new DeconToolsPeakDetectorV2();
peakDetector.PeakToBackgroundRatio = 1.3;
peakDetector.SignalToNoiseThreshold = 2;
peakDetector.PeakFitType = Globals.PeakFitType.QUADRATIC;
peakDetector.IsDataThresholded = true;
run.CurrentScanSet = scan;
msgen.Execute(run.ResultCollection);
var peaks = peakDetector.FindPeaks(run.XYData.Xvalues, run.XYData.Yvalues, 400, 1000);
var expectedPeaks = new List <Peak>();
// 3 most abundant peaks
expectedPeaks.Add(new Peak(481.274, 13084440F, 0.0079F));
expectedPeaks.Add(new Peak(639.822, 9063344F, 0.0119F));
expectedPeaks.Add(new Peak(579.63, 7917913F, 0.0104F));
// 3 medium abundance peaks
expectedPeaks.Add(new Peak(907.961, 416092.1F, 0.0187F));
expectedPeaks.Add(new Peak(607.305, 415606.4F, 0.0114F));
expectedPeaks.Add(new Peak(515.945, 415311F, 0.0086F));
// 3 least abundant peaks
expectedPeaks.Add(new Peak(861.366, 199058.3F, 0.0192F));
expectedPeaks.Add(new Peak(479.754, 198565.2F, 0.0071F));
expectedPeaks.Add(new Peak(935.447, 198530.2F, 0.0206F));
var sb = new StringBuilder();
sb.Append("Looking for " + expectedPeaks.Count + " expected peaks" + Environment.NewLine);
sb.Append("Index\tXVal \tYVal \tWidth" + Environment.NewLine);
// Look for each expected peak in the actual peaks
foreach (var expectedPeak in (from peak in expectedPeaks orderby peak.XValue select peak))
{
var found = false;
foreach (var peak in peaks)
{
if (Math.Abs(expectedPeak.XValue - peak.XValue) < 0.01)
{
var widthIsDifferent = Math.Abs(expectedPeak.Width - peak.Width) > 0.001;
sb.Append(peak.DataIndex + "\t" + peak.XValue.ToString("0.000").PadRight(8) + "\t" + peak.Height.ToString("0").PadRight(8) + "\t" + peak.Width.ToString("0.0000") + Environment.NewLine);
found = true;
break;
}
}
if (!found)
{
sb.Append("Expected peak not found: ");
sb.Append(expectedPeak.DataIndex + "\t" + expectedPeak.XValue + "\t" + expectedPeak.Height + "\t" + expectedPeak.Width.ToString("0.0000"));
}
Assert.IsTrue(found);
}
Console.WriteLine(sb.ToString());
// Console.WriteLine("Full peak list");
// TestUtilities.DisplayPeaks(peaks);
}
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
}
