private void RemoveIsotopicIons(PeakList <T> t, T ion)
{
var is1 = ion.Mz + Atom.C13_GAP / ion.Charge;
var is1Ions = FindPeakConsideringCharge(t, is1, ion.Charge, ion.Intensity);
if (is1Ions.Count > 0)
{
is1Ions.ForEach(m => t.Remove(m));
var is2 = ion.Mz + Atom.C13_GAP * 2 / ion.Charge;
var is2Ions = FindPeakConsideringCharge(t, is2, ion.Charge, ion.Intensity);
is2Ions.ForEach(m => t.Remove(m));
}
}
public static List <PeakList <T> > GetEnvelopes <T>(PeakList <T> pkl, double ppmTolerance) where T : IPeak
{
var tmp = new PeakList <T>(pkl);
var result = new List <PeakList <T> >();
while (tmp.Count > 0)
{
double mzTolerance = 2 * PrecursorUtils.ppm2mz(tmp[0].Mz, ppmTolerance);
PeakList <T> envelope = tmp.FindEnvelope(tmp[0], mzTolerance, true);
result.Add(envelope);
foreach (T peak in envelope)
{
//Remove all peaks around current peak
PeakList <T> findPeaks = tmp.FindPeak(peak.Mz, peak.Charge, mzTolerance);
foreach (T findPeak in findPeaks)
{
tmp.Remove(findPeak);
}
}
}
/*
* Console.Out.WriteLine("---before merge");
* foreach (PeakList<T> pkl in result)
* {
* Console.Out.WriteLine("---");
* foreach (Peak p in pkl)
* {
* Console.Out.WriteLine(p);
* }
* }
*
* result.Sort(new PeakListMzAscendingComparer<T>());
*
* int current = 0;
*
* while (current < result.Count - 1)
* {
* PeakList<T> currentPkl = result[current];
* if (currentPkl[0].Charge > 0)
* {
* double expectMz = currentPkl[currentPkl.Count - 1].Mz + ChargeDeconvolution.C_GAP / currentPkl[0].Charge;
* double mzTolerance = 4 * Precursor.ppm2mz(currentPkl[0].Mz, ppmTolerance);
* int next = current + 1;
* while (next < result.Count)
* {
* double gap = result[next][0].Mz - expectMz;
* if (gap >= 2.0)
* {
* break;
* }
*
* if (Math.Abs(gap) > mzTolerance)
* {
* next++;
* continue;
* }
*
* if (result[next][0].Charge != currentPkl[0].Charge)
* {
* next++;
* continue;
* }
*
* Console.Out.WriteLine("Current----");
* foreach (T p in currentPkl)
* {
* Console.Out.WriteLine(p);
* }
* Console.Out.WriteLine("Add----");
* foreach (T p in result[next])
* {
* Console.Out.WriteLine(p);
* }
*
* currentPkl.AddRange(result[next]);
*
* Console.Out.WriteLine("To----");
* foreach (T p in currentPkl)
* {
* Console.Out.WriteLine(p);
* }
*
* result.RemoveAt(next);
* }
* }
*
* current++;
* }
*
* Console.Out.WriteLine("---after merge");
* foreach (PeakList<T> pkl in result)
* {
* Console.Out.WriteLine("---");
* foreach (Peak p in pkl)
* {
* Console.Out.WriteLine(p);
* }
* }
*/
return(result);
}
public PeakList <T> Process(PeakList <T> t)
{
if (t.PrecursorCharge > 0)
{
var isobaricList = new List <T>();
var mzPrecursor = PrecursorUtils.ppm2mz(t.PrecursorMZ, options.PPMTolerance);
var precursurIons = FindPeakConsideringCharge(t, t.PrecursorMZ, t.PrecursorCharge, mzPrecursor);
//First of all, we need to find precursor
if (precursurIons.Count > 0)
{
precursurIons.ForEach(m => { t.Remove(m); });
isobaricList.Add(new T()
{
Mz = t.PrecursorMZ,
Charge = t.PrecursorCharge,
Intensity = mzPrecursor
});
if (options.RemoveChargeMinus1Precursor && t.PrecursorCharge > 1)
{
//Get charge-1 precursor
var p1mz = PrecursorUtils.MHToMz(PrecursorUtils.MzToMH(t.PrecursorMZ, t.PrecursorCharge, true), t.PrecursorCharge - 1, true);
var p1Window = PrecursorUtils.ppm2mz(p1mz, options.PPMTolerance);
var p1Ions = FindPeakConsideringCharge(t, p1mz, t.PrecursorCharge - 1, p1Window);
if (p1Ions.Count > 0)
{
p1Ions.ForEach(m => { t.Remove(m); });
isobaricList.Add(new T()
{
Mz = p1mz,
Charge = t.PrecursorCharge - 1,
Intensity = p1Window
});
}
}
if (options.RemoveIsotopicIons)
{
foreach (var ion in isobaricList)
{
RemoveIsotopicIons(t, ion);
}
}
}
foreach (var offset in offsets)
{
var mz = t.PrecursorMZ + offset / t.PrecursorCharge;
var mzWindow = PrecursorUtils.ppm2mz(mz, options.PPMTolerance);
var minMz = mz - mzWindow;
var maxMz = mz + mzWindow;
t.RemoveAll(m =>
{
if (m.Charge == t.PrecursorCharge || m.Charge == 0)
{
return(m.Mz >= minMz && m.Mz <= maxMz);
}
else
{
return(false);
}
});
}
if (options.RemoveIonLargerThanPrecursor)
{
var pmass = PrecursorUtils.MzToMH(t.PrecursorMZ, t.PrecursorCharge, true);
t.RemoveAll(m =>
{
var mass = m.Charge > 0 ? PrecursorUtils.MzToMH(m.Mz, m.Charge, true) : m.Mz;
return(mass >= pmass);
});
}
}
return(t);
}
