public double ScoreLipidDissimilarity(LipidGroupSearchResult lipidGroupSearchResult)
{
var relatedScoreModelUnits = GetRelatedScoreModelUnits(lipidGroupSearchResult);
var spectrumSearchResult = lipidGroupSearchResult.SpectrumSearchResult;
var cidResultList = spectrumSearchResult.CidSearchResultList;
var hcdResultList = spectrumSearchResult.HcdSearchResultList;
var cidMaxIntensity = spectrumSearchResult.CidSpectrum.Peaks.Any() ? spectrumSearchResult.CidSpectrum.Peaks.Max(x => x.Intensity) : 1;
var hcdMaxIntensity = spectrumSearchResult.HcdSpectrum.Peaks.Any() ? spectrumSearchResult.HcdSpectrum.Peaks.Max(x => x.Intensity) : 1;
double lipidScore = 0;
if (cidMaxIntensity > 1)
{
// Score CID Results
lipidScore += ScoreSingleFragmentationTypeDissimilarity(cidResultList, relatedScoreModelUnits, FragmentationType.CID, cidMaxIntensity);
}
if (hcdMaxIntensity > 1)
{
// Score CID Results
lipidScore += ScoreSingleFragmentationTypeDissimilarity(hcdResultList, relatedScoreModelUnits, FragmentationType.HCD, hcdMaxIntensity);
}
return(lipidScore);
}
public static void AddHeaderForScoring(LipidGroupSearchResult lipidGroupSearchResult, TextWriter textWriter)
{
var stringBuilder = new StringBuilder();
stringBuilder.Append("Dataset,Lipid,");
var spectrumSearchResult = lipidGroupSearchResult.SpectrumSearchResult;
var cidResultList = spectrumSearchResult.CidSearchResultList;
var hcdResultList = spectrumSearchResult.HcdSearchResultList;
foreach (var cidResult in cidResultList)
{
stringBuilder.Append("CID-" + cidResult.TheoreticalPeak.Description + ",");
}
foreach (var hcdResult in hcdResultList)
{
stringBuilder.Append("HCD-" + hcdResult.TheoreticalPeak.Description + ",");
}
textWriter.WriteLine(stringBuilder.ToString());
}
private List <ScoreModelUnit> GetRelatedScoreModelUnits(LipidGroupSearchResult lipidGroupSearchResult)
{
var lipidTarget = lipidGroupSearchResult.LipidTarget;
return(GetRelatedScoreModelUnits(lipidTarget));
}
public static List <LipidGroupSearchResult> RunGlobalWorkflow(IEnumerable <Lipid> lipidList, LcMsRun lcmsRun, double hcdMassError, double cidMassError, ScoreModel scoreModel, IProgress <int> progress = null)
{
//TextWriter textWriter = new StreamWriter("outputNeg.tsv");
var lipidGroupSearchResultList = new List <LipidGroupSearchResult>();
var hcdTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm);
var cidTolerance = new Tolerance(cidMassError, ToleranceUnit.Ppm);
//var lipidsGroupedByTarget = lipidList.OrderBy(x => x.LipidTarget.Composition.Mass).GroupBy(x => x.LipidTarget).ToList(); //order by mz
var lipidsGroupedByTarget = lipidList.OrderBy(x => x.LipidTarget.MzRounded).GroupBy(x => x.LipidTarget).ToList();
var minLcScan = lcmsRun.MinLcScan;
double maxLcScan = lcmsRun.MaxLcScan;
var activationMethodCombination = FigureOutActivationMethodCombination(lcmsRun);
if (activationMethodCombination == ActivationMethodCombination.Unsupported)
{
throw new SystemException("Unsupported activation method.");
}
var useTwoScans = activationMethodCombination == ActivationMethodCombination.CidThenHcd || activationMethodCombination == ActivationMethodCombination.HcdThenCid;
for (var i = minLcScan; i <= maxLcScan; i++)
{
// Lookup the MS/MS Spectrum
var firstMsMsSpectrum = lcmsRun.GetSpectrum(i) as ProductSpectrum;
if (firstMsMsSpectrum == null)
{
continue;
}
// Lookup the MS/MS Spectrum
ProductSpectrum secondMsMsSpectrum = null;
if (useTwoScans)
{
secondMsMsSpectrum = lcmsRun.GetSpectrum(i + 1) as ProductSpectrum;
if (secondMsMsSpectrum == null)
{
continue;
}
// If m/z values of the MS/MS spectrums do not match, just move on
var deltaMz = firstMsMsSpectrum.IsolationWindow.IsolationWindowTargetMz -
