public override double GetFragmentScore(Composition prefixFragmentComposition, Composition suffixFragmentComposition)
{
var score = 0.0;
foreach (var baseIonType in BaseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? prefixFragmentComposition + baseIonType.OffsetComposition
: suffixFragmentComposition + baseIonType.OffsetComposition;
if (fragmentComposition.Mass < Ms2Spectrum.Peaks[0].Mz)
{
continue;
}
var chargeRange = GetMinMaxChargeRange(fragmentComposition);
var containsIon = false;
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
if (Ms2Spectrum.GetCorrScore(ion, Tolerance) > _corrScoreThreshold)
{
containsIon = true;
break;
}
}
if (containsIon)
{
score += 1.0;
}
}
return(score);
}
/// <summary>
/// Find the praks that match the provided composition
/// </summary>
/// <param name="fragmentComposition"></param>
/// <param name="corrThreshold"></param>
/// <param name="distThreshold"></param>
/// <returns></returns>
protected IEnumerable <DeconvolutedPeak> FindMatchedPeaks(Composition fragmentComposition,
double corrThreshold, double distThreshold)
{
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMass = fragmentComposition.Mass;
//var matchedPeak = new MatchedFragmentPeak();
//var deconvPeak = new DeconvolutedPeak()
if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz)
{
yield break;
}
var prevObservedCharge = 0;
var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null)
{
if (prevObservedCharge > 0 && charge - prevObservedCharge > 1)
{
yield break;
}
continue;
}
var distCorr = GetDistCorr(ion, observedPeaks);
if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold)
{
if (prevObservedCharge > 0 && charge - prevObservedCharge > 1)
{
yield break;
}
continue;
}
var matchedPeak = new DeconvolutedPeak(fragmentIonMass, observedPeaks[mostAbundantIsotopeIndex].Intensity, charge, distCorr.Item2, distCorr.Item1, observedPeaks);
prevObservedCharge = charge;
yield return(matchedPeak);
}
}
/*
* protected Peak[] FindMostAbundantPeak(Composition.Composition fragmentComposition,
* double corrThreshold, double distThreshold,
* out int observedCharge, out double envelopeCorr, out double envelopeDist)
* {
* //Peak[] intenseObservedPeaks = null;
* var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
* var fragmentIonMass = fragmentComposition.Mass;
* observedCharge = 0;
* envelopeCorr = 0d;
* envelopeDist = 1.0d;
*
* if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz) return null;
*
* var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
* var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
*
* for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
* {
* var ion = new Ion(fragmentComposition, charge);
*
* var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
* if (observedPeaks == null) continue;
*
* var distCorr = GetDistCorr(ion, observedPeaks);
* if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold) continue;
* //var mostAbuPeak = observedPeaks[mostAbundantIsotopeIndex];
* //if (intenseObservedPeaks == null || mostAbuPeak.Intensity > intenseObservedPeaks[mostAbundantIsotopeIndex].Intensity)
* //{
* //intenseObservedPeaks = observedPeaks;
* observedCharge = charge;
* envelopeDist = distCorr.Item1;
* envelopeCorr = distCorr.Item2;
* return observedPeaks;
* //}
* }
* return null;
* }
*/
/// <summary>
/// Find the highest-intensity peak that matches the provided fragment composition
/// </summary>
/// <param name="fragmentComposition"></param>
/// <param name="corrThreshold"></param>
/// <param name="distThreshold"></param>
/// <param name="observedCharge"></param>
/// <param name="envelopeCorr"></param>
/// <param name="envelopeDist"></param>
/// <returns></returns>
protected Peak[] FindMostIntensePeak(Composition fragmentComposition, double corrThreshold, double distThreshold, out int observedCharge, out double envelopeCorr, out double envelopeDist)
{
Peak[] intenseObservedPeaks = null;
var mostAbundantIsotopeIndex = fragmentComposition.GetMostAbundantIsotopeZeroBasedIndex();
var fragmentIonMass = fragmentComposition.Mass;
observedCharge = 0;
envelopeCorr = 0d;
envelopeDist = 1.0d;
if (fragmentIonMass < Ms2Spectrum.Peaks.First().Mz)
{
return(null);
}
var fragmentIonMostAbuMass = fragmentIonMass + Constants.C13MinusC12 * mostAbundantIsotopeIndex;
var chargeRange = GetMinMaxChargeRange(fragmentIonMostAbuMass);
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
var observedPeaks = Ms2Spectrum.GetAllIsotopePeaks(ion, Tolerance, RelativeIsotopeIntensityThreshold);
if (observedPeaks == null)
{
continue;
}
var distCorr = GetDistCorr(ion, observedPeaks);
if (distCorr.Item2 < corrThreshold && distCorr.Item1 > distThreshold)
{
continue;
}
var mostAbuPeak = observedPeaks[mostAbundantIsotopeIndex];
if (intenseObservedPeaks == null || mostAbuPeak.Intensity > intenseObservedPeaks[mostAbundantIsotopeIndex].Intensity)
{
intenseObservedPeaks = observedPeaks;
observedCharge = charge;
envelopeDist = distCorr.Item1;
envelopeCorr = distCorr.Item2;
}
}
return(intenseObservedPeaks);
}
public override double GetFragmentScore(Composition prefixFragmentComposition, Composition suffixFragmentComposition,
AminoAcid nTerminalResidue = null,
AminoAcid cTerminalResidue = null)
{
var score = 0.0;
foreach (var baseIonType in BaseIonTypes)
{
var fragmentComposition = baseIonType.IsPrefix
? prefixFragmentComposition + baseIonType.OffsetComposition
: suffixFragmentComposition + baseIonType.OffsetComposition;
if (fragmentComposition.Mass < Ms2Spectrum.Peaks[0].Mz)
{
continue;
}
var chargeRange = GetMinMaxChargeRange(fragmentComposition);
var containsIon = false;
for (var charge = chargeRange.Min; charge <= chargeRange.Max; charge++)
{
var ion = new Ion(fragmentComposition, charge);
if (Ms2Spectrum.ContainsIon(ion, Tolerance, RelativeIsotopeIntensityThreshold))
{
containsIon = true;
break;
}
}
if (containsIon)
{
score += 1.0;
}
}
return(score);
}
