/// <summary>
/// Constructor
/// </summary>
/// <param name="peaks"></param>
/// <param name="scanNum"></param>
public DeconvolutedSpectrum(ICollection <DeconvolutedPeak> peaks, int scanNum) : base(scanNum)
{
var dPeaks = new DeconvolutedPeak[peaks.Count];
peaks.CopyTo(dPeaks, 0);
Peaks = dPeaks;
}
/// <summary>
/// Constructor
/// </summary>
/// <param name="originalSpec"></param>
/// <param name="peaks"></param>
public DeconvolutedSpectrum(Spectrum originalSpec, DeconvolutedPeak[] peaks)
: base(originalSpec.ScanNum)
{
MsLevel = originalSpec.MsLevel;
NativeId = originalSpec.NativeId;
ElutionTime = originalSpec.ElutionTime;
TotalIonCurrent = originalSpec.TotalIonCurrent;
var ms2Spec = originalSpec as ProductSpectrum;
if (ms2Spec == null)
{
ActivationMethod = ActivationMethod.Unknown;
}
else
{
ActivationMethod = ms2Spec.ActivationMethod;
IsolationWindow = new IsolationWindow(ms2Spec.IsolationWindow.IsolationWindowTargetMz, ms2Spec.IsolationWindow.IsolationWindowLowerOffset, ms2Spec.IsolationWindow.IsolationWindowUpperOffset, ms2Spec.IsolationWindow.MonoisotopicMz, ms2Spec.IsolationWindow.Charge);
}
var dPeaks = new DeconvolutedPeak[peaks.Length];
peaks.CopyTo(dPeaks, 0);
Peaks = dPeaks;
}
private void UpdateDeconvPeak(int binNum, DeconvolutedPeak newPeak)
{
if (newPeak == null) return;
DeconvolutedPeak existingPeak;
if (_massBinToPeakMap.TryGetValue(binNum, out existingPeak))
{
if (existingPeak.Intensity < newPeak.Intensity) _massBinToPeakMap[binNum] = newPeak;
}
else
{
_massBinToPeakMap[binNum] = newPeak;
}
}
/// <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);
}
}
/// <summary>
/// Store the peaks in the Peaks, assuring that each peak is an instance of DeconvolutedPeak
/// </summary>
/// <param name="peaks"></param>
private void StorePeaks(IReadOnlyList <DeconvolutedPeak> peaks)
{
var dPeaks = new DeconvolutedPeak[peaks.Count];
for (var i = 0; i < peaks.Count; i++)
{
dPeaks[i] = peaks[i];
}
// Store the deconvoluted peaks in Peaks
// ReSharper disable once CoVariantArrayConversion
Peaks = new DeconvolutedPeak[dPeaks.Length];
for (var i = 0; i < dPeaks.Length; i++)
{
Peaks[i] = dPeaks[i];
}
}
public DeconvolutedSpectrum(Spectrum originalSpec, DeconvolutedPeak[] peaks)
: base(originalSpec.ScanNum)
{
Peaks = new DeconvolutedPeak[peaks.Length];
peaks.CopyTo(Peaks, 0);
MsLevel = originalSpec.MsLevel;
var ms2Spec = originalSpec as ProductSpectrum;
if (ms2Spec == null)
{
ActivationMethod = ActivationMethod.Unknown;
}
else
{
ActivationMethod = ms2Spec.ActivationMethod;
}
MsLevel = originalSpec.MsLevel;
}
public DeconvolutedSpectrum(Spectrum originalSpec, DeconvolutedPeak[] peaks)
: base(originalSpec.ScanNum)
{
Peaks = new DeconvolutedPeak[peaks.Length];
peaks.CopyTo(Peaks, 0);
MsLevel = originalSpec.MsLevel;
var ms2Spec = originalSpec as ProductSpectrum;
if (ms2Spec == null)
{
ActivationMethod = ActivationMethod.Unknown;
}
else
{
ActivationMethod = ms2Spec.ActivationMethod;
}
MsLevel = originalSpec.MsLevel;
}
/// <summary>
/// Find a neutral monoisotopic peak corrsponding to a single compound/
/// </summary>
/// <param name="composition">The compound to look for.</param>
/// <param name="tolerance">The peak tolerance to use.</param>
/// <returns>The neutral monoisotopic peak.</returns>
public DeconvolutedPeak FindPeak(Composition.Composition composition, Tolerance tolerance)
{
double mass = composition.Mass;
DeconvolutedPeak deconvolutedPeak = null;
double maxIntensity = 0.0;
for (int charge = this.minCharge; charge <= this.maxCharge; charge++)
{
var ion = new Ion(composition, charge);
var isotopePeaks = this.spectrum.GetAllIsotopePeaks(ion, tolerance);
