//Calculate score based on All possible Products Masses for inter- or intra- crosslinks and deadend.
public static void XlLocalizationForLoopCrosslink(Ms2ScanWithSpecificMass theScan, PsmCross psmCross, double modMass, CrosslinkerTypeClass crosslinker, List <ProductType> lp, Tolerance fragmentTolerance, List <int> linkPos)
{
var pmmhList = PsmCross.XlCalculateTotalProductMassesForLoopCrosslink(psmCross, modMass, crosslinker, lp, linkPos);
List <double> scoreList = new List <double>();
List <MatchedIonInfo> miil = new List <MatchedIonInfo>();
foreach (var pmm in pmmhList)
{
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, fragmentTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
miil.Add(matchedIonMassesListPositiveIsMatch);
scoreList.Add(pmmScore);
}
psmCross.XLBestScore = scoreList.Max();
psmCross.MatchedIonInfo = miil[scoreList.IndexOf(scoreList.Max())];
psmCross.XlPos = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos + 1;
psmCross.XlPos2 = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos2 + 1;
}
//Calculate score based on Product Masses.
public static double XlMatchIons(IMsDataScan <IMzSpectrum <IMzPeak> > thisScan, Tolerance productMassTolerance, double[] sorted_theoretical_product_masses_for_this_peptide, string[] sorted_theoretical_product_name_for_this_peptide, MatchedIonInfo matchedIonMassesListPositiveIsMatch)
{
var TotalProductsHere = sorted_theoretical_product_masses_for_this_peptide.Length;
if (TotalProductsHere == 0)
{
return(0);
}
int MatchingProductsHere = 0;
double MatchingIntensityHere = 0;
// speed optimizations
double[] experimental_mzs = thisScan.MassSpectrum.XArray;
double[] experimental_intensities = thisScan.MassSpectrum.YArray;
int[] experimental_intensities_rank = GenerateIntensityRanks(experimental_mzs, experimental_intensities);
int num_experimental_peaks = experimental_mzs.Length;
int currentTheoreticalIndex = -1;
double currentTheoreticalMass;
do
{
currentTheoreticalIndex++;
currentTheoreticalMass = sorted_theoretical_product_masses_for_this_peptide[currentTheoreticalIndex];
} while (double.IsNaN(currentTheoreticalMass) && currentTheoreticalIndex < sorted_theoretical_product_masses_for_this_peptide.Length - 1);
if (double.IsNaN(currentTheoreticalMass))
{
return(0);
}
double currentTheoreticalMz = currentTheoreticalMass + Constants.protonMass;
int testTheoreticalIndex;
double testTheoreticalMZ;
double testTheoreticalMass;
// Loop over all experimenal indices
for (int experimentalIndex = 0; experimentalIndex < num_experimental_peaks; experimentalIndex++)
{
double currentExperimentalMZ = experimental_mzs[experimentalIndex];
// If found match
if (productMassTolerance.Within(currentExperimentalMZ, currentTheoreticalMz))
{
MatchingProductsHere++;
MatchingIntensityHere += experimental_intensities[experimentalIndex];
matchedIonMassesListPositiveIsMatch.MatchedIonMz[currentTheoreticalIndex] = currentTheoreticalMass;
matchedIonMassesListPositiveIsMatch.MatchedIonIntensity[currentTheoreticalIndex] = experimental_intensities[experimentalIndex];
matchedIonMassesListPositiveIsMatch.MatchedIonName[currentTheoreticalIndex] = sorted_theoretical_product_name_for_this_peptide[currentTheoreticalIndex];
matchedIonMassesListPositiveIsMatch.MatchedIonIntensityRank[currentTheoreticalIndex] = experimental_intensities_rank[experimentalIndex];
currentTheoreticalIndex++;
if (currentTheoreticalIndex == TotalProductsHere)
{
break;
}
currentTheoreticalMass = sorted_theoretical_product_masses_for_this_peptide[currentTheoreticalIndex];
currentTheoreticalMz = currentTheoreticalMass + Constants.protonMass;
}
// Else if for sure did not reach the next theoretical yet, move to next experimental
else if (currentExperimentalMZ < currentTheoreticalMz)
{
continue;
}
// Else if for sure passed a theoretical
else
{
// Mark the theoretical as missed
matchedIonMassesListPositiveIsMatch.MatchedIonMz[currentTheoreticalIndex] = -currentTheoreticalMass;
// Move on to next index and never come back!
