//If XlSites is of same types
private PsmCross XlSitesSame(Ms2ScanWithSpecificMass theScan, PsmCross psmCrossAlpha, PsmCross psmCrossBeta,
CrosslinkerTypeClass crosslinker, int ind, int inx)
{
PsmCross psmCross = null;
var xlPosAlpha = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker.CrosslinkerModSites);
var xlPosBeta = PsmCross.XlPosCal(psmCrossBeta.compactPeptide, crosslinker.CrosslinkerModSites);
if (xlPosAlpha.Count() >= 1 && xlPosBeta.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossAlpha, psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, ProductTypes, commonParameters.ProductMassTolerance, Charge_2_3, Charge_2_3_PrimeFragment, xlPosAlpha);
PsmCross.XlLocalization(theScan, psmCrossBeta, psmCrossAlpha.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, ProductTypes, commonParameters.ProductMassTolerance, Charge_2_3, Charge_2_3_PrimeFragment, xlPosBeta);
if (psmCrossAlpha.XLBestScore < psmCrossBeta.XLBestScore)
{
var swap = psmCrossAlpha;
psmCrossAlpha = psmCrossBeta;
psmCrossBeta = swap;
}
psmCrossAlpha.XlRank = new int[] { ind, inx };
psmCrossAlpha.XLTotalScore = psmCrossAlpha.XLBestScore + psmCrossBeta.XLBestScore;
psmCrossAlpha.XLQvalueTotalScore = Math.Sqrt(psmCrossAlpha.XLBestScore) * psmCrossBeta.XLBestScore;
psmCrossAlpha.BetaPsmCross = psmCrossBeta;
if (crosslinker.Cleavable)
{
psmCrossAlpha.ParentIonMaxIntensityRanks.AddRange(psmCrossBeta.ParentIonMaxIntensityRanks);
psmCrossAlpha.ParentIonExistNum += psmCrossBeta.ParentIonExistNum;
}
psmCrossAlpha.CrossType = PsmCrossType.Cross;
psmCross = psmCrossAlpha;
}
return(psmCross);
}
//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;
}
//Targetting function: to find two peptides that in the Top matched peptides
private PsmCross FindCrosslinkedPeptide(Ms2ScanWithSpecificMass theScan, List <BestPeptideScoreNotch> theScanBestPeptide, int i)
{
List <PsmCross> bestPsmCrossList = new List <PsmCross>();
PsmCross bestPsmCross = null;
string crosslinkerModSitesAll = new string((Crosslinker.CrosslinkerModSites + Crosslinker.CrosslinkerModSites2).ToCharArray().Distinct().ToArray());
for (int ind = 0; ind < theScanBestPeptide.Count; ind++)
{
//Single Peptide
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods) >= 0)
{
var productMasses = theScanBestPeptide[ind].BestPeptide.ProductMassesMightHaveDuplicatesAndNaNs(ProductTypes);
Array.Sort(productMasses);
double score = CalculatePeptideScoreOld(theScan.TheScan, commonParameters.ProductMassTolerance, productMasses, theScan.PrecursorMass, DissociationTypes, AddComplementaryIons, 0);
var psmCrossSingle = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, score, i, theScan, commonParameters.DigestionParams);
psmCrossSingle.XLTotalScore = psmCrossSingle.Score;
psmCrossSingle.CrossType = PsmCrossType.Singe;
bestPsmCrossList.Add(psmCrossSingle);
}
//Deadend Peptide
else if (QuenchTris && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + Crosslinker.DeadendMassTris) >= 0)
{
var psmCrossEnd = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan, commonParameters.DigestionParams);
var xlPos = PsmCross.XlPosCal(psmCrossEnd.compactPeptide, crosslinkerModSitesAll);
if (xlPos.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossEnd, Crosslinker.DeadendMassTris, Crosslinker, ProductTypes, commonParameters.ProductMassTolerance, false, false, xlPos);
psmCrossEnd.XLTotalScore = psmCrossEnd.XLBestScore;
psmCrossEnd.CrossType = PsmCrossType.DeadEndTris;
bestPsmCrossList.Add(psmCrossEnd);
}
}
else if (QuenchH2O && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + Crosslinker.DeadendMassH2O) >= 0)
{
var psmCrossEnd = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan, commonParameters.DigestionParams);
var xlPos = PsmCross.XlPosCal(psmCrossEnd.compactPeptide, crosslinkerModSitesAll);