var intensity = isotopePeaks.Max(peak => peak.Intensity);
var corrCos = this.GetCorrCos(ion, isotopePeaks);
if (intensity > maxIntensity)
{
deconvolutedPeak = new DeconvolutedPeak(mass, intensity, charge, corrCos.Item1, corrCos.Item2, isotopePeaks);
}
}
return(deconvolutedPeak);
}
protected IEnumerable<DeconvolutedPeak> FindMatchedPeaks(Composition.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;
}
}
public double GetNodeScoreWithoutMassError(ActivationMethod activationMethod, bool isPrefix, DeconvolutedPeak matchedPeak, double refIntensity)
{
return GetNodeScoreWithoutMassError(activationMethod, isPrefix, matchedPeak.Mass, matchedPeak.Charge, matchedPeak.Corr, matchedPeak.Dist, matchedPeak.Intensity / refIntensity);
}
public double GetNodeScore(ActivationMethod activationMethod, bool isPrefix, double fragmentIonMass, DeconvolutedPeak matchedPeak, double refIntensity)
{
var massErrorPpm = 1e6 * ((matchedPeak.Mass - fragmentIonMass) / fragmentIonMass);
return GetNodeScore(activationMethod, isPrefix, fragmentIonMass, matchedPeak.Charge, matchedPeak.Corr, matchedPeak.Dist, matchedPeak.Intensity / refIntensity, massErrorPpm);
}
// 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 the deconvoluted peaks, selecting the best peak within +/- filteringWindowSize
/// </summary>
/// <param name="scanNum">Scan number (included in any exceptions that are caught)</param>
/// <param name="peaks"></param>
/// <param name="minCharge"></param>
/// <param name="maxCharge"></param>
/// <param name="isotopeOffsetTolerance"></param>
/// <param name="filteringWindowSize"></param>
/// <param name="tolerance"></param>
/// <param name="corrScoreThreshold"></param>
/// <returns></returns>
public static List <DeconvolutedPeak> GetDeconvolutedPeaks(
int scanNum, Peak[] peaks,
int minCharge, int maxCharge,
int isotopeOffsetTolerance, double filteringWindowSize,
Tolerance tolerance, double corrScoreThreshold)
{
try
{
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;
//var bestScore = 0.0;
//DeconvolutedPeak bestPeak = null;
for (var charge = maxCharge; charge >= minCharge; charge--)
{
var mass = (peak.Mz * charge) - charge * Constants.Proton;
//var isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(mass);
//var mostAbundantIsotopeIndex = isotopomerEnvelope.MostAbundantIsotopeIndex;
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.Envelope;
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;
//var score = corr / (bcDist * ((double)Math.Abs(isotopeIndex - mostAbundantIsotopeIndex) / envelop.Length));
if (corr < corrScoreThreshold && bcDist > 0.03)
{
continue;
}
// monoIsotopeMass is valid
//if (score >= bestScore)
//{
// bestScore = score;
// bestPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks);
//}
var deconvPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks);
monoIsotopePeakList.Add(deconvPeak);
}
}
//if (bestPeak != null)
//{
// monoIsotopePeakList.Add(bestPeak);
//}
}
monoIsotopePeakList.Sort();
return(monoIsotopePeakList);
}
catch (Exception ex)
{
throw new Exception(string.Format("Error getting deconvoluted peaks for scan {0} in GetDeconvolutedPeaks: {1}", scanNum, ex.Message), ex);
}
}
/// <summary>
/// Get the deconvoluted peaks that correspond to the provided peak list
/// </summary>
/// <param name="peaks"></param>
/// <param name="minCharge"></param>
/// <param name="maxCharge"></param>
/// <param name="isotopeOffsetTolerance"></param>
/// <param name="tolerance"></param>
/// <param name="corrScoreThreshold"></param>
/// <returns></returns>
public static List <DeconvolutedPeak> GetDeconvolutedPeaks_new(
