private (List <LabeledMs2DataPoint>, int, int, int) SearchMS2Spectrum(IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > ms2DataScan, Proteomics.Peptide peptide, int peptideCharge, PeptideSpectralMatch identification)
{
List <LabeledMs2DataPoint> result = new List <LabeledMs2DataPoint>();
int numMs2MassChargeCombinationsConsidered = 0;
int numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks = 0;
int numFragmentsIdentified = 0;
if (ms2DataScan.MassSpectrum.Size == 0)
{
return(result, numMs2MassChargeCombinationsConsidered, numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks, numFragmentsIdentified);
}
// Key: mz value, Value: error
var addedPeaks = new Dictionary <double, double>();
var countForThisMS2 = 0;
var countForThisMS2a = 0;
var scanWindowRange = ms2DataScan.ScanWindowRange;
IHasChemicalFormula[] fragmentList = peptide.Fragment(fragmentTypesForCalibration, true).OfType <IHasChemicalFormula>().ToArray();
foreach (var fragment in fragmentList)
{
bool fragmentIdentified = false;
bool computedIsotopologues = false;
double[] masses = new double[0];
double[] intensities = new double[0];
// First look for monoisotopic masses, do not compute distribution spectrum!
for (int chargeToLookAt = 1; chargeToLookAt <= peptideCharge; chargeToLookAt++)
{
var monoisotopicMZ = fragment.MonoisotopicMass.ToMz(chargeToLookAt);
if (monoisotopicMZ > scanWindowRange.Maximum)
{
continue;
}
if (monoisotopicMZ < scanWindowRange.Minimum)
{
break;
}
var closestPeakMZ = ms2DataScan.MassSpectrum.GetClosestPeakXvalue(monoisotopicMZ);
if (mzToleranceForMs2Search.Within(closestPeakMZ.Value, monoisotopicMZ) && !computedIsotopologues)
{
var dist = IsotopicDistribution.GetDistribution(fragment.ThisChemicalFormula, fineResolutionForIsotopeDistCalculation, 0.001);
masses = dist.Masses.ToArray();
intensities = dist.Intensities.ToArray();
Array.Sort(intensities, masses, Comparer <double> .Create((x, y) => y.CompareTo(x)));
computedIsotopologues = true;
break;
}
}
if (computedIsotopologues)
{
bool startingToAdd = false;
for (int chargeToLookAt = 1; chargeToLookAt <= peptideCharge; chargeToLookAt++)
{
if (masses.First().ToMz(chargeToLookAt) > scanWindowRange.Maximum)
{
continue;
}
if (masses.Last().ToMz(chargeToLookAt) < scanWindowRange.Minimum)
{
break;
}
var trainingPointsToAverage = new List <LabeledMs2DataPoint>();
foreach (double a in masses)
{
double theMZ = a.ToMz(chargeToLookAt);
var npwr = ms2DataScan.MassSpectrum.NumPeaksWithinRange(mzToleranceForMs2Search.GetMinimumValue(theMZ), mzToleranceForMs2Search.GetMaximumValue(theMZ));
if (npwr == 0)
{
break;
}
numMs2MassChargeCombinationsConsidered++;
if (npwr > 1)
{
numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks++;
continue;
}
var closestPeakIndex = ms2DataScan.MassSpectrum.GetClosestPeakIndex(theMZ);
var closestPeakMZ = ms2DataScan.MassSpectrum.XArray[closestPeakIndex.Value];
if (!addedPeaks.ContainsKey(closestPeakMZ))
{
addedPeaks.Add(closestPeakMZ, Math.Abs(closestPeakMZ - theMZ));
trainingPointsToAverage.Add(new LabeledMs2DataPoint(closestPeakMZ, double.NaN, double.NaN, double.NaN, Math.Log(ms2DataScan.MassSpectrum.YArray[closestPeakIndex.Value]), theMZ, null));
}
}
// If started adding and suddnely stopped, go to next one, no need to look at higher charges
if (trainingPointsToAverage.Count == 0 && startingToAdd)
{
break;
}
if (trainingPointsToAverage.Count < Math.Min(minMS2isotopicPeaksNeededForConfirmedIdentification, intensities.Count()))
{
}
else
{
startingToAdd = true;
if (!fragmentIdentified)
{
fragmentIdentified = true;
numFragmentsIdentified += 1;
}
countForThisMS2 += trainingPointsToAverage.Count;
countForThisMS2a++;
result.Add(new LabeledMs2DataPoint(trainingPointsToAverage.Select(b => b.mz).Average(),
ms2DataScan.RetentionTime,
Math.Log(ms2DataScan.TotalIonCurrent),
ms2DataScan.InjectionTime.HasValue ? Math.Log(ms2DataScan.InjectionTime.Value) : double.NaN,
trainingPointsToAverage.Select(b => b.logIntensity).Average(),
trainingPointsToAverage.Select(b => b.expectedMZ).Average(),
identification));
}
}
}
}
return(result, numMs2MassChargeCombinationsConsidered, numMs2MassChargeCombinationsThatAreIgnoredBecauseOfTooManyPeaks, numFragmentsIdentified);
}
