| public static CalculateMassError ( double experimental, double theoretical, MassToleranceUnits massErrorUnits ) : double | ||
| experimental | double | |
| theoretical | double | |
| massErrorUnits | MassToleranceUnits | |
| return | double | |
private static List<MSPeak> Deisotope(IEnumerable<MSPeak> peaks, int maxAbsoluteCharge, int polarity, MassTolerance isotopicMZTolerance)
{
List<MSPeak> new_peaks = new List<MSPeak>(peaks);
int p = new_peaks.Count - 1;
while(p >= 1)
{
int q = p - 1;
bool removed = false;
while(q >= 0)
{
if(new_peaks[p].MZ > (new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE) + isotopicMZTolerance)
{
break;
}
if(new_peaks[p].Intensity < new_peaks[q].Intensity)
{
if(polarity == 0)
{
if(Math.Abs(MassTolerance.CalculateMassError(new_peaks[p].MZ, new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE, isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.RemoveAt(p);
removed = true;
break;
}
}
else
{
for(int c = polarity; polarity > 0 ? c <= maxAbsoluteCharge : c >= -maxAbsoluteCharge; c += polarity)
{
if(Math.Abs(MassTolerance.CalculateMassError(new_peaks[p].MZ, new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE / Math.Abs(c), isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.RemoveAt(p);
removed = true;
break;
}
}
}
if(removed)
{
break;
}
}
q--;
}
p--;
}
return new_peaks;
}
private static List<MSPeak> AssignChargeStates(IList<MSPeak> peaks, int maxAbsoluteCharge, int polarity, MassTolerance isotopicMZTolerance)
{
List<MSPeak> new_peaks = new List<MSPeak>();
for(int i = 0; i < peaks.Count; i++)
{
int j = i + 1;
List<int> charges = new List<int>();
while(j < peaks.Count)
{
if(peaks[j].MZ > (peaks[i].MZ + Constants.C12_C13_MASS_DIFFERENCE) + isotopicMZTolerance)
{
break;
}
for(int c = polarity * maxAbsoluteCharge; polarity > 0 ? c >= 1 : c <= -1; c -= polarity)
{
// remove harmonic charges, e.g. don't consider peak as a +2 (0.5 Th spacing) if it could be a +4 (0.25 Th spacing)
if(HARMONIC_CHARGE_DETECTION)
{
bool harmonic = false;
foreach(int c2 in charges)
{
if(c2 % c == 0)
{
harmonic = true;
break;
}
}
if(harmonic)
{
continue;
}
}
if(Math.Abs(MassTolerance.CalculateMassError(peaks[j].MZ, peaks[i].MZ + Constants.C12_C13_MASS_DIFFERENCE / c, isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.Add(new MSPeak(peaks[i].MZ, peaks[i].Intensity, c, polarity));
charges.Add(c);
}
}
j++;
}
if(charges.Count == 0)
{
new_peaks.Add(new MSPeak(peaks[i].MZ, peaks[i].Intensity, 0, polarity));
}
}
return new_peaks;
}