/// <summary>
///
/// </summary>
private CrosslinkSpectralMatch FindCrosslinkedPeptide(Ms2ScanWithSpecificMass theScan, List <BestPeptideScoreNotch> theScanBestPeptide, int scanIndex)
{
List <CrosslinkSpectralMatch> possibleMatches = new List <CrosslinkSpectralMatch>();
for (int alphaIndex = 0; alphaIndex < theScanBestPeptide.Count; alphaIndex++)
{
PeptideWithSetModifications bestPeptide = theScanBestPeptide[alphaIndex].BestPeptide;
//Single Peptide
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass) >= 0)
{
List <Product> products = bestPeptide.Fragment(CommonParameters.DissociationType, FragmentationTerminus.Both).ToList();
var matchedFragmentIons = MatchFragmentIons(theScan, products, CommonParameters);
double score = CalculatePeptideScore(theScan.TheScan, matchedFragmentIons);
var psmCrossSingle = new CrosslinkSpectralMatch(bestPeptide, theScanBestPeptide[alphaIndex].BestNotch, score, scanIndex, theScan, CommonParameters.DigestionParams, matchedFragmentIons)
{
CrossType = PsmCrossType.Single,
XlRank = new List <int> {
alphaIndex
}
};
possibleMatches.Add(psmCrossSingle);
}
// Deadend Peptide
else if (QuenchTris && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.DeadendMassTris) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Any())
{
// tris deadend
possibleMatches.Add(LocalizeDeadEndSite(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, TrisDeadEnd, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
else if (QuenchH2O && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.DeadendMassH2O) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Any())
{
// H2O deadend
possibleMatches.Add(LocalizeDeadEndSite(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, H2ODeadEnd, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
else if (QuenchNH2 && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.DeadendMassNH2) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Any())
{
// NH2 deadend
possibleMatches.Add(LocalizeDeadEndSite(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, NH2DeadEnd, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
// loop peptide
else if (Crosslinker.LoopMass != 0 && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.LoopMass) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Count >= 2)
{
possibleMatches.Add(LocalizeLoopSites(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, Loop, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
// Cross-linked peptide
else if (theScan.PrecursorMass - bestPeptide.MonoisotopicMass >= (CommonParameters.DigestionParams.MinPeptideLength * 50))
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (!possibleCrosslinkLocations.Any())
{
continue;
}
PeptideWithSetModifications alphaPeptide = bestPeptide;
for (int betaIndex = 0; betaIndex < theScanBestPeptide.Count; betaIndex++)
{
PeptideWithSetModifications betaPeptide = theScanBestPeptide[betaIndex].BestPeptide;
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, alphaPeptide.MonoisotopicMass + betaPeptide.MonoisotopicMass + Crosslinker.TotalMass) >= 0)
{
List <int> possibleBetaCrosslinkSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, betaPeptide);
if (!possibleBetaCrosslinkSites.Any())
{
continue;
}
CrosslinkSpectralMatch csm = LocalizeCrosslinkSites(theScan, theScanBestPeptide[alphaIndex], theScanBestPeptide[betaIndex], Crosslinker, alphaIndex, betaIndex);
possibleMatches.Add(csm);
}
}
}
}
// get the best match for this spectrum
// bestPsmCross will be null if there are no valid hits
possibleMatches.RemoveAll(v => v == null);
possibleMatches = possibleMatches.OrderByDescending(p => p.XLTotalScore).ToList();
var bestPsmCross = possibleMatches.FirstOrDefault();
// resolve ambiguities
if (bestPsmCross != null)
{
bestPsmCross.ResolveAllAmbiguities();
if (bestPsmCross.BetaPeptide != null)
{
bestPsmCross.BetaPeptide.ResolveAllAmbiguities();
}
}
// calculate delta score
if (possibleMatches.Count > 1)
{
bestPsmCross.DeltaScore = possibleMatches[0].XLTotalScore - possibleMatches[1].XLTotalScore;
}
return(bestPsmCross);
}
/// <summary>
/// Localizes the crosslink position on the alpha and beta peptides
/// </summary>
private CrosslinkSpectralMatch LocalizeCrosslinkSites(Ms2ScanWithSpecificMass theScan, BestPeptideScoreNotch alphaPeptide, BestPeptideScoreNotch betaPeptide, Crosslinker crosslinker, int ind, int inx)
{
CrosslinkSpectralMatch localizedCrosslinkedSpectralMatch = null;