secondMsMsSpectrum.IsolationWindow.IsolationWindowTargetMz;
if (Math.Abs(deltaMz) > 0.01)
{
continue;
}
}
//textWriter.WriteLine(i);
//Console.WriteLine(DateTime.Now + "\tProcessing Scan" + i);
// Grab Precursor Spectrum
var precursorScanNumber = 0;
if (lcmsRun.MinMsLevel == 1) //Make sure there are precursor scans in file
{
precursorScanNumber = lcmsRun.GetPrecursorScanNum(i);
}
var precursorSpectrum = lcmsRun.GetSpectrum(precursorScanNumber);
// Assign each MS/MS spectrum to HCD or CID
ProductSpectrum hcdSpectrum;
ProductSpectrum cidSpectrum;
if (firstMsMsSpectrum.ActivationMethod == ActivationMethod.HCD)
{
hcdSpectrum = firstMsMsSpectrum;
cidSpectrum = secondMsMsSpectrum;
}
else
{
hcdSpectrum = secondMsMsSpectrum;
cidSpectrum = firstMsMsSpectrum;
}
var msMsPrecursorMz = firstMsMsSpectrum.IsolationWindow.IsolationWindowTargetMz;
var mzToSearchTolerance = hcdMassError * msMsPrecursorMz / 1000000;
var lowMz = msMsPrecursorMz - mzToSearchTolerance;
var highMz = msMsPrecursorMz + mzToSearchTolerance;
foreach (var grouping in lipidsGroupedByTarget)
{
var lipidTarget = grouping.Key;
var lipidMz = lipidTarget.MzRounded;
// If we reached the point where the m/z is too high, we can exit
if (lipidMz > highMz)
{
break;
}
if (lipidMz > lowMz)
{
// Find the MS1 data
//Xic xic = lcmsRun.GetPrecursorExtractedIonChromatogram(lipidMz, hcdTolerance, i);
var xic = lcmsRun.GetFullPrecursorIonExtractedIonChromatogram(lipidMz, hcdTolerance);
// Bogus data
if (precursorSpectrum != null && (xic.GetApexScanNum() < 0 || xic.GetSumIntensities() <= 0))
{
continue;
}
// Grab the MS/MS peak to search for
IEnumerable <MsMsSearchUnit> msMsSearchUnits = lipidTarget.GetMsMsSearchUnits();
// Get all matching peaks
var hcdSearchResultList = hcdSpectrum != null ? (from msMsSearchUnit in msMsSearchUnits let peak = hcdSpectrum.FindPeak(msMsSearchUnit.Mz, hcdTolerance) select new MsMsSearchResult(msMsSearchUnit, peak)).ToList() : new List <MsMsSearchResult>();
var cidSearchResultList = cidSpectrum != null ? (from msMsSearchUnit in msMsSearchUnits let peak = cidSpectrum.FindPeak(msMsSearchUnit.Mz, cidTolerance) select new MsMsSearchResult(msMsSearchUnit, peak)).ToList() : new List <MsMsSearchResult>();
// Create spectrum search results
SpectrumSearchResult spectrumSearchResult;
LipidGroupSearchResult lipidGroupSearchResult;
if (precursorSpectrum != null)
{
spectrumSearchResult = new SpectrumSearchResult(hcdSpectrum, cidSpectrum, precursorSpectrum, hcdSearchResultList, cidSearchResultList, xic, lcmsRun)
{
PrecursorTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm)
};
lipidGroupSearchResult = new LipidGroupSearchResult(lipidTarget, grouping.ToList(), spectrumSearchResult, scoreModel);
}
else //If there are no precursor scans in this file
{
spectrumSearchResult = new SpectrumSearchResult(hcdSpectrum, cidSpectrum, hcdSearchResultList, cidSearchResultList, lcmsRun)
{
PrecursorTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm)
};
lipidGroupSearchResult = new LipidGroupSearchResult(lipidTarget, grouping.ToList(), spectrumSearchResult, scoreModel);
}
lipidGroupSearchResultList.Add(lipidGroupSearchResult);
}
}
// Skip an extra scan if we look at 2 at a time
if (useTwoScans)
{
i++;
}
// Report progress
if (progress != null)
{
var currentProgress = (int)(i / maxLcScan * 100);
progress.Report(currentProgress);
}
}
//textWriter.Close();
return(lipidGroupSearchResultList);
}
/*
* public static List<LipidGroupSearchResult> RunGlobalWorkflow(IEnumerable<Lipid> lipidList, DataReader ImsRun, IEnumerable<ImsFeature> FeatureTargets, double hcdMassError,double cidMassError, ScoreModel scoreModel, IProgress<int> progress = null)
* {
