/* 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);
}
private static SpectrumData GenerateMergedSpectrum(SpectrumData allPeakDataInEachGroup)
{
// adMSMS data(20ev-50ev-MS) of each group is treated by first calculating relative intensities among group,
// then calculating the average intensities in each CID, next taking the max of the value among CIDs
SpectrumData mergedSpectrum = new SpectrumData();
mergedSpectrum = CalMaxAverageIntensity(IdMSMS_Deconvolution.CalRelativeIntensity(allPeakDataInEachGroup));
return(mergedSpectrum);
}
static void Main(string[] args)
{
Stopwatch watch = new Stopwatch();
watch.Start();
string rootPath = @"E:\Different tissues\idMSMS different tissue\MIX Results\";
/**
* Fill 0 values in XCMS peaktable
*/
//string fillpeaksPath = rootPath + "NormPeakArea.csv";
//string nonefillpeaksPath = rootPath + "data_minfrac0.1_sn3_nonfill.csv";
//string outPath = rootPath + "NormPeakArea_fill0.csv";
//Data_Operation.Fill0Peaks(fillpeaksPath, nonefillpeaksPath, outPath);
/**
* export precursors (change parapeters to export all/without isotope/only adducts)
*/
//string CSVFilePath = rootPath + "NormPeakArea.csv";
//List<SpectrumData> allSpectraList = IdMSMS_Deconvolution.ProcessPeaktableToSpectralist(CSVFilePath);
//Data_Operation.FindPrecursorMZ(allSpectraList, outPrecursorPath);
/**
* Assemble idMS/MS with multi-eV
*/
string CSVFilePath = rootPath + "AllDeconvolutedSpectra_MS_pvals_9s.csv";
string outputFilePath = rootPath + "idmsms_3_6_0.9_minCor_rmv50_50ev.csv";
string NLOutputFilePath = rootPath + "NL_motif.csv";
string NDPmatrixPath = rootPath + "NDPmatrix.csv";
List <SpectrumData> allMergedList = IdMSMS_Deconvolution.MergeIdMSMSOfDiffCIDs(CSVFilePath);
FileProcess.WriteSpectrumList(allMergedList, outputFilePath); //output idMSMS spectra
FileProcess.OutputNeutralLoss(allMergedList, NLOutputFilePath); //output NL_motif
string commonNLPath = rootPath + "Common NL table.csv";
string outNLHitPath = rootPath + "NLmatrix.csv";
FileProcess.OutputSelectedNLto360Spec(allMergedList, commonNLPath, outNLHitPath); //output binary NL hit table
//List<SpectrumData> allSpectraList = FileProcess.ReadSpectralCSVFile(CSVFilePath); // use if there is spectra list to read
//List<SpectrumData> allKnownSpectraList = FileProcess.ReadKnownMSMSSpectraList(knownMSMSPath); // use if there is known spectra list
List <SpectrumData> allKnownSpectraList = allMergedList;
List <double[]> NDPResultList = new List <double[]>();
string[] queryTitleLine = new string[allMergedList.Count]; // add QueryTitle line to result
for (int i = 0; i < allMergedList.Count; i++)
{
queryTitleLine[i] = allMergedList[i].group.ToString();
}
string[] libraryTitleLine = new string[allKnownSpectraList.Count]; // add Library title to result
for (int i = 0; i < allKnownSpectraList.Count; i++)
{
libraryTitleLine[i] = allKnownSpectraList[i].peakList[0].sampleName;
}
for (int i = 0; i < allMergedList.Count; i++)
{
double[] line = new double[allMergedList.Count]; //
for (int j = 0; j < allMergedList.Count; j++) //
{
line[j] = Cal_Cosine_Product.CalCosineProduct(allMergedList[i], allMergedList[j]); //
}
NDPResultList.Add(line);
}
FileProcess.WriteNDPListToFile(NDPResultList, queryTitleLine, queryTitleLine, NDPmatrixPath); // output NDPmatrix
watch.Stop();
Console.WriteLine("weight: " + IdMSMS_Deconvolution.weight + " minSamp:" + IdMSMS_Deconvolution.minSampleNrForCor + " ndpThreh:" + IdMSMS_Deconvolution.ndpThreshold);
Console.WriteLine("Deconvoluted spectra number: " + allMergedList.Count);
Console.WriteLine("calculation time: " + watch.Elapsed);
Console.WriteLine("OK");
Console.Read();
}
/* 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);
}
