public void getTheorIsotopicProfileXYDataTest1()
{
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);
TestUtilities.DisplayIsotopicProfileData(mt.IsotopicProfile);
XYData xydata = TheorXYDataCalculationUtilities.Get_Theoretical_IsotopicProfileXYData(mt.IsotopicProfile, 0.02);
TestUtilities.DisplayXYValues(xydata);
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
MassTag mt = TestUtilities.GetMassTagStandard(1);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = mt;
Task theorFeatureGen = new TomTheorFeatureGenerator();
theorFeatureGen.Execute(run.ResultCollection);
int numPeaksForExtractingChrom = 3;
int toleranceInPPM = 25;
IsotopicProfileMultiChromatogramExtractor multiChromExtractor = new IsotopicProfileMultiChromatogramExtractor(
numPeaksForExtractingChrom, toleranceInPPM);
List <int> ms1Levels = run.GetMSLevelScanValues();
Dictionary <MSPeak, XYData> chromDataForIsotopicProfile = multiChromExtractor.GetChromatogramsForIsotopicProfilePeaks(run.ResultCollection.MSPeakResultList, run.CurrentMassTag.IsotopicProfile, true, ms1Levels);
multiChromExtractor.SmoothChromatograms(chromDataForIsotopicProfile, new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2));
XYData xydata1 = chromDataForIsotopicProfile.Values.First();
XYData xydata2 = chromDataForIsotopicProfile.Values.ElementAt(1);
XYData xydata3 = chromDataForIsotopicProfile.Values.ElementAt(2);
TestUtilities.DisplayXYValues(xydata3);
}
private clsMassTag convertDeconToolsMassTagToMultialignMassTag(MassTag mt)
{
clsMassTag multialignMassTag = new clsMassTag();
multialignMassTag.Id = mt.ID;
multialignMassTag.Charge1FScore = 0;
multialignMassTag.Charge2FScore = 0;
multialignMassTag.Charge3FScore = 0;
multialignMassTag.ChargeState = mt.ChargeState;
multialignMassTag.CleavageState = -1;
multialignMassTag.DiscriminantMax = 0;
//multialignMassTag.DriftTime = 0;
multialignMassTag.HighPeptideProphetProbability = 0;
multialignMassTag.Mass = mt.MonoIsotopicMass;
multialignMassTag.ModCount = -1;
multialignMassTag.Modifications = String.Empty;
multialignMassTag.MSGFSpecProbMax = 0;
multialignMassTag.MSMSObserved = mt.ObsCount;
multialignMassTag.NetAverage = mt.NETVal;
multialignMassTag.NetPredicted = -1;
multialignMassTag.NetStandardDeviation = 0;
multialignMassTag.Peptide = mt.PeptideSequence;
multialignMassTag.PeptideEx = String.Empty;
multialignMassTag.XCorr = -1;
return(multialignMassTag);
}
public void test2()
{
MassTag massTag = new MassTag();
massTag.ID = 56488;
massTag.MonoIsotopicMass = 2275.1694779;
massTag.ChargeState = 3;
massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649;
Run run = new XCaliburRun(xcaliburTestfile);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = massTag;
Task peakChromGen = new PeakChromatogramGenerator(10);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector();
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
TestUtilities.DisplayPeaks(run.PeakList);
TestUtilities.DisplayXYValues(run.ResultCollection);
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
MassTag mt = mass_tagList[0];
run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
run.CurrentMassTag = mt;
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(0.01);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
msgen.Execute(run.ResultCollection);
//run.XYData.Display();
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
Console.WriteLine("Fit val = " + result.IsotopicProfile.Score);
/*
*
*
* ------------------- MassTag = 24769---------------------------
* monoMass = 2086.0595; monoMZ = 1044.0370; ChargeState = 2; NET = 0.452; Sequence = DFNEALVHQVVVAYAANAR
*
****** Match ******
******NET = 0.452
******ChromPeak ScanNum = 9016.48992535631
******ChromPeak NETVal = 0.453
******ScanSet = { 9010, 9017, 9024, }
******Observed MZ and intensity = 1044.03290771556 1.269842E+07
******------------------------------ end --------------------------
*
*
*
*
*
*/
}
public void test3()
{
MassTag massTag = new MassTag();
massTag.ID = 56488;
massTag.MonoIsotopicMass = 2275.1694779;
massTag.ChargeState = 3;
massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649;
massTag.NETVal = 0.3520239f;
Run run = new XCaliburRun(xcaliburTestfile);
ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo();
