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);
}
public double GetTheoreticalMz()
{
return(PrecursorUtils.MHToMz(TheoreticalMH, Query.Charge, IsPrecursorMonoisotopic));
}
public PeakList <T> ReadFromFile(string dtaFilename)
{
var fi = new FileInfo(dtaFilename);
if (!fi.Exists)
{
throw new FileNotFoundException("Cannot find the file " + dtaFilename);
}
var result = new PeakList <T>();
SequestFilename sf = SequestFilename.Parse(fi.Name);
result.Experimental = sf.Experimental;
result.ScanTimes.Add(new ScanTime(sf.FirstScan, 0.0));
if (sf.FirstScan != sf.LastScan)
{
result.ScanTimes.Add(new ScanTime(sf.LastScan, 0.0));
}
result.PrecursorCharge = sf.Charge;
using (var filein = new StreamReader(new FileStream(dtaFilename, FileMode.Open, FileAccess.Read)))
{
string lastline;
while ((lastline = filein.ReadLine()) != null)
{
if (lastline.Trim().Length > 0)
{
break;
}
}
if (lastline == null)
{
return(null);
}
string[] parts = Regex.Split(lastline, @"\s+");
double precursorMass = MyConvert.ToDouble(parts[0]);
result.PrecursorCharge = int.Parse(parts[1]);
result.PrecursorMZ = PrecursorUtils.MHToMz(precursorMass, result.PrecursorCharge, true);
while ((lastline = filein.ReadLine()) != null)
{
if (lastline.Length == 0)
{
continue;
}
if (lastline[0] == '>')
{
break;
}
string[] peakParts = Regex.Split(lastline, @"\s+");
var peak = new T();
peak.Mz = MyConvert.ToDouble(peakParts[0]);
peak.Intensity = MyConvert.ToDouble(peakParts[1]);
if (peakParts.Length > 2)
{
peak.Charge = int.Parse(peakParts[2]);
}
result.Add(peak);
}
return(result);
}
}
public double GetPrecursorMz()
{
return(PrecursorUtils.MHToMz(ExperimentalMH, Query.Charge, IsPrecursorMonoisotopic));
}