if (xlPos.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossEnd, Crosslinker.DeadendMassH2O, Crosslinker, ProductTypes, commonParameters.ProductMassTolerance, false, false, xlPos);
psmCrossEnd.XLTotalScore = psmCrossEnd.XLBestScore;
psmCrossEnd.CrossType = PsmCrossType.DeadEndH2O;
bestPsmCrossList.Add(psmCrossEnd);
}
}
else if (QuenchNH2 && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + Crosslinker.DeadendMassNH2) >= 0)
{
var psmCrossEnd = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan, commonParameters.DigestionParams);
var xlPos = PsmCross.XlPosCal(psmCrossEnd.compactPeptide, crosslinkerModSitesAll);
if (xlPos.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossEnd, Crosslinker.DeadendMassNH2, Crosslinker, ProductTypes, commonParameters.ProductMassTolerance, false, false, xlPos);
psmCrossEnd.XLTotalScore = psmCrossEnd.XLBestScore;
psmCrossEnd.CrossType = PsmCrossType.DeadEndNH2;
bestPsmCrossList.Add(psmCrossEnd);
}
}
//loop peptide
else if (Crosslinker.LoopMass != 0 && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + Crosslinker.LoopMass) >= 0)
{
var psmCrossLoop = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan, commonParameters.DigestionParams);
var xlPos = PsmCross.XlPosCal(psmCrossLoop.compactPeptide, Crosslinker.CrosslinkerModSites);
if (xlPos.Count() >= 2)
{
PsmCross.XlLocalizationForLoopCrosslink(theScan, psmCrossLoop, Crosslinker.LoopMass, Crosslinker, ProductTypes, commonParameters.ProductMassTolerance, xlPos);
psmCrossLoop.XLTotalScore = psmCrossLoop.XLBestScore;
psmCrossLoop.CrossType = PsmCrossType.Loop;
bestPsmCrossList.Add(psmCrossLoop);
}
}
//Cross-linked peptide
else if (theScan.PrecursorMass - theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods >= 200)
{
var x = theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods;
for (int inx = ind; inx < theScanBestPeptide.Count; inx++)
{
var y = theScanBestPeptide[inx].BestPeptide.MonoisotopicMassIncludingFixedMods;
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, x + y + Crosslinker.TotalMass) >= 0)
{
var psmCrossAlpha = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan, commonParameters.DigestionParams);
var psmCrossBeta = new PsmCross(theScanBestPeptide[inx].BestPeptide, theScanBestPeptide[inx].BestNotch, theScanBestPeptide[inx].BestScore, i, theScan, commonParameters.DigestionParams);
PsmCross psmCross = null;
if (Crosslinker.CrosslinkerModSites == Crosslinker.CrosslinkerModSites2)
{
psmCross = XlSitesSame(theScan, psmCrossAlpha, psmCrossBeta, Crosslinker, ind, inx);
}
else
{
psmCross = XlSitesTwoDiff(theScan, psmCrossAlpha, psmCrossBeta, Crosslinker, ind, inx);
}
if (psmCross != null)
{
bestPsmCrossList.Add(psmCross);
}
}
}
}
}
if (bestPsmCrossList.Count != 0)
{
bestPsmCross = bestPsmCrossList.OrderByDescending(p => p.XLTotalScore).First();
if (bestPsmCrossList.Count > 1)
{
bestPsmCross.DScore = Math.Abs(bestPsmCrossList.First().XLTotalScore - bestPsmCrossList[1].XLTotalScore);
}
}
return(bestPsmCross);
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static List <ProductMassesMightHave> XlCalculateTotalProductMassesForLoopCrosslink(PsmCross psmCross, double modMass, CrosslinkerTypeClass crosslinker, List <ProductType> lp, List <int> linkPos)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
ProductMassesMightHave pmmhTop = new ProductMassesMightHave();
List <ProductMassesMightHave> pmmhList = new List <ProductMassesMightHave>();
if (linkPos.Count() >= 2)
{
for (int ipos = 0; ipos < linkPos.Count() - 1; ipos++)
{
for (int jpos = ipos + 1; jpos < linkPos.Count(); jpos++)
{
var pmmhCurr = new ProductMassesMightHave();
pmmhCurr.XlPos = linkPos[ipos];
pmmhCurr.XlPos2 = linkPos[jpos];
List <double> x = new List <double>();
List <string> y = new List <string>();
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm < linkPos[ipos] + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
}
if ((cr == 'y' || cr == 'z') && nm < length - linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