chromAligner.Execute(run);
PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile);
peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList);
run.CurrentMassTag = massTag;
Task peakChromGen = new PeakChromatogramGenerator(20);
Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2);
Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector();
Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.1);
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
peakChromGen.Execute(run.ResultCollection);
smoother.Execute(run.ResultCollection);
peakDet.Execute(run.ResultCollection);
chromPeakSel.Execute(run.ResultCollection);
Console.WriteLine("Now generating MS....");
msgen.Execute(run.ResultCollection);
Console.WriteLine("----------- RESULTS ----------------------\n");
TestUtilities.DisplayPeaks(run.PeakList);
MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[massTag];
massTagResult.DisplayToConsole();
Assert.AreEqual(5512, massTagResult.ScanSet.PrimaryScanNumber);
}
public void createPeptideObjectTest1()
{
MassTag mt = new MassTag();
mt.ID = 56488;
mt.MonoIsotopicMass = 2275.1694779;
mt.PeptideSequence = "TTPSIIAYTDDETIVGQPAKR";
mt.NETVal = 0.3520239f;
mt.CreatePeptideObject();
Assert.AreNotEqual(null, mt.Peptide);
Assert.AreEqual(2275.16959115176m, (decimal)mt.Peptide.MonoIsotopicMass);
}
public MassTag createMassTag1()
{
MassTag mt = new MassTag();
mt.ID = 24769;
mt.MonoIsotopicMass = 2086.0595;
mt.ChargeState = 2;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
mt.PeptideSequence = "DFNEALVHQVVVAYAANAR";
mt.CreatePeptideObject();
return(mt);
}
public static MassTag GetMassTagStandard(int standardNum)
{
MassTag mt = new MassTag();
mt.ID = 86963986;
mt.MonoIsotopicMass = 1516.791851;
mt.PeptideSequence = "AAKEGISCEIIDLR";
mt.NETVal = 0.2284955f;
mt.CreatePeptideObject();
mt.ChargeState = 2;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
return(mt);
}
public static List <MassTag> CreateO16O18TestMassTagList1()
{
List <MassTag> mtList = new List <MassTag>();
MassTag mt = new MassTag();
mt.ID = 1142;
mt.MonoIsotopicMass = 921.4807035;
mt.ChargeState = 2;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
mt.PeptideSequence = "AEFVEVTK";
mt.CreatePeptideObject();
mtList.Add(mt);
return(mtList);
}
public static List <MassTag> CreateTestMassTagList()
{
List <MassTag> mtList = new List <MassTag>();
MassTag mt = new MassTag();
mt.ID = 24769;
mt.MonoIsotopicMass = 2086.0595;
mt.ChargeState = 2;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
mt.PeptideSequence = "DFNEALVHQVVVAYAANAR";
mt.CreatePeptideObject();
mtList.Add(mt);
return(mtList);
}
public static List <MassTag> CreateN14N15TestMassTagList()
{
List <MassTag> mtList = new List <MassTag>();
MassTag mt = new MassTag();
mt.ID = 23085473;
mt.NETVal = 0.3807834F;
mt.MonoIsotopicMass = 2538.33284203802;
mt.ChargeState = 3;
mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS;
mt.PeptideSequence = "AIHQPAPTFAEQSTTSEILVTGIK";
mt.CreatePeptideObject();
mtList.Add(mt);
return(mtList);
}
public void test1()
{
Run run = new XCaliburRun(xcaliburTestfile);
List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList();
MassTag mt = mass_tagList[0];
run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 });
run.CurrentMassTag = mt;
MSGeneratorFactory msgenFactory = new MSGeneratorFactory();
Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType);
DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC);
Task mspeakDet = new DeconToolsPeakDetector(peakParams);
Task theorFeatureGen = new TomTheorFeatureGenerator();
Task targetedFeatureFinder = new BasicTFF(0.01);
IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator();
Task exporter = new BasicMTResultSQLiteExporter(exporterOutputFile1);
msgen.Execute(run.ResultCollection);
//run.XYData.Display();
mspeakDet.Execute(run.ResultCollection);
theorFeatureGen.Execute(run.ResultCollection);
targetedFeatureFinder.Execute(run.ResultCollection);
fitScoreCalc.Execute(run.ResultCollection);
exporter.Execute(run.ResultCollection);
exporter.Cleanup();
MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt);
TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile);
}
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);
}
