public void OnUpdateTargetAdductFragmentation(Adduct adduct, FragmentationMode fragmode)
{
TargetAdduct = adduct;
TargetFragmentationMode = fragmode;
OnPropertyChanged("TargetAdduct");
OnPropertyChanged("TargetFragmentationMode");
}
public SpecificFragment(LipidClass lipidClass, LipidType lipidType, string fragmentDescription, FragmentationMode fragmentationMode, FragmentationType fragmentationType)
{
LipidClass = lipidClass;
LipidType = lipidType;
FragmentDescription = fragmentDescription;
FragmentationMode = fragmentationMode;
FragmentationType = fragmentationType;
}
public LipidGroupSearchResult(SpectrumSearchResult spectrumSearchResult, FragmentationMode fragmentationMode, Adduct adduct)
{
var msmsSpec = spectrumSearchResult.CidSpectrum ?? spectrumSearchResult.HcdSpectrum;
LipidTarget = new LipidTarget(msmsSpec.IsolationWindow.ToString(), LipidClass.Unknown, fragmentationMode, null, null, adduct);
LipidList = null;
SpectrumSearchResult = spectrumSearchResult;
DisplayScanNum = msmsSpec.ScanNum;
DisplayMz = msmsSpec.IsolationWindow.IsolationWindowTargetMz;
ShouldExport = false;
Score = 0;
}
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 LipidTarget(
string commonName,
LipidClass lipidClass,
FragmentationMode fragmentationMode,
Composition composition,
IEnumerable <AcylChain> acylChainList,
Adduct adduct = Adduct.Hydrogen, int charge = 1)
{
CommonName = commonName;
LipidClass = lipidClass;
FragmentationMode = fragmentationMode;
Composition = composition;
AcylChainList = acylChainList.ToList();
Adduct = adduct;
Charge = charge;
LipidType = FigureOutLipidType();
}
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 OnProcessAllTarget(double hcdError, double cidError, FragmentationMode fragmentationMode, int numResultsPerScanToInclude)
{
IProgress <int> progress = new Progress <int>(ReportGlobalWorkflowProgress);
// Make sure to only look at targets that match the fragmentation mode
var targetsToProcess = LipidTargetList.Where(x => x.LipidTarget.FragmentationMode == fragmentationMode);
// Run global analysis
LipidGroupSearchResultList = new List <LipidGroupSearchResult>();
IEnumerable <IGrouping <double, LipidGroupSearchResult> > resultsGrouped;
List <LipidGroupSearchResult> lipidGroupSearchResultList;
if (AverageSpec)
{
lipidGroupSearchResultList = GlobalWorkflow.RunGlobalWorkflowAvgSpec(targetsToProcess, LcMsRun, hcdError, cidError, ScoreModel, progress);
resultsGrouped = lipidGroupSearchResultList.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum?.IsolationWindow.IsolationWindowTargetMz ?? x.SpectrumSearchResult.CidSpectrum.IsolationWindow.IsolationWindowTargetMz);
}
else
{
lipidGroupSearchResultList = GlobalWorkflow.RunGlobalWorkflow(targetsToProcess, LcMsRun, hcdError, cidError, ScoreModel, progress);
resultsGrouped = lipidGroupSearchResultList.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum?.ScanNum ?? (double)x.SpectrumSearchResult.CidSpectrum.ScanNum);
}
// Group results of same scan together
// Grab the result(s) with the best score
foreach (var group in resultsGrouped)
{
var groupOrdered = group.OrderByDescending(x => x.Score).ToList();
for (var i = 0; i < numResultsPerScanToInclude && i < groupOrdered.Count; i++)
{
var resultToAdd = groupOrdered[i];
LipidGroupSearchResultList.Add(resultToAdd);
}
}
OnPropertyChanged("LipidGroupSearchResultList");
progress.Report(0);
}
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());
}
}
public int CompareTo(ScoreModelUnit other)
{
if (!LipidClass.Equals(other.LipidClass))
{
return(LipidClass.CompareTo(other.LipidClass));
}
if (!LipidType.Equals(other.LipidType))
{
return(LipidType.CompareTo(other.LipidType));
}
if (!FragmentDescription.Equals(other.FragmentDescription))
{
return(String.Compare(FragmentDescription, other.FragmentDescription, StringComparison.Ordinal));
}
if (!FragmentationMode.Equals(other.FragmentationMode))
{
return(FragmentationMode.CompareTo(other.FragmentationMode));
}
if (!FragmentationType.Equals(other.FragmentationType))
{
return(FragmentationType.CompareTo(other.FragmentationType));
}
return(IntensityMax.CompareTo(other.IntensityMax));
}
public int CompareTo(SpecificFragment other)
{
if (!LipidClass.Equals(other.LipidClass))
{
return(LipidClass.CompareTo(other.LipidClass));
}
if (!LipidType.Equals(other.LipidType))
{
return(LipidType.CompareTo(other.LipidType));
}
if (!FragmentDescription.Equals(other.FragmentDescription))
{
return(String.Compare(FragmentDescription, other.FragmentDescription, StringComparison.Ordinal));
}
if (!FragmentationMode.Equals(other.FragmentationMode))
{
return(FragmentationMode.CompareTo(other.FragmentationMode));
}
return(FragmentationType.CompareTo(other.FragmentationType));
}
public void OnBuildLibrary(IList <string> filesList, double hcdError, double cidError, FragmentationMode fragmentationMode, int numResultsPerScanToInclude)
{
foreach (var file in filesList)
{
using (var reader = new StreamReader(new FileStream(file, FileMode.Open, FileAccess.Read, FileShare.ReadWrite)))
{
if (reader.EndOfStream)
{
continue;
}
var headerLine = reader.ReadLine();
if (string.IsNullOrWhiteSpace(headerLine))
{
// Empty header line
continue;
}
var header = headerLine.Split('\t').ToList();
var index = header.IndexOf("Raw Data File");
if (index == -1)
{
continue;
}
if (reader.EndOfStream)
{
continue;
}
try
{
var dataLine = reader.ReadLine();
if (string.IsNullOrWhiteSpace(dataLine))
{
// Empty data line
continue;
}
var rawFileName = dataLine.Split('\t')[index];
LibraryBuilder.AddDmsDataset(rawFileName);
UpdateRawFileLocation(rawFileName);
OnProcessAllTarget(hcdError, cidError, fragmentationMode, numResultsPerScanToInclude);
LoadLipidIdentifications(file);
OnExportGlobalResults(file.Replace(".tsv", ".msp"));
//Delete the raw files we copied from DMS to save space
LcMsRun.Close();
LcMsRun = null;
OnPropertyChanged("LcMsRun");
GC.Collect();
//File.Delete(rawFileName);
var pbfFilePath = Path.ChangeExtension(rawFileName, ".pbf");
if (string.IsNullOrWhiteSpace(pbfFilePath))
{
continue;
}
var pbfFile = new FileInfo(pbfFilePath);
if (pbfFile.Exists)
{
pbfFile.Delete();
}
}
catch (Exception)
{
// Ignore the error
}
}
}
}