currentTheoreticalIndex++;
if (currentTheoreticalIndex == TotalProductsHere)
{
break;
}
currentTheoreticalMass = sorted_theoretical_product_masses_for_this_peptide[currentTheoreticalIndex];
currentTheoreticalMz = currentTheoreticalMass + Constants.protonMass;
// Start with the current ones
testTheoreticalIndex = currentTheoreticalIndex;
testTheoreticalMZ = currentTheoreticalMz;
testTheoreticalMass = currentTheoreticalMass;
// Mark the skipped theoreticals as not found. The last one is not for sure, might be flipped!
while (currentExperimentalMZ > testTheoreticalMZ)
{
matchedIonMassesListPositiveIsMatch.MatchedIonMz[testTheoreticalIndex] = -currentTheoreticalMass;
// Store old info for possible reuse
currentTheoreticalMass = testTheoreticalMass;
currentTheoreticalMz = testTheoreticalMZ;
currentTheoreticalIndex = testTheoreticalIndex;
// Update test stuff!
testTheoreticalIndex++;
if (testTheoreticalIndex == TotalProductsHere)
{
break;
}
testTheoreticalMass = sorted_theoretical_product_masses_for_this_peptide[testTheoreticalIndex];
testTheoreticalMZ = testTheoreticalMass + Constants.protonMass;
}
experimentalIndex--;
}
}
return(MatchingProductsHere + MatchingIntensityHere / thisScan.TotalIonCurrent);
}
//Calculate score based on All possible Products Masses for inter- or intra- crosslinks and deadend.
public static void XlLocalization(Ms2ScanWithSpecificMass theScan, PsmCross psmCross, double modMass,
CrosslinkerTypeClass crosslinker, List <ProductType> lp, Tolerance fragmentTolerance, bool Charge_2_3, bool Charge_2_3_PrimeFragment, List <int> linkPos)
{
var pmmhList = PsmCross.XlCalculateTotalProductMasses(psmCross, modMass, crosslinker, lp, Charge_2_3, Charge_2_3_PrimeFragment, linkPos);
List <double> scoreList = new List <double>();
List <MatchedIonInfo> miil = new List <MatchedIonInfo>();
foreach (var pmm in pmmhList)
{
var matchedIonMassesListPositiveIsMatch = new MatchedIonInfo(pmm.ProductMz.Length);
double pmmScore = PsmCross.XlMatchIons(theScan.TheScan, fragmentTolerance, pmm.ProductMz, pmm.ProductName, matchedIonMassesListPositiveIsMatch);
miil.Add(matchedIonMassesListPositiveIsMatch);
scoreList.Add(pmmScore);
}
psmCross.XLBestScore = scoreList.Max();
psmCross.MatchedIonInfo = miil[scoreList.IndexOf(scoreList.Max())];
psmCross.XlPos = pmmhList[scoreList.IndexOf(scoreList.Max())].XlPos + 1;
if (crosslinker.Cleavable)
{
psmCross.ParentIonMaxIntensityRanks = new List <int>();
if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Contains("PepS")))
{
psmCross.ParentIonExist += "PepS";
psmCross.ParentIonExistNum += 1;
}
if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Contains("PepL")))
{
psmCross.ParentIonExist += "PepL";
psmCross.ParentIonExistNum += 1;
}
//if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Equals("PepS2")))
//{
// psmCross.ParentIonExist += "PepS2";
// psmCross.ParentIonExistNum += 1;
//}
//if (psmCross.MatchedIonInfo.MatchedIonName.Any(p => p != null && p.Equals("PepL2")))
//{
// psmCross.ParentIonExist += "PepL2";
// psmCross.ParentIonExistNum += 1;
//}
for (int i = 0; i < psmCross.MatchedIonInfo.MatchedIonName.Length; i++)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i] != null)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i].Contains("Pep"))
{
psmCross.ParentIonMaxIntensityRanks.Add(psmCross.MatchedIonInfo.MatchedIonIntensityRank[i]);
}
}
}
}
if (Charge_2_3 || Charge_2_3_PrimeFragment)
{
int Charge2IonExist = 0;
for (int i = 0; i < psmCross.MatchedIonInfo.MatchedIonName.Length; i++)
{
if (psmCross.MatchedIonInfo.MatchedIonName[i] != null && (psmCross.MatchedIonInfo.MatchedIonName[i].Contains("t2") || psmCross.MatchedIonInfo.MatchedIonName[i].Contains("t3")))
{
Charge2IonExist++;
}
}
psmCross.Charge2IonExist = Charge2IonExist;
}
}
