//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);
}
//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);
}
//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);
}