}
if (cr == 'b' && nm >= linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1b" + nm.ToString());
}
if (cr == 'c' && nm >= linkPos[jpos] + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1c" + nm.ToString());
}
if (cr == 'y' && (nm >= length - linkPos[ipos] + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1y" + nm.ToString());
}
if (cr == 'z' && (nm >= length - linkPos[ipos] + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1z" + nm.ToString());
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
pmmhList.Add(pmmhCurr);
}
}
}
return(pmmhList);
}
//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;
}
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static List <ProductMassesMightHave> XlCalculateTotalProductMasses(PsmCross psmCross, double modMass,
CrosslinkerTypeClass crosslinker, List <ProductType> lp, bool Charge_2_3, bool Charge_2_3_PrimeFragment, List <int> linkPos)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
ProductMassesMightHave pmmhTop = new ProductMassesMightHave();
List <ProductMassesMightHave> pmmhList = new List <ProductMassesMightHave>();
foreach (var ipos in linkPos)
{
var pmmhCurr = new ProductMassesMightHave();
pmmhCurr.XlPos = ipos;
List <double> x = new List <double>();
List <string> y = new List <string>();
if (crosslinker.Cleavable)
{
x.Add((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassShort);
y.Add("PepS");
x.Add(((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassShort) / 2);
y.Add("PepS2");
x.Add((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassLong);
y.Add("PepL");
x.Add(((double)psmCross.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.CleaveMassLong) / 2);
y.Add("PepL2");
}
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm < ipos + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'b')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2b" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3b" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'c')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2c" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3c" + nm.ToString());
}
}
if ((cr == 'y' || cr == 'z') && nm < length - ipos + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'y')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2y" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3y" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'z')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2z" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3z" + nm.ToString());
}
}
if (cr == 'b' && nm >= ipos + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1b" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2b" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3b" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sb" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lb" + nm.ToString());
}
}
if (cr == 'c' && nm >= ipos + 1)
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1c" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2c" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3c" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sc" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lc" + nm.ToString());
}
}
if (cr == 'y' && (nm >= length - ipos + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1y" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2y" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3y" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sy" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("ly" + nm.ToString());
}
}
if (cr == 'z' && (nm >= length - ipos + 1))
{
x.Add(pmmh.ProductMz[i] + modMass);
y.Add("t1z" + nm.ToString());
if (Charge_2_3)
{
x.Add((pmmh.ProductMz[i] + modMass) / 2);
y.Add("t2z" + nm.ToString());
x.Add((pmmh.ProductMz[i] + modMass) / 3);
y.Add("t3z" + nm.ToString());
}
