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 getVeryLowN15ProfileWithIterativeTFFTest1()
{
var n14n15Util = new N14N15TestingUtilities();
//get sample MS from Test Data
var rf = new RunFactory();
var run = rf.CreateRun(N14N15TestingUtilities.MS_AMTTag23085904_z2_sum1_lowN15);
run.XYData = N14N15TestingUtilities.GetTestSpectrum(N14N15TestingUtilities.MS_AMTTag23085904_z2_sum1_lowN15);
var mt23140708 = n14n15Util.CreateMT23085904_Z2();
run.CurrentMassTag = mt23140708;
run.ResultCollection.ResultType = Globals.ResultType.N14N15_TARGETED_RESULT;
var theorN14FeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005);
theorN14FeatureGen.GenerateTheorFeature(mt23140708);
var theorN15FeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
theorN15FeatureGen.GenerateTheorFeature(mt23140708);
var parameters = new IterativeTFFParameters();
parameters.IsotopicProfileType = Globals.IsotopicProfileType.LABELLED;
parameters.ToleranceInPPM = 30;
var itff = new IterativeTFF(parameters);
itff.Execute(run.ResultCollection);
// IsotopicProfile iso = itff.iterativelyFindMSFeature(run, mt23140708.IsotopicProfileLabelled);
var result = (N14N15_TResult)run.ResultCollection.GetTargetedResult(run.CurrentMassTag);
Assert.IsNotNull(result.IsotopicProfileLabeled);
Assert.AreEqual(82280, (int)result.IntensityAggregate);
Assert.AreEqual(3, result.IsotopicProfileLabeled.MonoIsotopicPeakIndex);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfileLabeled);
}
