/// <summary>
/// Constructor
/// </summary>
/// <param name="peaks"></param>
/// <param name="scanNum"></param>
public Spectrum(ICollection <Peak> peaks, int scanNum)
{
Peaks = new Peak[peaks.Count];
peaks.CopyTo(Peaks, 0);
ScanNum = scanNum;
}
// Select the best peak within +/- filteringWindowSize
public static List <DeconvolutedPeak> GetDeconvolutedPeaks(
Peak[] peaks, int minCharge, int maxCharge,
int isotopeOffsetTolerance, double filteringWindowSize,
Tolerance tolerance, double corrScoreThreshold)
{
var monoIsotopePeakList = new List <DeconvolutedPeak>();
for (var peakIndex = 0; peakIndex < peaks.Length; peakIndex++)
{
var peak = peaks[peakIndex];
// Check whether peak has the maximum intensity within the window
var isBest = true;
var prevIndex = peakIndex - 1;
while (prevIndex >= 0)
{
var prevPeak = peaks[prevIndex];
if ((peak.Mz - prevPeak.Mz) > filteringWindowSize)
{
break;
}
if (prevPeak.Intensity > peak.Intensity)
{
isBest = false;
break;
}
prevIndex--;
}
if (!isBest)
{
continue;
}
var nextIndex = peakIndex + 1;
while (nextIndex < peaks.Length)
{
var nextPeak = peaks[nextIndex];
if ((nextPeak.Mz - peak.Mz) > filteringWindowSize)
{
break;
}
if (nextPeak.Intensity > peak.Intensity)
{
isBest = false;
break;
}
nextIndex++;
}
if (!isBest)
{
continue;
}
// peak has the maximum intensity, window = [prevIndex+1,nextIndex-1]
var window = new Peak[nextIndex - prevIndex - 1];
Array.Copy(peaks, prevIndex + 1, window, 0, window.Length);
var windowSpectrum = new Spectrum(window, 1);
var peakMz = peak.Mz;
for (var charge = maxCharge; charge >= minCharge; charge--)
{
var mass = peak.Mz * charge;
var mostAbundantIsotopeIndex = Averagine.GetIsotopomerEnvelope(mass).MostAbundantIsotopeIndex;
for (var isotopeIndex = mostAbundantIsotopeIndex - isotopeOffsetTolerance; isotopeIndex <= mostAbundantIsotopeIndex + isotopeOffsetTolerance; isotopeIndex++)
{
var monoIsotopeMass = Ion.GetMonoIsotopicMass(peakMz, charge, isotopeIndex);
var isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(monoIsotopeMass);
var observedPeaks = windowSpectrum.GetAllIsotopePeaks(monoIsotopeMass, charge, isotopomerEnvelope, tolerance, 0.1);
if (observedPeaks == null)
{
continue;
}
var envelop = isotopomerEnvelope.Envolope;
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
var sim = FitScoreCalculator.GetDistanceAndCorrelation(envelop, observedIntensities);
var bcDist = sim.Item1;
var corr = sim.Item2;
if (corr < corrScoreThreshold && bcDist > 0.03)
{
continue;
}
// monoIsotopeMass is valid
var deconvPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks);
monoIsotopePeakList.Add(deconvPeak);
}
}
}
monoIsotopePeakList.Sort();
return(monoIsotopePeakList);
}
/// <summary>
/// Get all isotope peaks that correspond to <paramref name="monoIsotopeMass"/>, <paramref name="charge"/>, <paramref name="envelope"/>, and <paramref name="tolerance"/>
/// </summary>
/// <param name="monoIsotopeMass"></param>
/// <param name="charge"></param>
/// <param name="envelope"></param>
/// <param name="tolerance"></param>
/// <param name="relativeIntensityThreshold"></param>
/// <returns></returns>
public Peak[] GetAllIsotopePeaks(double monoIsotopeMass, int charge, IsotopomerEnvelope envelope, Tolerance tolerance, double relativeIntensityThreshold = 0.1)
{
var mostAbundantIsotopeIndex = envelope.MostAbundantIsotopeIndex;
var isotopomerEnvelope = envelope.Envelope;
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.GetToleranceAsMz(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.GetToleranceAsMz(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);
}
