public void OnMsMsSearchResultChange(SpectrumSearchResult spectrumSearchResult)
{
CurrentSpectrumSearchResult = spectrumSearchResult;
CurrentLipidTarget = LipidUtil.CreateLipidTarget((spectrumSearchResult.HcdSpectrum ?? spectrumSearchResult.CidSpectrum).IsolationWindow.IsolationWindowTargetMz, TargetFragmentationMode, TargetAdduct);
OnPropertyChanged("CurrentSpectrumSearchResult");
OnPropertyChanged("CurrentLipidTarget");
}
public LipidTarget CreateLipidTarget()
{
Adduct adduct;
FragmentationMode fragmentationMode;
if (AdductFull == "[M+H]+")
{
adduct = Adduct.Hydrogen;
fragmentationMode = FragmentationMode.Positive;
}
else if (AdductFull == "[M+NH4]+")
{
adduct = Adduct.Ammonium;
fragmentationMode = FragmentationMode.Positive;
}
else if (AdductFull == "[M+Na]+")
{
adduct = Adduct.Sodium;
fragmentationMode = FragmentationMode.Positive;
}
else if (AdductFull == "[M+K]+")
{
adduct = Adduct.Potassium;
fragmentationMode = FragmentationMode.Positive;
}
else if (AdductFull == "[M+Oac]-")
{
adduct = Adduct.Acetate;
fragmentationMode = FragmentationMode.Negative;
}
else if (AdductFull == "[M-H]-")
{
adduct = Adduct.Hydrogen;
fragmentationMode = FragmentationMode.Negative;
}
else if (AdductFull == "[M-2H]--")
{
adduct = Adduct.Dihydrogen;
fragmentationMode = FragmentationMode.Negative;
}
else
{
throw new SystemException("Unknown adduct: " + AdductFull);
}
var lipidTarget = LipidUtil.CreateLipidTarget(CommonName, fragmentationMode, adduct);
return(lipidTarget);
}
public void SearchForTarget(string commonName, Adduct adduct, FragmentationMode fragmentationMode, double hcdMassError, double cidMassError)
{
CurrentLipidTarget = LipidUtil.CreateLipidTarget(commonName, fragmentationMode, adduct);
OnPropertyChanged("CurrentLipidTarget");
SpectrumSearchResultList = InformedWorkflow.RunInformedWorkflow(CurrentLipidTarget, LcMsRun, hcdMassError, cidMassError, ScoreModel);
OnPropertyChanged("SpectrumSearchResultList");
if (SpectrumSearchResultList.Any())
{
var spectrumSearchResult = SpectrumSearchResultList.OrderByDescending(x => x.NumMatchingMsMsPeaks).First();
OnSpectrumSearchResultChange(spectrumSearchResult);
}
else
{
CurrentSpectrumSearchResult = null;
}
}
public void SearchForFragments(double hcdError, double cidError, FragmentationMode fragmentationMode, int numResultsPerScanToInclude, int minMatches, Adduct adduct)
{
IProgress <int> progress = new Progress <int>(ReportFragmentSearchProgress);
SpectrumSearchResultList = InformedWorkflow.RunFragmentWorkflow(FragmentSearchList, LcMsRun, hcdError, cidError, minMatches, progress);
OnPropertyChanged("SpectrumSearchResultList");
progress.Report(0);
if (SpectrumSearchResultList.Any())
{
var spectrumSearchResult =
SpectrumSearchResultList.OrderByDescending(x => x.ApexScanNum).First();
CurrentLipidTarget = LipidUtil.CreateLipidTarget((spectrumSearchResult.HcdSpectrum ?? spectrumSearchResult.CidSpectrum).IsolationWindow.IsolationWindowTargetMz, fragmentationMode, adduct);
//OnMsMsSearchResultChange(spectrumSearchResult);
OnSpectrumSearchResultChange(spectrumSearchResult);
}
else
{
CurrentSpectrumSearchResult = null;
}
}
public void TestSingleTarget()
{
// Testing PC(16:0/18:1) +H
const string commonName = "PC(16:0/18:1)";
const string empiricalFormula = "C42H83NO8P";
const LipidClass lipidClass = LipidClass.PC;
const FragmentationMode fragmentationMode = FragmentationMode.Positive;
var acylChainList = new List <AcylChain> {
new AcylChain("16:0"), new AcylChain("18:1")
};
var lipidTarget = LipidUtil.CreateLipidTarget(commonName, empiricalFormula, lipidClass, fragmentationMode, acylChainList);
var rawFileLocation = @"../../../testFiles/XGA121_lipid_Skin_1.raw";
var informedWorkflow = new InformedWorkflow(rawFileLocation);
var resultList = informedWorkflow.RunInformedWorkflow(lipidTarget, 30, 500);
foreach (var result in resultList.OrderByDescending(x => x.GetNumMatchingMsMsPeaks()))
{
Console.WriteLine(result.Xic.GetApexScanNum() + " - " + result.HcdSpectrum.ScanNum + " - " + result.CidSpectrum.ScanNum + " - " + result.GetNumMatchingMsMsPeaks());
}
}
public void TestSingleConfidentTarget()
{
// Testing PE(18:3/20:5) +H
const string commonName = "PE(18:3/20:5)";
const string empiricalFormula = "C43H71NO8P";
const LipidClass lipidClass = LipidClass.PE;
const FragmentationMode fragmentationMode = FragmentationMode.Positive;
var acylChainList = new List <AcylChain> {
new AcylChain("18:3"), new AcylChain("20:5")
};
var lipidTarget = LipidUtil.CreateLipidTarget(commonName, empiricalFormula, lipidClass, fragmentationMode, acylChainList);
var rawFileLocation = @"../../../testFiles/Daphnia_gut_TLE_POS_Gimli_21Jan14_13-07-01.raw";
var informedWorkflow = new InformedWorkflow(rawFileLocation);
var resultList = informedWorkflow.RunInformedWorkflow(lipidTarget, 30, 500);
foreach (var result in resultList.OrderByDescending(x => x.GetNumMatchingMsMsPeaks()))
{
Console.WriteLine(result.Xic.GetApexScanNum() + " - " + result.HcdSpectrum.ScanNum + " - " + result.CidSpectrum.ScanNum + " - " + result.GetNumMatchingMsMsPeaks());
}
}