* Tolerance hcdTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm);
* Tolerance cidTolerance = new Tolerance(cidMassError, ToleranceUnit.Ppm);
*
* var lipidsGroupedByTarget = lipidList.OrderBy(x => x.LipidTarget.Composition.Mass).GroupBy(x => x.LipidTarget).ToList();
* int MS1Frames = ImsRun.GetNumberOfFrames(DataReader.FrameType.MS1);
* int MS2Frames = ImsRun.GetNumberOfFrames(DataReader.FrameType.MS2);
*
* var gp = ImsRun.GetGlobalParams();
* var framelist = ImsRun.GetMasterFrameList();
*
* ActivationMethodCombination activationMethodCombination = MS2Frames > 0 ? ActivationMethodCombination.CidOnly : ActivationMethodCombination.Unsupported;
* if (activationMethodCombination == ActivationMethodCombination.Unsupported) throw new SystemException("Unsupported activation method.");
*
* List<Spectrum> Spectra = new List<Spectrum>();
* foreach (var feature in FeatureTargets)
* {
* double mzToSearchTolerance = hcdMassError * feature.Mz / 1000000;
* double lowMz = feature.Mz - mzToSearchTolerance;
* double highMz = feature.Mz + mzToSearchTolerance;
*
* double[] mzArray;
* int[] intensityArray;
* ImsRun.GetSpectrum(feature.LcStart, feature.LcEnd, DataReader.FrameType.MS1, feature.ImsStart,
* feature.ImsEnd, out mzArray, out intensityArray);
*
* foreach (var mz in mzArray)
* {
* if (mz > highMz) break;
* if (mz > lowMz)
* {
* //Target IMS feature found in this scan
* double[] MS2Mz;
* int[] MS2Ints;
* ImsRun.GetSpectrum(feature.LcStart, feature.LcEnd, DataReader.FrameType.MS2, feature.ImsStart,
* feature.ImsEnd, out MS2Mz, out MS2Ints);
* var MS2Intensity = (from intensity in MS2Ints select (double) (intensity)).ToArray();
* Spectrum spec = new ProductSpectrum(MS2Mz, MS2Intensity, feature.ImsScan);
* spec.MsLevel = 2;
* Spectra.Add(spec);
* }
* }
*
*
* /*
* for (int lcScan = feature.LcStart; lcScan <= feature.LcEnd; lcScan++)
* {
* if (framelist[lcScan] == DataReader.FrameType.MS1)
* {
* for (int imsScan = feature.ImsStart; imsScan <= feature.ImsEnd; imsScan++)
* {
* double[] mzArray;
* int[] intensityArray;
* ImsRun.GetSpectrum(lcScan, lcScan, DataReader.FrameType.MS1, imsScan, imsScan, out mzArray, out intensityArray);
*
* foreach (var mz in mzArray)
* {
* if (mz > highMz) break;
* if (mz > lowMz)
* {
* //Target IMS feature found in this scan
* feature.AddCoord(lcScan, imsScan);
* }
* }
* }
* }
* }
* }
*
* return new List<LipidGroupSearchResult>();
* }
*/
public static List <LipidGroupSearchResult> RunGlobalWorkflowAvgSpec(
IEnumerable <Lipid> lipidList,
LcMsRun lcmsRun,
double hcdMassError,
double cidMassError,
ScoreModel scoreModel,
IProgress <int> progress = null)
{
var lipidGroupSearchResultList = new List <LipidGroupSearchResult>();
var hcdTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm);
var cidTolerance = new Tolerance(cidMassError, ToleranceUnit.Ppm);
var lipidsGroupedByTarget = lipidList.OrderBy(x => x.LipidTarget.MzRounded).GroupBy(x => x.LipidTarget).ToList();
var minLcScan = lcmsRun.MinLcScan;
double maxLcScan = lcmsRun.MaxLcScan;
var ms2scans = lcmsRun.GetScanNumbers(2);
var ms2spectra = ms2scans.Select(scan => lcmsRun.GetSpectrum(scan) as ProductSpectrum).ToList();
var uniqueMz = (from spectrum in ms2spectra select spectrum.IsolationWindow.IsolationWindowTargetMz).ToList().Distinct().ToList();
foreach (var mz in uniqueMz)
{
var hcdScans = ms2spectra.Where(x => Math.Abs(x.IsolationWindow.IsolationWindowTargetMz - mz) < float.Epsilon && x.ActivationMethod == ActivationMethod.HCD).Select(x => x.ScanNum).ToList();
var summedSpec = lcmsRun.GetSummedSpectrum(hcdScans);
var summedHcdSpec = new ProductSpectrum(summedSpec.Peaks, 0)
{
ActivationMethod = ActivationMethod.HCD
};
