private static int? ValidateFormulaWithMz(SrmDocument document, ref string moleculeFormula, double mz, int? charge, out double monoMass, out double averageMass, out double? mzCalc)
{
// Is the ion's formula the old style where user expected us to add a hydrogen?
var tolerance = document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
int massShift;
var ion = new DocNodeCustomIon(moleculeFormula);
monoMass = ion.GetMass(MassType.Monoisotopic);
averageMass = ion.GetMass(MassType.Average);
double mass = (document.Settings.TransitionSettings.Prediction.FragmentMassType == MassType.Monoisotopic)
? monoMass
: averageMass;
// Does given charge, if any, agree with mass and mz?
mzCalc = charge.HasValue ? BioMassCalc.CalculateIonMz(mass, charge.Value) : (double?)null;
if (mzCalc.HasValue && tolerance >= (Math.Abs(mzCalc.Value - mz)))
{
return charge;
}
int nearestCharge;
charge = TransitionCalc.CalcCharge(mass, mz, tolerance, true, TransitionGroup.MIN_PRECURSOR_CHARGE,
TransitionGroup.MAX_PRECURSOR_CHARGE, new int[0],
TransitionCalc.MassShiftType.none, out massShift, out nearestCharge);
if (!charge.HasValue)
{
// That formula and this mz don't yield a reasonable charge state - try adding an H
var ion2 = new DocNodeCustomIon(BioMassCalc.AddH(ion.Formula));
monoMass = ion2.GetMass(MassType.Monoisotopic);
averageMass = ion2.GetMass(MassType.Average);
mass = (document.Settings.TransitionSettings.Prediction.FragmentMassType == MassType.Monoisotopic)
? monoMass
: averageMass;
charge = TransitionCalc.CalcCharge(mass, mz, tolerance, true, TransitionGroup.MIN_PRECURSOR_CHARGE,
TransitionGroup.MAX_PRECURSOR_CHARGE, new int[0], TransitionCalc.MassShiftType.none, out massShift, out nearestCharge);
if (charge.HasValue)
{
moleculeFormula = ion2.Formula;
}
else
{
monoMass = 0;
averageMass = 0;
}
}
return charge;
}
private double ValidateFormulaWithCharge(SrmDocument document, string moleculeFormula, int charge, out double monoMass, out double averageMass)
{
var massType = document.Settings.TransitionSettings.Prediction.PrecursorMassType;
var ion = new DocNodeCustomIon(moleculeFormula);
double mass = ion.GetMass(massType);
monoMass = ion.GetMass(MassType.Monoisotopic);
averageMass = ion.GetMass(MassType.Average);
return BioMassCalc.CalculateIonMz(mass, charge);
}