if (crosslinker.Cleavable)
{
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassShort);
y.Add("sz" + nm.ToString());
x.Add(pmmh.ProductMz[i] + crosslinker.CleaveMassLong);
y.Add("lz" + nm.ToString());
}
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
pmmhList.Add(pmmhCurr);
}
return(pmmhList);
}
//Calculate All possible Products Masses based on ModMass and linkPos
public static ProductMassesMightHave XlCalculateTotalProductMassesForSingle(PsmCross psmCross, List <ProductType> lp, bool Charge_2_3_PrimeFragment)
{
int length = psmCross.compactPeptide.NTerminalMasses.Length;
var pmmh = psmCross.ProductMassesMightHaveDuplicatesAndNaNs(lp);
var pmmhCurr = new ProductMassesMightHave();
List <double> x = new List <double>();
List <string> y = new List <string>();
for (int i = 0; i < pmmh.ProductMz.Length; i++)
{
var cr = pmmh.ProductName[i][0];
//get the position of amino acid
var nm = Int32.Parse(System.Text.RegularExpressions.Regex.Match(pmmh.ProductName[i], @"\d+").Value);
if ((cr == 'b' || cr == 'c') && nm <= length + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'b')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2b" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3b" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'c')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2c" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3c" + nm.ToString());
}
}
if ((cr == 'y' || cr == 'z') && nm <= length + 1)
{
x.Add(pmmh.ProductMz[i]);
y.Add(pmmh.ProductName[i]);
if (Charge_2_3_PrimeFragment && cr == 'y')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2y" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3y" + nm.ToString());
}
if (Charge_2_3_PrimeFragment && cr == 'z')
{
x.Add(pmmh.ProductMz[i] / 2);
y.Add("t2z" + nm.ToString());
x.Add(pmmh.ProductMz[i] / 3);
y.Add("t3z" + nm.ToString());
}
}
}
pmmhCurr.ProductMz = x.ToArray();
pmmhCurr.ProductName = y.ToArray();
Array.Sort(pmmhCurr.ProductMz, pmmhCurr.ProductName);
return(pmmhCurr);
}
//Targetting function: to find two peptides that in the Top matched peptides
private PsmCross FindCrosslinkedPeptide(Ms2ScanWithSpecificMass theScan, List <BestPeptideScoreNotch> theScanBestPeptide, int i)
{
List <PsmCross> bestPsmCrossList = new List <PsmCross>();
PsmCross bestPsmCross = null;
for (int ind = 0; ind < theScanBestPeptide.Count; ind++)
{
//Single Peptide
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods) >= 0)
{
var productMasses = theScanBestPeptide[ind].BestPeptide.ProductMassesMightHaveDuplicatesAndNaNs(lp);
Array.Sort(productMasses);
double score = CalculatePeptideScore(theScan.TheScan, CommonParameters.ProductMassTolerance, productMasses, theScan.PrecursorMass, dissociationTypes, addCompIons, 0);
var psmCrossSingle = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, score, i, theScan);
psmCrossSingle.XLTotalScore = psmCrossSingle.Score;
psmCrossSingle.CrossType = PsmCrossType.Singe;
bestPsmCrossList.Add(psmCrossSingle);
}
//Deadend Peptide
else if (quench_Tris && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.DeadendMassTris) >= 0)
{
var psmCrossEnd = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan);
var xlPos = PsmCross.XlPosCal(psmCrossEnd.compactPeptide, crosslinker);
if (xlPos.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossEnd, crosslinker.DeadendMassTris, crosslinker, lp, CommonParameters.ProductMassTolerance, false, false, xlPos);
psmCrossEnd.XLTotalScore = psmCrossEnd.XLBestScore;
psmCrossEnd.CrossType = PsmCrossType.DeadEndTris;
bestPsmCrossList.Add(psmCrossEnd);
}
}
else if (quench_H2O && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.DeadendMassH2O) >= 0)
{
var psmCrossEnd = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan);
var xlPos = PsmCross.XlPosCal(psmCrossEnd.compactPeptide, crosslinker);