var cidScans = ms2spectra.Where(x => Math.Abs(x.IsolationWindow.IsolationWindowTargetMz - mz) < float.Epsilon && x.ActivationMethod == ActivationMethod.CID).Select(x => x.ScanNum).ToList();
summedSpec = lcmsRun.GetSummedSpectrum(cidScans);
var summedCidSpec = new ProductSpectrum(summedSpec.Peaks, 0)
{
ActivationMethod = ActivationMethod.CID
};
var HcdPresent = summedHcdSpec.Peaks.Any();
var CidPresent = summedCidSpec.Peaks.Any();
if (HcdPresent)
{
summedHcdSpec.IsolationWindow = new IsolationWindow(mz, hcdMassError, hcdMassError);
}
if (CidPresent)
{
summedCidSpec.IsolationWindow = new IsolationWindow(mz, cidMassError, cidMassError);
}
var mzToSearchTolerance = hcdMassError * mz / 1000000;
var lowMz = mz - mzToSearchTolerance;
var highMz = mz + mzToSearchTolerance;
var hcdSpectrum = summedHcdSpec;
var cidSpectrum = summedCidSpec;
Spectrum precursorSpectrum = null;
foreach (var grouping in lipidsGroupedByTarget)
{
var lipidTarget = grouping.Key;
var lipidMz = lipidTarget.MzRounded;
// If we reached the point where the m/z is too high, we can exit
if (lipidMz > highMz)
{
break;
}
if (lipidMz > lowMz)
{
// Find the MS1 data
//Xic xic = lcmsRun.GetPrecursorExtractedIonChromatogram(lipidMz, hcdTolerance, i);
var xic = lcmsRun.GetFullPrecursorIonExtractedIonChromatogram(lipidMz, hcdTolerance);
// Bogus data
if (precursorSpectrum != null && (xic.GetApexScanNum() < 0 || xic.GetSumIntensities() <= 0))
{
continue;
}
// Grab the MS/MS peak to search for
IEnumerable <MsMsSearchUnit> msMsSearchUnits = lipidTarget.GetMsMsSearchUnits();
// Get all matching peaks
var hcdSearchResultList = hcdSpectrum != null ? (from msMsSearchUnit in msMsSearchUnits let peak = hcdSpectrum.FindPeak(msMsSearchUnit.Mz, hcdTolerance) select new MsMsSearchResult(msMsSearchUnit, peak)).ToList() : new List <MsMsSearchResult>();
var cidSearchResultList = cidSpectrum != null ? (from msMsSearchUnit in msMsSearchUnits let peak = cidSpectrum.FindPeak(msMsSearchUnit.Mz, cidTolerance) select new MsMsSearchResult(msMsSearchUnit, peak)).ToList() : new List <MsMsSearchResult>();
// Create spectrum search results
SpectrumSearchResult spectrumSearchResult;
LipidGroupSearchResult lipidGroupSearchResult;
if (precursorSpectrum != null)
{
spectrumSearchResult = new SpectrumSearchResult(hcdSpectrum, cidSpectrum, precursorSpectrum, hcdSearchResultList, cidSearchResultList, xic, lcmsRun)
{
PrecursorTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm)
};
lipidGroupSearchResult = new LipidGroupSearchResult(lipidTarget, grouping.ToList(), spectrumSearchResult, scoreModel);
}
else //If there are no precursor scans in this file
{
spectrumSearchResult = new SpectrumSearchResult(hcdSpectrum, cidSpectrum, hcdSearchResultList, cidSearchResultList, lcmsRun)
{
PrecursorTolerance = new Tolerance(hcdMassError, ToleranceUnit.Ppm)
};
lipidGroupSearchResult = new LipidGroupSearchResult(lipidTarget, grouping.ToList(), spectrumSearchResult, scoreModel);
}
lipidGroupSearchResultList.Add(lipidGroupSearchResult);
//textWriter.WriteLine(lipidTarget.CommonName + "\t" + spectrumSearchResult.Score);
//Console.WriteLine(lipidTarget.CommonName + "\t" + spectrumSearchResult.Score);
}
}
}
//var summedHcdSpectra = uniqueMz.Select(mz => new Tuple<double, ProductSpectrum>(mz, lcmsRun.GetSummedMs2Spectrum(mz, minLcScan, (int)maxLcScan, 1, 2, ActivationMethod.HCD))).ToDictionary(x => x.Item1, x => x.Item2);
//if (summedHcdSpectra != null) { foreach (var spec in summedHcdSpectra) { spec.Value.IsolationWindow = new IsolationWindow(spec.Key, spec.Key, spec.Key); } }
//var summedCidSpectra = uniqueMz.Select(mz => lcmsRun.GetSummedMs2Spectrum(mz, minLcScan, (int)maxLcScan, 1, 2, ActivationMethod.CID)).ToList();
return(lipidGroupSearchResultList);
}