/* This method is to extract all the precursors' mz values.
* [M+H]+; [M+Na]+; [M+K]+; [M+NH4]+
* //*/
public static void FindPrecursorMZ(List <SpectrumData> allSpectraList, string outputFilePath)
{
List <double> mzList = new List <double>();
for (int i = 0; i < allSpectraList.Count; i++)
{
for (int j = 0; j < allSpectraList[i].peakList.Count; j++)
{
string iso = allSpectraList[i].peakList[j].isotopes;
if (!IdMSMS_Deconvolution.IsIsotope(iso))
{
//if (true) {
mzList.Add(allSpectraList[i].peakList[j].mz);
}
}
}
using (StreamWriter sw = new StreamWriter(outputFilePath)) {
for (int i = 0; i < mzList.Count; i++)
{
if (i == mzList.Count - 1)
{
sw.Write(mzList[i]);
}
else
{
sw.Write(mzList[i] + ",");
//if (i%300==0&&i!=0) {
// sw.WriteLine();
//}
}
}
}
Console.WriteLine(mzList.Count);
}
/* This method is to calculate all the neutral loss in each spectrum.
* cross over all peaks!
* //*/
public static List <double> FindNeutralLoss(SpectrumData spectrum)
{
List <double> neutralLossList = new List <double>();
List <PeakData> sortedPeakList = spectrum.peakList.OrderByDescending(x => x.mz).Where(x => !IdMSMS_Deconvolution.IsIsotope(x.isotopes)).ToList(); //并计算和isotope的NL
double mzPrecursor = double.Parse(spectrum.group.Split('_')[0]);
for (int i = 0; i < sortedPeakList.Count; i++) // add precursor neutral loss
{
double neutralLoss = mzPrecursor - sortedPeakList[i].mz;
if (neutralLoss > 14)
{
neutralLossList.Add(neutralLoss);
}
}
for (int i = 0; i < sortedPeakList.Count; i++) // add peaks neutral loss
{
for (int j = i + 1; j < sortedPeakList.Count; j++)
{
double neutralLoss = sortedPeakList[i].mz - sortedPeakList[j].mz;
if (neutralLoss > 14)
{
neutralLossList.Add(neutralLoss);
}
}
}
neutralLossList = neutralLossList.Distinct().ToList();
return(neutralLossList);
}