/// <summary>
///
/// </summary>
/// <param name="centroidData"></param>
/// <param name="parentMZ"></param>
/// <param name="possibleChargeStates"></param>
/// <param name="assignedChargeState"></param>
/// <returns></returns>
static (int charge, double mass) GetMonoIsotopicMassCharge(CentroidStreamData centroidData, double parentMZ, List <int> possibleChargeStates, int assignedChargeState)
{
Dictionary <(int charge, double monoIsoMass), (double distance, double correlation)> scores =
new Dictionary <(int charge, double monoIsoMass), (double distance, double correlation)>();;
List <double> possibleMonoIsoMasses;
Averagine averagine = new Averagine();
double[] masses, intensities;
(masses, intensities) = AdditionalMath.SubsetMsData(centroidData.Masses, centroidData.Intensities, parentMZ - 2.2, parentMZ + 5);
if (masses.Length == 0)
{
return(assignedChargeState, parentMZ);
}
foreach (int charge in possibleChargeStates)
{
// populate a list of possible monoisotopic masses
possibleMonoIsoMasses = new List <double>()
{
parentMZ
};
for (int i = 1; i < 4; i++)
{
double isotope = parentMZ - i * Masses.C13MinusC12 / charge;
if (masses.withinTolerance(isotope, 10))
{
possibleMonoIsoMasses.Add(isotope);
}
else
{
break;
}
}
if (possibleChargeStates.Count() == 1 & possibleMonoIsoMasses.Count() == 1)
{
// only one possible monoisotopic mass was found, so just return that
return(possibleChargeStates.First(), parentMZ);
}
// now score
foreach (double monoisoMZ in possibleMonoIsoMasses)
{
// calculate the actual mass and intensity envelope of the potential monoisotopicMZ
double monoIsotopeMass = (monoisoMZ - Masses.Proton) * charge;
double[] isotopomerEnvelope = Averagine.GetIsotopomerEnvelope(monoIsotopeMass).Envelope;
// get out the observed intensities corresponding to the isotope envelope
List <double> observedIntensities = new List <double>();
int currentIndex = masses.ToList().IndexOf(monoisoMZ);
for (int i = 0; i < isotopomerEnvelope.Count(); i++)
{
if ((masses.withinTolerance(monoisoMZ + i * Masses.C13MinusC12 / charge, 10)))
{
if (currentIndex < intensities.Count())
{
int index = masses.indexOfClosest(monoisoMZ + i * Masses.C13MinusC12 / charge);
observedIntensities.Add(intensities[index]);
}
else
{
// we've run out of ions
double[] temp = new double[observedIntensities.Count()];
for (int j = 0; j < temp.Length; j++)
{
temp[j] = isotopomerEnvelope[j];
}
isotopomerEnvelope = temp;
}
}
else
{
observedIntensities.Add(0);
}
currentIndex++;
}
// normalize the observed intensities
double maxInt = observedIntensities.Max();
for (int i = 0; i < observedIntensities.Count(); i++)
{
observedIntensities[i] = observedIntensities[i] / maxInt;
}
// calculate distance and correlation
double distance, correlation;
(distance, correlation) = FitScores.GetDistanceAndCorrelation(observedIntensities.ToArray(), isotopomerEnvelope);
if (distance < 0.3)
{
scores.Add((charge, monoisoMZ), (distance, correlation));
}
}
}
double smallestDistance = 1;
double massOut = 0;
int chargeOut = assignedChargeState;
if (scores.Keys.Count == 0)
{
return(chargeOut, parentMZ);
}
foreach (var key in scores?.Keys)
{
if (scores[key].distance < smallestDistance)
{
smallestDistance = scores[key].distance;
massOut = key.monoIsoMass;
chargeOut = key.charge;
}
}
return(chargeOut, massOut);
}
static Averagine()
{
DefaultAveragine = new Averagine();
}