private static Tuple <Peak, int>[] GetAllIsotopePeaks(
Spectrum spec,
double monoisotopicMass,
int charge,
IsotopomerEnvelope envelope,
Tolerance tolerance,
double relativeIntensityThreshold)
{
var mostAbundantIsotopeIndex = envelope.MostAbundantIsotopeIndex;
var isotopomerEnvelope = envelope.Envelope;
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(monoisotopicMass, charge, mostAbundantIsotopeIndex);
var mostAbundantIsotopePeakIndex = spec.FindPeakIndex(mostAbundantIsotopeMz, tolerance);
if (mostAbundantIsotopePeakIndex < 0)
{
return(null);
}
var observedPeaks = new Tuple <Peak, int> [isotopomerEnvelope.Length];
observedPeaks[mostAbundantIsotopeIndex] = new Tuple <Peak, int>(spec.Peaks[mostAbundantIsotopePeakIndex], mostAbundantIsotopePeakIndex);
// go down
var peakIndex = mostAbundantIsotopePeakIndex - 1;
for (var isotopeIndex = mostAbundantIsotopeIndex - 1; isotopeIndex >= 0; isotopeIndex--)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = Ion.GetIsotopeMz(monoisotopicMass, charge, isotopeIndex);
var tolTh = tolerance.GetToleranceAsMz(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex; i >= 0; i--)
{
var peakMz = spec.Peaks[i].Mz;
if (peakMz < minMz)
{
peakIndex = i;
break;
}
if (peakMz <= maxMz) // find match, move to prev isotope
{
var peak = spec.Peaks[i];
if (observedPeaks[isotopeIndex] == null ||
peak.Intensity > observedPeaks[isotopeIndex].Item1.Intensity)
{
observedPeaks[isotopeIndex] = new Tuple <Peak, int>(peak, peakIndex);
}
}
}
}
// go up
peakIndex = mostAbundantIsotopePeakIndex + 1;
for (var isotopeIndex = mostAbundantIsotopeIndex + 1; isotopeIndex < isotopomerEnvelope.Length; isotopeIndex++)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = Ion.GetIsotopeMz(monoisotopicMass, charge, isotopeIndex);
var tolTh = tolerance.GetToleranceAsMz(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex; i < spec.Peaks.Length; i++)
{
var peakMz = spec.Peaks[i].Mz;
if (peakMz > maxMz)
{
peakIndex = i;
break;
}
if (peakMz >= minMz) // find match, move to prev isotope
{
var peak = spec.Peaks[i];
if (observedPeaks[isotopeIndex] == null ||
peak.Intensity > observedPeaks[isotopeIndex].Item1.Intensity)
{
observedPeaks[isotopeIndex] = new Tuple <Peak, int>(peak, peakIndex);
}
}
}
}
return(observedPeaks);
}
public Peak[] GetAllIsotopePeaks(double monoIsotopeMass, int charge, IsotopomerEnvelope envelope, Tolerance tolerance, double relativeIntensityThreshold)
{
var mostAbundantIsotopeIndex = envelope.MostAbundantIsotopeIndex;
var isotopomerEnvelope = envelope.Envolope;
var mostAbundantIsotopeMz = Ion.GetIsotopeMz(monoIsotopeMass, charge, mostAbundantIsotopeIndex);
var mostAbundantIsotopePeakIndex = FindPeakIndex(mostAbundantIsotopeMz, tolerance);
if (mostAbundantIsotopePeakIndex < 0)
{
return(null);
}
var observedPeaks = new Peak[isotopomerEnvelope.Length];
observedPeaks[mostAbundantIsotopeIndex] = Peaks[mostAbundantIsotopePeakIndex];
// go down
var peakIndex = mostAbundantIsotopePeakIndex - 1;
for (var isotopeIndex = mostAbundantIsotopeIndex - 1; isotopeIndex >= 0; isotopeIndex--)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = Ion.GetIsotopeMz(monoIsotopeMass, charge, isotopeIndex);
var tolTh = tolerance.GetToleranceAsTh(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex; i >= 0; i--)
{
var peakMz = Peaks[i].Mz;
if (peakMz < minMz)
{
peakIndex = i;
break;
}
if (peakMz <= maxMz) // find match, move to prev isotope
{
var peak = Peaks[i];
if (observedPeaks[isotopeIndex] == null ||
peak.Intensity > observedPeaks[isotopeIndex].Intensity)
{
observedPeaks[isotopeIndex] = peak;
}
}
}
}
// go up
peakIndex = mostAbundantIsotopePeakIndex + 1;
for (var isotopeIndex = mostAbundantIsotopeIndex + 1; isotopeIndex < isotopomerEnvelope.Length; isotopeIndex++)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = Ion.GetIsotopeMz(monoIsotopeMass, charge, isotopeIndex);
var tolTh = tolerance.GetToleranceAsTh(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex; i < Peaks.Length; i++)
{
var peakMz = Peaks[i].Mz;
if (peakMz > maxMz)
{
peakIndex = i;
break;
}
if (peakMz >= minMz) // find match, move to prev isotope
{
var peak = Peaks[i];
if (observedPeaks[isotopeIndex] == null ||
peak.Intensity > observedPeaks[isotopeIndex].Intensity)
{
observedPeaks[isotopeIndex] = peak;
}
}
}
}
return(observedPeaks);
}