//MsDeconv Score peak
private static double MsDeconvScore_peak(MzPeak experiment, MzPeak theory, double mass_error_tolerance = 0.02)
{
double score = 0;
double mass_error = Math.Abs(experiment.Mz - theory.Mz);
double mass_accuracy = 0;
if (mass_error <= 0.02)
{
mass_accuracy = 1 - mass_error / mass_error_tolerance;
}
double abundance_diff = 0;
if (experiment.Intensity < theory.Intensity && (theory.Intensity - experiment.Intensity) / experiment.Intensity <= 1)
{
abundance_diff = 1 - (theory.Intensity - experiment.Intensity) / experiment.Intensity;
}
else if (experiment.Intensity >= theory.Intensity && (experiment.Intensity - theory.Intensity) / experiment.Intensity <= 1)
{
abundance_diff = Math.Sqrt(1 - (experiment.Intensity - theory.Intensity) / experiment.Intensity);
}
score = Math.Sqrt(theory.Intensity) * mass_accuracy * abundance_diff;
return(score);
}
//Scale Theoretical Envelope
private static MzPeak[] ScaleTheoEnvelop(MzPeak[] experiment, MzPeak[] theory, string method = "sum")
{
var scale_Theory = new MzPeak[theory.Length];
switch (method)
{
case "sum":
var total_abundance = experiment.Sum(p => p.Intensity);
scale_Theory = theory.Select(p => new MzPeak(p.Mz, p.Intensity * total_abundance)).ToArray();
break;
default:
break;
}
return(scale_Theory);
}
//Change the workflow for different score method.
public static IsoEnvelop GetETEnvelopForPeakAtChargeState(MzSpectrumXY mzSpectrumXY, double candidateForMostIntensePeakMz, int chargeState, DeconvolutionParameter deconvolutionParameter, double noiseLevel, out List <int> arrayOfTheoPeakIndexes)
{
var testMostIntenseMass = candidateForMostIntensePeakMz.ToMass(chargeState);
var massIndex = GetClosestIndexInArray(testMostIntenseMass, mostIntenseMasses).Value;
var differenceBetweenTheorAndActual = candidateForMostIntensePeakMz.ToMass(chargeState) - mostIntenseMasses[massIndex];
var theoryIsoEnvelopLength = 0;
for (int i = 0; i < allIntensities[massIndex].Length; i++)
{
theoryIsoEnvelopLength++;
if (allIntensities[massIndex][i] / allIntensities[massIndex][0] <= 0.05 && i >= 2)
{
break;
}
}
var arrayOfPeaks = new MzPeak[theoryIsoEnvelopLength];
var arrayOfTheoPeaks = new MzPeak[theoryIsoEnvelopLength];
arrayOfTheoPeakIndexes = new List <int>(); //For top-down to calculate MsDeconvSignificance
for (int indexToLookAt = 0; indexToLookAt < theoryIsoEnvelopLength; indexToLookAt++)
{
double theorMassThatTryingToFind = allMasses[massIndex][indexToLookAt] + differenceBetweenTheorAndActual;
arrayOfTheoPeaks[indexToLookAt] = new MzPeak(theorMassThatTryingToFind.ToMz(chargeState), allIntensities[massIndex][indexToLookAt]);
var closestPeakToTheorMassIndex = GetClosestIndexInArray(theorMassThatTryingToFind.ToMz(chargeState), mzSpectrumXY.XArray);
var closestPeakmz = mzSpectrumXY.XArray[closestPeakToTheorMassIndex.Value];
var closestPeakIntensity = mzSpectrumXY.YArray[closestPeakToTheorMassIndex.Value];
if (!deconvolutionParameter.DeconvolutionAcceptor.Within(theorMassThatTryingToFind, closestPeakmz.ToMass(chargeState)) || closestPeakIntensity < noiseLevel)
{
closestPeakmz = theorMassThatTryingToFind.ToMz(chargeState);
closestPeakIntensity = 0;
}
else
{
//if the peak was matched
arrayOfTheoPeakIndexes.Add(closestPeakToTheorMassIndex.Value);
}
arrayOfPeaks[indexToLookAt] = new MzPeak(closestPeakmz, closestPeakIntensity);
}
if (FilterEEnvelop(arrayOfPeaks))
{
var scaleArrayOfTheoPeaks = ScaleTheoEnvelop(arrayOfPeaks, arrayOfTheoPeaks);
//The following 3 lines are for calculating monoisotopicMass, origin from Stephan, I don't understand it, and may optimize it in the future. (Lei)
//var extrapolatedMonoisotopicMass = candidateForMostIntensePeakMz.ToMass(chargeState) - diffToMonoisotopic[massIndex]; // Optimized for proteoforms!!
//var lowestMass = arrayOfPeaks.Min(b => b.Mz).ToMass(chargeState); // But may actually observe this small peak
//var monoisotopicMass = Math.Abs(extrapolatedMonoisotopicMass - lowestMass) < 0.5 ? lowestMass : extrapolatedMonoisotopicMass;
var monoisotopicMass = candidateForMostIntensePeakMz.ToMass(chargeState) - diffToMonoisotopic[massIndex];
IsoEnvelop isoEnvelop = new IsoEnvelop(arrayOfPeaks, scaleArrayOfTheoPeaks, monoisotopicMass, chargeState, arrayOfTheoPeakIndexes);
return(isoEnvelop);
}
return(null);
}