public void getPeakChromatogramTest2()
{
var mt = TestUtilities.GetMassTagStandard(1);
Run run = new XCaliburRun2(FileRefs.RawDataMSFiles.OrbitrapStdFile1);
var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(FileRefs.PeakDataFiles.OrbitrapPeakFile_scans5500_6500);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = mt;
var unlabelledTheorGenerator = new TomTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var peakChromGen = new PeakChromatogramGenerator(10, Globals.ChromatogramGeneratorMode.TOP_N_PEAKS);
peakChromGen.TopNPeaksLowerCutOff = 0.4;
peakChromGen.Execute(run.ResultCollection);
Assert.AreEqual(133, run.XYData.Xvalues.Length);
Assert.AreEqual(5543, (int)run.XYData.Xvalues[35]);
//Assert.AreEqual(7319569, (int)run.XYData.Yvalues[35]);
run.XYData.Display();
}
public override void Execute(ResultCollection resultList)
{
Check.Require(resultList.Run.CurrentMassTag != null, string.Format("{0} failed. Mass tags haven't been defined.", Name));
if (resultList.Run.CurrentMassTag == null)
{
return;
}
resultList.ResultType = Globals.ResultType.N14N15_TARGETED_RESULT;
_FeatureGenerator.GenerateTheorFeature(resultList.Run.CurrentMassTag); //generate theor profile for unlabeled feature
var labeledProfile = _N15IsotopicProfileGenerator.GetN15IsotopicProfile(resultList.Run.CurrentMassTag, 0.005);
var chromExtractor = new IsotopicProfileMultiChromatogramExtractor(
NumPeaksForGeneratingChrom, ToleranceInPPM);
var massTagResult = resultList.CurrentTargetedResult;
if (!(massTagResult is N14N15_TResult n14n15result))
{
throw new InvalidOperationException(string.Format("{0} failed. There was a problem with the Result type; massTagResult is not class N14N15_TResult ", Name));
}
n14n15result.UnlabeledPeakChromData = chromExtractor.GetChromatogramsForIsotopicProfilePeaks(resultList.MSPeakResultList, resultList.Run.CurrentMassTag.IsotopicProfile);
n14n15result.LabeledPeakChromData = chromExtractor.GetChromatogramsForIsotopicProfilePeaks(resultList.MSPeakResultList, labeledProfile);
}
public void test1()
{
Run run = new XCaliburRun(bsaO16O18file1);
MSGeneratorFactory msgenFact = new MSGeneratorFactory();
Task msgen = msgenFact.CreateMSGenerator(run.MSFileType);
DeconToolsPeakDetector peakDet = new DeconToolsPeakDetector(1.3, 2, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true);
O16O18FeatureFinder finder = new O16O18FeatureFinder();
List <MassTag> massTagList = TestUtilities.CreateO16O18TestMassTagList1();
run.CurrentMassTag = massTagList[0];
TomTheorFeatureGenerator theorFeatureGen = new TomTheorFeatureGenerator();
theorFeatureGen.GenerateTheorFeature(run.CurrentMassTag);
run.CurrentScanSet = new ScanSet(3294);
msgen.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
IsotopicProfile o16O18profile = finder.FindFeature(run.PeakList, run.CurrentMassTag.IsotopicProfile, 10, true);
TestUtilities.DisplayIsotopicProfileData(o16O18profile);
}
public void TomGenerateTheorProfileTest1()
{
var mt = TestDataCreationUtilities.CreateN14N15TestMassTagList().First(p => p.ID == 23085473);
var theorGenerator = new TomTheorFeatureGenerator();
theorGenerator.GenerateTheorFeature(mt);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
//TODO: add an Assert, with a manually confirmed number.
}
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 TomGenerateN15LabelledTheorProfileTest1()
{
var mt = TestDataCreationUtilities.CreateN14N15TestMassTagList().First(p => p.ID == 23085473);
var unlabelledTheorGenerator = new TomTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var n15theorGenerator = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
n15theorGenerator.GenerateTheorFeature(mt);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfileLabelled);
//TODO: add an Assert, with a manually confirmed number.
}
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);
}
public void TomGenerateN15LabelledTheorProfileTest2()
{
var mt = TestDataCreationUtilities.CreateN14N15TestMassTagList().First(p => p.ID == 23085470);
mt.EmpiricalFormula = mt.GetEmpiricalFormulaFromTargetCode();
Console.WriteLine("Total nitrogens = " + mt.GetAtomCountForElement("N"));
var unlabelledTheorGenerator = new TomTheorFeatureGenerator();
unlabelledTheorGenerator.GenerateTheorFeature(mt);
var n15theorGenerator = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005);
n15theorGenerator.GenerateTheorFeature(mt);
//TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfileLabelled);
//TODO: add an Assert, with a manually confirmed number.
}
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
}