Peak[] peaks,
int minCharge,
int maxCharge,
int isotopeOffsetTolerance,
Tolerance tolerance,
double corrScoreThreshold)
{
var spectrum = new Spectrum(peaks, 0);
var monoIsotopePeakList = new List <DeconvolutedPeak>();
var sortedPeaks = peaks.OrderByDescending(peak => peak.Intensity).ToArray();
var peakUsed = new bool[peaks.Length];
foreach (var peak in sortedPeaks)
{
var peakIndex = Array.BinarySearch(peaks, peak);
if (peakUsed[peakIndex])
{
continue;
}
var bestScore = 0.0;
DeconvolutedPeak bestPeak = null;
Tuple <Peak, int>[] bestObservedPeaks = null;
for (var charge = minCharge; charge <= maxCharge; charge++)
{
var mass = peak.Mz * charge - (charge * Constants.Proton);
if (mass > MaxMass)
{
continue;
}
var isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(mass);
var mostAbundantIsotopeIndex = isotopomerEnvelope.MostAbundantIsotopeIndex;
var offsetTolerance = isotopeOffsetTolerance;
if (isotopeOffsetTolerance < 0)
{
offsetTolerance = isotopomerEnvelope.Envelope.Length;
}
for (var isotopeIndex = mostAbundantIsotopeIndex - offsetTolerance;
isotopeIndex <= mostAbundantIsotopeIndex + offsetTolerance;
isotopeIndex++)
{
var monoIsotopeMass = Ion.GetMonoIsotopicMass(peak.Mz, charge, isotopeIndex);
var observedPeaks = GetAllIsotopePeaks(spectrum, monoIsotopeMass, charge, isotopomerEnvelope, tolerance, 0.1);
if (observedPeaks == null)
{
continue;
}
var envelop = isotopomerEnvelope.Envelope;
var observedIntensities = new double[observedPeaks.Length];
var observedPeakCount = 0;
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
if (observedPeak != null && peakUsed[observedPeak.Item2])
{
observedPeak = null;
observedPeaks[i] = null;
}
observedPeakCount += observedPeak != null ? 1 : 0;
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Item1.Intensity : 0.0;
}
var sim = FitScoreCalculator.GetDistanceAndCorrelation(envelop, observedIntensities);
var bcDist = sim.Item1;
var corr = sim.Item2;
var foundPeakRatio = observedPeakCount / ((double)envelop.Length);
var interferenceScore = 10.0;
var filteredObserved = observedPeaks.Where(p => p != null).ToArray();
if (filteredObserved.Length >= 2)
{
var allPeaks =
spectrum.Peaks.Where(p => p.Mz >= filteredObserved[0].Item1.Mz && p.Mz <= filteredObserved[filteredObserved.Length - 1].Item1.Mz).ToArray();
interferenceScore = CalculateInterferenceScore(allPeaks, filteredObserved);
}
bcDist = Math.Max(bcDist, double.Epsilon);
if (corr < corrScoreThreshold && bcDist > 0.1)
{
continue;
}
var score = (foundPeakRatio * corr) / (bcDist * (Math.Abs(mostAbundantIsotopeIndex - isotopeIndex) + 1) * interferenceScore);
//if (corr < corrScoreThreshold) continue;
// monoIsotopeMass is valid
if (score >= bestScore)
{
bestScore = score;
bestPeak = new DeconvolutedPeak(monoIsotopeMass, observedIntensities[mostAbundantIsotopeIndex], charge, corr, bcDist, observedPeaks.Where(p => p != null).Select(p => p.Item1).ToArray());
bestObservedPeaks = observedPeaks;
}
}
}
if (bestPeak != null)
{
monoIsotopePeakList.Add(bestPeak);
foreach (var p in bestObservedPeaks)
{
if (p != null)
{
bestPeak.ObservedPeakIndices.Add(p.Item2);
peakUsed[p.Item2] = true;
}
}
}
}
monoIsotopePeakList.Sort();
return(monoIsotopePeakList);
}
// 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);
}
private double GetMatchedIonPeakScore(bool isPrefixIon, DeconvolutedPeak peak)
{
var param = (isPrefixIon) ? ScoreParam.Prefix : ScoreParam.Suffix;
var score = param.Count;
score += param.Intensity * Math.Min(peak.Intensity / ReferencePeakIntensity, 1.0d);
score += param.Corr * peak.Corr;
score += param.Dist * peak.Dist;
return score;
}