/// <summary>
/// Find the index of the peak that matches the m/z and tolerance
/// </summary>
/// <param name="mz"></param>
/// <param name="tolerance"></param>
/// <returns></returns>
public int FindPeakIndex(double mz, Tolerance tolerance)
{
var tolTh = tolerance.GetToleranceAsMz(mz);
var minMz = mz - tolTh;
var maxMz = mz + tolTh;
return(FindPeakIndex(minMz, maxMz));
}
/// <summary>
/// Filter noise peaks out using an intensity histogram
/// </summary>
public void FilterNoiseByIntensityHistogram()
{
var filteredPeaks = new List <Peak>();
var intensities = new double[Peaks.Length];
var tolerance = new Tolerance(10000);
var st = 0;
var ed = 0;
foreach (var peak in Peaks)
{
var mzWindowWidth = tolerance.GetToleranceAsMz(peak.Mz);
var intensity = peak.Intensity;
var mzStart = peak.Mz - mzWindowWidth;
var mzEnd = peak.Mz + mzWindowWidth;
while (st < Peaks.Length)
{
if (st < Peaks.Length - 1 && Peaks[st].Mz < mzStart)
{
st++;
}
else
{
break;
}
}
while (ed < Peaks.Length)
{
if (ed < Peaks.Length - 1 && Peaks[ed].Mz < mzEnd)
{
ed++;
}
else
{
break;
}
}
var abundantIntensityBucket = GetMostAbundantIntensity(st, ed);
if (abundantIntensityBucket.LowerBound < intensity && intensity < abundantIntensityBucket.UpperBound)
{
continue;
}
filteredPeaks.Add(peak);
}
filteredPeaks.Sort();
Peaks = filteredPeaks.ToArray();
}
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);
}
/// <summary>
/// Filter noise peaks out using a local window
/// </summary>
/// <param name="signalToNoiseRatio"></param>
/// <param name="windowPpm"></param>
public void FilterNoiseByLocalWindow(double signalToNoiseRatio = 1.4826, int windowPpm = 10000)
{
var filteredPeaks = new List <Peak>();
var tolerance = new Tolerance(windowPpm);
var st = 0;
var ed = 0;
var prevSt = 0;
var prevEd = 0;
var intensityValues = new SortedSet <double>();
foreach (var peak in Peaks)
{
var mzWindowWidth = tolerance.GetToleranceAsMz(peak.Mz);
var mzStart = peak.Mz - mzWindowWidth;
var mzEnd = peak.Mz + mzWindowWidth;
while (st < Peaks.Length)
{
if (st < Peaks.Length - 1 && Peaks[st].Mz < mzStart)
{
st++;
}
else
{
break;
}
}
while (ed < Peaks.Length)
{
if (ed < Peaks.Length - 1 && Peaks[ed].Mz < mzEnd)
{
ed++;
}
else
{
break;
}
}
if (ed - st + 1 < 2)
{
filteredPeaks.Add(peak);
continue;
}
if (intensityValues.Count < 1)
{
for (var i = st; i <= ed; i++)
{
intensityValues.Add(Peaks[i].Intensity);
}
}
else
{
if (prevEd >= st)
{
for (var i = prevSt; i < ed; i++)
{
intensityValues.Remove(Peaks[i].Intensity);
}
for (var i = prevEd + 1; i <= ed; i++)
{
intensityValues.Add(Peaks[i].Intensity);
}
}
else
{
for (var i = prevSt; i <= prevEd; i++)
{
intensityValues.Remove(Peaks[i].Intensity);
}
}
}
var intensityMedian = intensityValues.Median();
if (peak.Intensity > intensityMedian * signalToNoiseRatio)
{
filteredPeaks.Add(peak);
}
prevSt = st;
prevEd = ed;
}
filteredPeaks.Sort();
Peaks = filteredPeaks.ToArray();
}
/// <summary>
/// Finds all isotope peaks corresponding to theoretical profiles with relative intensity higher than the threshold
/// </summary>
/// <param name="ion">ion</param>
/// <param name="tolerance">tolerance</param>
/// <param name="relativeIntensityThreshold">relative intensity threshold of the theoretical isotope profile</param>