if (xlPos.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossEnd, crosslinker.DeadendMassH2O, crosslinker, lp, CommonParameters.ProductMassTolerance, false, false, xlPos);
psmCrossEnd.XLTotalScore = psmCrossEnd.XLBestScore;
psmCrossEnd.CrossType = PsmCrossType.DeadEndH2O;
bestPsmCrossList.Add(psmCrossEnd);
}
}
else if (quench_NH2 && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.DeadendMassNH2) >= 0)
{
var psmCrossEnd = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan);
var xlPos = PsmCross.XlPosCal(psmCrossEnd.compactPeptide, crosslinker);
if (xlPos.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossEnd, crosslinker.DeadendMassNH2, crosslinker, lp, CommonParameters.ProductMassTolerance, false, false, xlPos);
psmCrossEnd.XLTotalScore = psmCrossEnd.XLBestScore;
psmCrossEnd.CrossType = PsmCrossType.DeadEndNH2;
bestPsmCrossList.Add(psmCrossEnd);
}
}
//loop peptide
else if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.LoopMass) >= 0)
{
var psmCrossLoop = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan);
var xlPos = PsmCross.XlPosCal(psmCrossLoop.compactPeptide, crosslinker);
if (xlPos.Count() >= 2)
{
PsmCross.XlLocalizationForLoopCrosslink(theScan, psmCrossLoop, crosslinker.LoopMass, crosslinker, lp, CommonParameters.ProductMassTolerance, xlPos);
psmCrossLoop.XLTotalScore = psmCrossLoop.XLBestScore;
psmCrossLoop.CrossType = PsmCrossType.Loop;
bestPsmCrossList.Add(psmCrossLoop);
}
}
//Cross-linked peptide
else if (theScan.PrecursorMass - theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods >= 200)
{
var x = theScanBestPeptide[ind].BestPeptide.MonoisotopicMassIncludingFixedMods;
for (int inx = ind; inx < theScanBestPeptide.Count; inx++)
{
var y = theScanBestPeptide[inx].BestPeptide.MonoisotopicMassIncludingFixedMods;
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, x + y + crosslinker.TotalMass) >= 0 && PsmCross.XlPosCal(theScanBestPeptide[ind].BestPeptide, crosslinker).Count != 0 && PsmCross.XlPosCal(theScanBestPeptide[inx].BestPeptide, crosslinker).Count != 0)
{
var psmCrossAlpha = new PsmCross(theScanBestPeptide[ind].BestPeptide, theScanBestPeptide[ind].BestNotch, theScanBestPeptide[ind].BestScore, i, theScan);
var psmCrossBeta = new PsmCross(theScanBestPeptide[inx].BestPeptide, theScanBestPeptide[inx].BestNotch, theScanBestPeptide[inx].BestScore, i, theScan);
var xlPosAlpha = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker);
var xlPosBeta = PsmCross.XlPosCal(psmCrossBeta.compactPeptide, crosslinker);
if (xlPosAlpha.Count() >= 1 && xlPosBeta.Count() >= 1)
{
PsmCross.XlLocalization(theScan, psmCrossAlpha, psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, lp, CommonParameters.ProductMassTolerance, charge_2_3, charge_2_3_PrimeFragment, xlPosAlpha);
PsmCross.XlLocalization(theScan, psmCrossBeta, psmCrossAlpha.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, lp, CommonParameters.ProductMassTolerance, charge_2_3, charge_2_3_PrimeFragment, xlPosBeta);
if (psmCrossAlpha.XLBestScore < psmCrossBeta.XLBestScore)
{
var swap = psmCrossAlpha;
psmCrossAlpha = psmCrossBeta;
psmCrossBeta = swap;
}
psmCrossAlpha.XlRank = new int[] { ind, inx };
psmCrossAlpha.XLTotalScore = psmCrossAlpha.XLBestScore + psmCrossBeta.XLBestScore;
psmCrossAlpha.XLQvalueTotalScore = Math.Sqrt(psmCrossAlpha.XLBestScore) * psmCrossBeta.XLBestScore;
psmCrossAlpha.BetaPsmCross = psmCrossBeta;
if (crosslinker.Cleavable)
{
psmCrossAlpha.ParentIonMaxIntensityRanks.AddRange(psmCrossBeta.ParentIonMaxIntensityRanks);
psmCrossAlpha.ParentIonExistNum += psmCrossBeta.ParentIonExistNum;
}
psmCrossAlpha.CrossType = PsmCrossType.Cross;
bestPsmCrossList.Add(psmCrossAlpha);
}
}
}
}
}
if (bestPsmCrossList.Count != 0)
{
bestPsmCross = bestPsmCrossList.OrderByDescending(p => p.XLTotalScore).First();
if (bestPsmCrossList.Count > 1)
{
bestPsmCross.DScore = Math.Abs(bestPsmCrossList.First().XLTotalScore - bestPsmCrossList[1].XLTotalScore);
}
}
return(bestPsmCross);
}
