public static IsoEnvelop MsDeconvExperimentPeak(MzSpectrumXY mzSpectrumXY, int candidateForMostIntensePeak, DeconvolutionParameter deconvolutionParameter, double noiseLevel)
{
IsoEnvelop bestIsotopeEnvelopeForThisPeak = null;
var candidateForMostIntensePeakMz = mzSpectrumXY.XArray[candidateForMostIntensePeak];
//Find possible chargeStates.
List <int> allPossibleChargeState = new List <int>();
for (int i = candidateForMostIntensePeak + 1; i < mzSpectrumXY.XArray.Length; i++)
{
if (mzSpectrumXY.XArray[i] - candidateForMostIntensePeakMz < 1.1) //In case charge is +1
{
var chargeDouble = 1.00289 / (mzSpectrumXY.XArray[i] - candidateForMostIntensePeakMz);
int charge = Convert.ToInt32(chargeDouble);
if (deconvolutionParameter.DeconvolutionAcceptor.Within(candidateForMostIntensePeakMz + 1.00289 / chargeDouble, mzSpectrumXY.XArray[i]) &&
charge >= deconvolutionParameter.DeconvolutionMinAssumedChargeState &&
charge <= deconvolutionParameter.DeconvolutionMaxAssumedChargeState &&
!allPossibleChargeState.Contains(charge))
{
allPossibleChargeState.Add(charge);
}
}
else
{
break;
}
}
foreach (var chargeState in allPossibleChargeState)
{
List <int> arrayOfTheoPeakIndexes; //Is not used here, is used in ChargeDecon
var isoEnvelop = GetETEnvelopForPeakAtChargeState(mzSpectrumXY, candidateForMostIntensePeakMz, chargeState, deconvolutionParameter, noiseLevel, out arrayOfTheoPeakIndexes);
if (MsDeconvScore(isoEnvelop) > MsDeconvScore(bestIsotopeEnvelopeForThisPeak))
{
var temp = bestIsotopeEnvelopeForThisPeak;
bestIsotopeEnvelopeForThisPeak = isoEnvelop;
//This is to refine mis charge ones. But not working perfect.
if (temp != null && bestIsotopeEnvelopeForThisPeak != null)
{
int cd = temp.Charge / bestIsotopeEnvelopeForThisPeak.Charge;
if (temp.ExperimentIsoEnvelop.Where(p => p.Intensity != 0).Count() >= bestIsotopeEnvelopeForThisPeak.ExperimentIsoEnvelop.Where(p => p.Intensity != 0).Count() + 3 &&
cd > 1 && temp.Charge == bestIsotopeEnvelopeForThisPeak.Charge * cd)
{
bestIsotopeEnvelopeForThisPeak = temp;
}
}
}
}
return(bestIsotopeEnvelopeForThisPeak);
}
public static List <IsoEnvelop> MsDeconv_Deconvolute(MzSpectrumXY mzSpectrumXY, MzRange theRange, DeconvolutionParameter deconvolutionParameter)
{
var isolatedMassesAndCharges = new List <IsoEnvelop>();
if (mzSpectrumXY.Size == 0)
{
return(isolatedMassesAndCharges);
}
////Deconvolution by MZ increasing order
//double intensityThread = mzSpectrumXY.TotalIntensity / mzSpectrumXY.Size;
for (int candidateForMostIntensePeak = 0; candidateForMostIntensePeak < mzSpectrumXY.XArray.Length - 1; candidateForMostIntensePeak++)
{
//if (mzSpectrumXY.YArray[candidateForMostIntensePeak] <= intensityThread)
//{
// continue;
//}
double noiseLevel = CalNoiseLevel();
//TO THINK: Only get one isoEnvelop per best peak. It is possible this is a overlap best peak with different charge state.
IsoEnvelop bestIsotopeEnvelopeForThisPeak = MsDeconvExperimentPeak(mzSpectrumXY, candidateForMostIntensePeak, deconvolutionParameter, noiseLevel);
if (bestIsotopeEnvelopeForThisPeak != null)
{
bestIsotopeEnvelopeForThisPeak.MsDeconvSignificance = CalIsoEnvelopNoise(mzSpectrumXY, bestIsotopeEnvelopeForThisPeak);
bestIsotopeEnvelopeForThisPeak.IntensityRatio = bestIsotopeEnvelopeForThisPeak.TotalIntensity / mzSpectrumXY.TotalIntensity;
isolatedMassesAndCharges.Add(bestIsotopeEnvelopeForThisPeak);
}
}
HashSet <double> seen = new HashSet <double>(); //Do we still need this
List <IsoEnvelop> isoEnvelops = new List <IsoEnvelop>();
//TO DO: consider peak overlap
foreach (var ok in isolatedMassesAndCharges.OrderByDescending(b => b.MsDeconvScore))
{
//if (seen.Overlaps(ok.ExperimentIsoEnvelop.Select(b => b.Mz)))
//{
// continue;
//}
int noOverlap = 0;
foreach (var ah in ok.ExistedExperimentPeak.Select(b => b.Mz))
{
if (!seen.Contains(ah))
{
noOverlap++;
}
}
if (noOverlap < 2)
{
continue;
}
foreach (var ah in ok.ExperimentIsoEnvelop.Select(b => b.Mz))
{
seen.Add(ah);
}
isoEnvelops.Add(ok);
}
var orderedIsoEnvelops = isoEnvelops.OrderBy(p => p.ExperimentIsoEnvelop.First().Mz).ToList();
return(orderedIsoEnvelops);
}
//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);
}