/// <returns>array of observed isotope peaks in the spectrum. null if no peak found.</returns>
public Peak[] GetAllIsotopePeaks(Ion ion, Tolerance tolerance, double relativeIntensityThreshold = 0.1)
{
var mostAbundantIsotopeIndex = ion.Composition.GetMostAbundantIsotopeZeroBasedIndex();
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var mostAbundantIsotopeMz = ion.GetIsotopeMz(mostAbundantIsotopeIndex);
var mostAbundantIsotopeMatchedPeakIndex = FindPeakIndex(mostAbundantIsotopeMz, tolerance);
if (mostAbundantIsotopeMatchedPeakIndex < 0)
{
return(null);
}
var observedPeaks = new Peak[isotopomerEnvelope.Length];
observedPeaks[mostAbundantIsotopeIndex] = Peaks[mostAbundantIsotopeMatchedPeakIndex];
// go down
var peakIndex = mostAbundantIsotopeMatchedPeakIndex - 1;
for (var isotopeIndex = mostAbundantIsotopeIndex - 1; isotopeIndex >= 0; isotopeIndex--)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = ion.GetIsotopeMz(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 = mostAbundantIsotopeMatchedPeakIndex + 1;
for (var isotopeIndex = mostAbundantIsotopeIndex + 1; isotopeIndex < isotopomerEnvelope.Length; isotopeIndex++)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = ion.GetIsotopeMz(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);
}
/// <summary>
/// Checks whether this spectrum contains all isotope peaks whose relative intensity is equal or larter than the threshold
/// </summary>
/// <param name="ion">ion</param>
/// <param name="tolerance">tolerance</param>
/// <param name="relativeIntensityThreshold">relative intensity threshold of the theoretical isotope profile</param>
/// <returns>true if spectrum contains all ions; false otherwise.</returns>
public bool ContainsIon(Ion ion, Tolerance tolerance, double relativeIntensityThreshold = 0.1)
{
var baseIsotopeIndex = ion.Composition.GetMostAbundantIsotopeZeroBasedIndex();
var isotopomerEnvelope = ion.Composition.GetIsotopomerEnvelopeRelativeIntensities();
var baseIsotopMz = ion.GetIsotopeMz(baseIsotopeIndex);
var baseIsotopePeakIndex = FindPeakIndex(baseIsotopMz, tolerance);
if (baseIsotopePeakIndex < 0)
{
return(false);
}
// go down
var peakIndex = baseIsotopePeakIndex;
for (var isotopeIndex = baseIsotopeIndex - 1; isotopeIndex >= 0; isotopeIndex--)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = ion.GetIsotopeMz(isotopeIndex);
var tolTh = tolerance.GetToleranceAsMz(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex - 1; i >= 0; i--)
{
var peakMz = Peaks[i].Mz;
if (peakMz < minMz)
{
return(false);
}
if (peakMz <= maxMz) // find match, move to prev isotope
{
peakIndex = i;
break;
}
}
}
// go up
peakIndex = baseIsotopePeakIndex;
for (var isotopeIndex = baseIsotopeIndex + 1; isotopeIndex < isotopomerEnvelope.Length; isotopeIndex++)
{
if (isotopomerEnvelope[isotopeIndex] < relativeIntensityThreshold)
{
break;
}
var isotopeMz = ion.GetIsotopeMz(isotopeIndex);
var tolTh = tolerance.GetToleranceAsMz(isotopeMz);
var minMz = isotopeMz - tolTh;
var maxMz = isotopeMz + tolTh;
for (var i = peakIndex + 1; i < Peaks.Length; i++)
{
var peakMz = Peaks[i].Mz;
if (peakMz > maxMz)
{
return(false);
}
if (peakMz >= minMz) // find match, move to prev isotope
{
peakIndex = i;
break;
}
}
}
return(true);
}
