private static GraphML_List <MsMsPeak> AssignChargeStatesbkp(GraphML_List <MsMsPeak> peaks, int maxCharge, MassTolerance isotopicMzTolerance)
{
GraphML_List <MsMsPeak> new_peaks = new GraphML_List <MsMsPeak>();
for (int i = 0; i < peaks.Count - 1; 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 = maxCharge; c >= 1; c--)
{
if (Math.Abs(Numerics.CalculateMassError(peaks[j].MZ, peaks[i].MZ + Constants.C12_C13_MASS_DIFFERENCE / (double)c, isotopicMzTolerance.Units)) <= isotopicMzTolerance.Value)
{
new_peaks.Add(new MsMsPeak(peaks[i].MZ, peaks[i].Intensity, c));
charges.Add(c);
}
}
j++;
}
if (charges.Count == 0)
{
new_peaks.Add(new MsMsPeak(peaks[i].MZ, peaks[i].Intensity, 0));
}
}
return(new_peaks);
}
}//*/
public IEnumerable <ProductMatch> GetProductMZs(DBOptions options, GraphML_List <MsMsPeak> peaks)//, List<double> theoretical_product_mzs = null)
{
// speed optimizations
//double[] experimental_masses = Query.spectrum.Masses;
//GraphML_List<MSPeak> peaks = Query.spectrum.Peaks;
int num_experimental_peaks = peaks.Count;
TotalTheoreticalProducts = 0;
TotalWeightedProducts = 0;
//New version that should include charged ions
//foreach (ProductMatch matchTheo in AllFragmentSearch.ComputeAllFragments(Peptide, Query.precursor.Charge, options))
foreach (ProductMatch matchTheo in options.fragments.ComputeFragmentsFast(Peptide.GetMasses(), Query.precursor.Charge, options))
//foreach (ProductMatch matchTheo in options.fragments.ComputeFragments(Peptide, Query.precursor.Charge, options))
{
TotalTheoreticalProducts++;
TotalWeightedProducts += matchTheo.weight;//++;
//TODO test what is most common between charged ions, and uncharged ions
//for (int charge = 1; charge <= Query.precursor.Charge; charge++)
//for (int charge = Query.precursor.Charge; charge >= 1; charge--)
//{
double massDiff = options.productMassTolerance.Value;
double bestMz = -1;
double bestInt = 0;
foreach (int index in Query.spectrum.GetIndexOfMZInRange(matchTheo.theoMz, options.productMassTolerance))
{
if (peaks[index].Charge <= 0 || peaks[index].Charge == matchTheo.charge)
{
double diff = Numerics.CalculateMassError(peaks[index].MZ, matchTheo.theoMz, options.productMassTolerance.Units);
//double diff = matchTheo.theoMz - peaks[index].MZ;// experimental_masses[index];//TODO DALTON ONLY : add product mass tolerance unit test
if (Math.Abs(diff) < options.productMassTolerance.Value)
{
if (Math.Abs(diff) < Math.Abs(massDiff))//TODO Priority to intensity, or precision?
