private static void OutputResultsToMspLibrary(IEnumerable <LipidGroupSearchResult> lipidGroupSearchResults, string fileLocation)
{
using (TextWriter textWriter = new StreamWriter(fileLocation))
{
foreach (var lipidGroupSearchResult in lipidGroupSearchResults)
{
var lipidTarget = lipidGroupSearchResult.LipidTarget;
var spectrumSearchResult = lipidGroupSearchResult.SpectrumSearchResult;
var massSpectrum = spectrumSearchResult.PrecursorSpectrum.Peaks;
var targetMz = lipidTarget.MzRounded;
var closestPeak = massSpectrum.OrderBy(x => Math.Abs(x.Mz - targetMz)).First();
var hcdResults = spectrumSearchResult.HcdSearchResultList;
var cidResults = spectrumSearchResult.CidSearchResultList;
var hcdSpectrum = spectrumSearchResult.HcdSpectrum;
var cidSpectrum = spectrumSearchResult.CidSpectrum;
var hcdCount = hcdSpectrum.Peaks.Length;
var cidCount = cidSpectrum.Peaks.Length;
var name = lipidTarget.StrippedDisplay;
var firstLipid = lipidGroupSearchResult.LipidList.FirstOrDefault();
string adduct;
if (firstLipid == null)
{
adduct = string.Empty;
}
else
{
adduct = firstLipid.AdductFull;
}
var observedMz = closestPeak.Mz;
var formula = lipidTarget.EmpiricalFormula;
var RT = spectrumSearchResult.RetentionTime;
double MW = 0;
if (lipidTarget.FragmentationMode == FragmentationMode.Positive)
{
MW = lipidTarget.Composition.Mass - LipidUtil.GetCompositionOfAdduct(lipidTarget.Adduct).Mass;
}
else if (lipidTarget.FragmentationMode == FragmentationMode.Negative)
{
MW = lipidTarget.Composition.Mass + LipidUtil.GetCompositionOfAdduct(lipidTarget.Adduct).Mass;
}
textWriter.WriteLine("Name: {0}; {1}", name, adduct);
textWriter.WriteLine("MW: {0}", MW);
textWriter.WriteLine("PRECURSORMZ: {0}", observedMz);
textWriter.WriteLine("RETENTIONTIME: {0}", RT);
textWriter.WriteLine("FORMULA: {0}", formula);
textWriter.WriteLine("Comment: CID");
textWriter.WriteLine("Num Peaks: {0}", cidCount);
foreach (var peak in cidSpectrum.Peaks)
{
var mz = peak.Mz;
var intensity = peak.Intensity;
var match = cidResults.Where(x => x.ObservedPeak != null).FirstOrDefault(x => x.ObservedPeak.Mz.Equals(peak.Mz));
if (match != null)
{
var annotation = match.TheoreticalPeak.DescriptionForUi;
textWriter.WriteLine("{0} {1} \"{2}\"", mz, intensity, annotation);
}
else
{
textWriter.WriteLine("{0} {1}", mz, intensity);
}
}
textWriter.WriteLine();
textWriter.WriteLine("Name: {0}; {1}", name, adduct);
textWriter.WriteLine("MW: {0}", MW);
textWriter.WriteLine("PRECURSORMZ: {0}", observedMz);
textWriter.WriteLine("RETENTIONTIME: {0}", RT);
textWriter.WriteLine("FORMULA: {0}", formula);
textWriter.WriteLine("Comment: HCD");
textWriter.WriteLine("Num Peaks: {0}", hcdCount);
foreach (var peak in hcdSpectrum.Peaks)
{
var mz = peak.Mz;
var intensity = peak.Intensity;
var match = hcdResults.Where(x => x.ObservedPeak != null).FirstOrDefault(x => x.ObservedPeak.Mz.Equals(peak.Mz));
if (match != null)
{
var annotation = match.TheoreticalPeak.DescriptionForUi;
textWriter.WriteLine("{0} {1} \"{2}\"", mz, intensity, annotation);
}
else
{
textWriter.WriteLine("{0} {1}", mz, intensity);
}
}
textWriter.WriteLine();
}
}
}
