public virtual IsotopicProfile IterativelyFindMSFeature(XYData massSpecXyData, IsotopicProfile theorIso, out List <Peak> peakList)
{
if (massSpecXyData == null)
{
peakList = new List <Peak>();
return(null);
}
IsotopicProfile iso = null;
this.MSPeakDetector.MinX = theorIso.MonoPeakMZ - 10;
this.MSPeakDetector.MaxX = theorIso.MonoPeakMZ + 20;
//start with high PeakBR and rachet it down, so as to detect more peaks with each pass. Stop when you find the isotopic profile.
peakList = new List <Peak>();
for (var d = PeakDetectorPeakBR; d >= PeakBRMin; d = d - PeakBRStep)
{
this.MSPeakDetector.PeakToBackgroundRatio = d;
peakList = MSPeakDetector.FindPeaks(massSpecXyData.Xvalues, massSpecXyData.Yvalues);
iso = FindMSFeature(peakList, theorIso);
bool isoIsGoodEnough;
if (iso == null)
{
isoIsGoodEnough = false;
}
else if (iso.Peaklist.Count < 2)
{
isoIsGoodEnough = false;
}
else
{
double maxIntensity = iso.getMostIntensePeak().Height;
double minIntensityPeak = iso.Peaklist.Min(p => p.Height);
if (minIntensityPeak / maxIntensity < MinRelIntensityForPeakInclusion)
{
isoIsGoodEnough = true;
}
else
{
isoIsGoodEnough = false;
}
}
if (isoIsGoodEnough)
{
break;
}
}
return(iso);
}
// Sipper's key method. Sipper will try to pull out low level C13-related peaks. So
// it will not stop as early as the BasicTFF, but will iterate more times to pull
// out the smaller intensity C13-related peaks
public override IsotopicProfile IterativelyFindMSFeature(XYData massSpecXyData, IsotopicProfile theorIso, out List <Peak> peakList)
{
IsotopicProfile foundIso = null;
//start with high PeakBR and rachet it down, so as to detect more peaks with each pass. Stop when you find the isotopic profile.
peakList = new List <Peak>();
for (var d = PeakDetectorPeakBR; d >= PeakBRMin; d = d - PeakBRStep)
{
MSPeakDetector.PeakToBackgroundRatio = d;
peakList = MSPeakDetector.FindPeaks(massSpecXyData.Xvalues, massSpecXyData.Yvalues);
var iso = FindMSFeature(peakList, theorIso);
if (foundIso == null)
{
foundIso = iso;
}
if (foundIso != null)
{
double toleranceInPPM = 20;
combineIsotopicProfiles(foundIso, iso, toleranceInPPM);
}
//TODO: decide that iso is good enough when a peak is found that is less than a certain relative intensity
var isoIsGoodEnough = (foundIso != null && foundIso.Peaklist.Count >= MaxPeaksToInclude);
if (isoIsGoodEnough)
{
break;
}
}
if (foundIso != null)
{
AddZeroIntensityPeaks(foundIso, theorIso, 0.02d);
}
return(foundIso);
}