{
massDiff = diff;
bestMz = peaks[index].MZ;
}
//if (peaks[index].Intensity > bestInt)
bestInt += peaks[index].Intensity;
}
}
}
if (bestMz >= 0)
{
ProductMatch pMatch = new ProductMatch();
pMatch.weight = matchTheo.weight;
pMatch.theoMz = matchTheo.theoMz; // Utilities.MZFromMzSingleCharge(theoMass, charge);
pMatch.obsMz = bestMz; // experimental_masses[bestIndex];
pMatch.mass_diff = massDiff;
pMatch.obsIntensity = bestInt; // Intensities[bestIndex];
pMatch.charge = matchTheo.charge; // peaks[bestIndex].Charge;
pMatch.Fragment = matchTheo.Fragment;
pMatch.fragmentPos = matchTheo.fragmentPos;
pMatch.normalizedIntensity = pMatch.obsIntensity / (Query.spectrum.InjectionTime * Query.spectrum.PrecursorIntensityPerMilliSecond);
yield return(pMatch);
//break;
}
}
}
private static GraphML_List <MsMsPeak> Deisotopebkp(GraphML_List <MsMsPeak> peaks, int maxCharge, MassTolerance isotopicMzTolerance)
{
GraphML_List <MsMsPeak> new_peaks = new GraphML_List <MsMsPeak>(peaks);
peaks.Sort(MsMsPeak.AscendingMzComparison);
for (int lowMassIndex = 0; lowMassIndex < new_peaks.Count - 1; lowMassIndex++)
{
if (new_peaks[lowMassIndex].Charge > 0)
{
int toRemove = -1;
double bestMassError = isotopicMzTolerance.Value;
double aim = Numerics.IsotopicMassShift(1, new_peaks[lowMassIndex].Charge) + new_peaks[lowMassIndex].MZ;
int potentialIsotopeIndex = lowMassIndex + 1;
while (potentialIsotopeIndex < new_peaks.Count && new_peaks[potentialIsotopeIndex].MZ < aim + bestMassError)
{
if (new_peaks[lowMassIndex].Intensity > new_peaks[potentialIsotopeIndex].Intensity)
{
double massError = Math.Abs(Numerics.CalculateMassError(new_peaks[potentialIsotopeIndex].MZ, aim, isotopicMzTolerance.Units));
if (massError < bestMassError)
{
bestMassError = massError;
toRemove = potentialIsotopeIndex;
}
}
potentialIsotopeIndex++;
}
if (toRemove > 0)
{
new_peaks[lowMassIndex].Intensity += new_peaks[toRemove].Intensity;
new_peaks.RemoveAt(toRemove);
}
}
}
return(new_peaks);
}
private static GraphML_List <MsMsPeak> AssignChargeStatesAndDeisotope(GraphML_List <MsMsPeak> peaks, int maxCharge, MassTolerance isotopicMzTolerance)
{
GraphML_List <MsMsPeak> new_peaks = new GraphML_List <MsMsPeak>(peaks);
//peaks.Sort(MSPeak.AscendingMzComparison);
int[] bestIsotopes = new int[4];
int[] currentIsotopes = new int[4];
for (int lowMassIndex = 0; lowMassIndex < new_peaks.Count - 1; lowMassIndex++)
{
double bestChargeScore = 0;
int bestCharge = 0;
bestIsotopes[0] = 0; bestIsotopes[1] = 0; bestIsotopes[2] = 0; bestIsotopes[3] = 0;
for (int charge = maxCharge; charge > 0; charge--)
{
currentIsotopes[0] = 0; currentIsotopes[1] = 0; currentIsotopes[2] = 0; currentIsotopes[3] = 0;
double score = 0;
int potentialIsotopeIndex = lowMassIndex + 1;
for (int isotope = 1; isotope <= 4; isotope++)
{
double bestMassError = isotopicMzTolerance.Value;
double aim = Numerics.IsotopicMassShift(isotope, charge) + new_peaks[lowMassIndex].MZ;
while (potentialIsotopeIndex < new_peaks.Count && new_peaks[potentialIsotopeIndex].MZ < aim + bestMassError)
{
if (new_peaks[lowMassIndex].Intensity > new_peaks[potentialIsotopeIndex].Intensity)
{
double massError = Math.Abs(Numerics.CalculateMassError(new_peaks[potentialIsotopeIndex].MZ, aim, isotopicMzTolerance.Units));
if (massError < bestMassError)
{
bestMassError = massError;
currentIsotopes[isotope - 1] = potentialIsotopeIndex;
}
}
potentialIsotopeIndex++;
}
score += isotopicMzTolerance.Value - bestMassError;
if (score == 0)
{
break;
}
;
}
if (score > bestChargeScore)
{
bestIsotopes[0] = currentIsotopes[0];
bestIsotopes[1] = currentIsotopes[1];
bestIsotopes[2] = currentIsotopes[2];
bestIsotopes[3] = currentIsotopes[3];
bestChargeScore = score;
bestCharge = charge;
}
}
new_peaks[lowMassIndex].Charge = bestCharge;
for (int i = 3; i >= 0; i--)
{
if (bestIsotopes[i] > 0)
{
new_peaks[lowMassIndex].Intensity += new_peaks[bestIsotopes[i]].Intensity;
new_peaks.RemoveAt(bestIsotopes[i]);
}
}
}
return(new_peaks);
}