List <Tuple <List <int>, List <int> > > pairs = new List <Tuple <List <int>, List <int> > >();
if (crosslinker.CrosslinkerModSites.Equals(crosslinker.CrosslinkerModSites2))
{
List <int> possibleAlphaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), alphaPeptide.BestPeptide);
List <int> possibleBetaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), betaPeptide.BestPeptide);
pairs.Add(new Tuple <List <int>, List <int> >(possibleAlphaXlSites, possibleBetaXlSites));
}
else
{
List <int> possibleAlphaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), alphaPeptide.BestPeptide);
List <int> possibleBetaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites2.ToCharArray(), betaPeptide.BestPeptide);
pairs.Add(new Tuple <List <int>, List <int> >(possibleAlphaXlSites, possibleBetaXlSites));
possibleAlphaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites2.ToCharArray(), alphaPeptide.BestPeptide);
possibleBetaXlSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), betaPeptide.BestPeptide);
pairs.Add(new Tuple <List <int>, List <int> >(possibleAlphaXlSites, possibleBetaXlSites));
}
foreach (var pair in pairs)
{
List <int> possibleAlphaXlSites = pair.Item1;
List <int> possibleBetaXlSites = pair.Item2;
if (possibleAlphaXlSites.Any() && possibleBetaXlSites.Any())
{
int bestAlphaSite = 0;
int bestBetaSite = 0;
List <MatchedFragmentIon> bestMatchedAlphaIons = new List <MatchedFragmentIon>();
List <MatchedFragmentIon> bestMatchedBetaIons = new List <MatchedFragmentIon>();
Dictionary <int, List <MatchedFragmentIon> > bestMatchedChildAlphaIons = new Dictionary <int, List <MatchedFragmentIon> >();
Dictionary <int, List <MatchedFragmentIon> > bestMatchedChildBetaIons = new Dictionary <int, List <MatchedFragmentIon> >();
double bestAlphaLocalizedScore = 0;
double bestBetaLocalizedScore = 0;
var fragmentsForEachAlphaLocalizedPossibility = CrosslinkedPeptide.XlGetTheoreticalFragments(CommonParameters.DissociationType,
Crosslinker, possibleAlphaXlSites, betaPeptide.BestPeptide.MonoisotopicMass, alphaPeptide.BestPeptide).ToList();
foreach (int possibleSite in possibleAlphaXlSites)
{
foreach (var setOfFragments in fragmentsForEachAlphaLocalizedPossibility.Where(v => v.Item1 == possibleSite))
{
var matchedChildAlphaIons = new Dictionary <int, List <MatchedFragmentIon> >();
var matchedIons = MatchFragmentIons(theScan, setOfFragments.Item2, CommonParameters);
double score = CalculatePeptideScore(theScan.TheScan, matchedIons);
// search child scans (MS2+MS3)
foreach (Ms2ScanWithSpecificMass childScan in theScan.ChildScans)
{
var matchedChildIons = ScoreChildScan(theScan, childScan, possibleSite, alphaPeptide, betaPeptide);
if (matchedChildIons == null)
{
continue;
}
matchedChildAlphaIons.Add(childScan.OneBasedScanNumber, matchedChildIons);
//double childScore = CalculatePeptideScore(childScan.TheScan, matchedChildIons);
//score += childScore;
}
if (score > bestAlphaLocalizedScore)
{
bestAlphaLocalizedScore = score;
bestAlphaSite = possibleSite;
bestMatchedAlphaIons = matchedIons;
bestMatchedChildAlphaIons = matchedChildAlphaIons;
}
}
}
var fragmentsForEachBetaLocalizedPossibility = CrosslinkedPeptide.XlGetTheoreticalFragments(CommonParameters.DissociationType,
Crosslinker, possibleBetaXlSites, alphaPeptide.BestPeptide.MonoisotopicMass, betaPeptide.BestPeptide).ToList();
var alphaMz = new HashSet <double>(bestMatchedAlphaIons.Select(p => p.Mz));
foreach (int possibleSite in possibleBetaXlSites)
{
foreach (var setOfFragments in fragmentsForEachBetaLocalizedPossibility.Where(v => v.Item1 == possibleSite))
{
var matchedIons = MatchFragmentIons(theScan, setOfFragments.Item2, CommonParameters);
var matchedChildBetaIons = new Dictionary <int, List <MatchedFragmentIon> >();
// remove any matched beta ions that also matched to the alpha peptide
matchedIons.RemoveAll(p => alphaMz.Contains(p.Mz));
double score = CalculatePeptideScore(theScan.TheScan, matchedIons);
// search child scans (MS2+MS3)
foreach (Ms2ScanWithSpecificMass childScan in theScan.ChildScans)
{
var matchedChildIons = ScoreChildScan(theScan, childScan, possibleSite, betaPeptide, alphaPeptide);
if (matchedChildIons == null)
{
continue;
}
matchedChildBetaIons.Add(childScan.OneBasedScanNumber, matchedChildIons);
//double childScore = CalculatePeptideScore(childScan.TheScan, matchedChildIons);
//score += childScore;
}
if (score > bestBetaLocalizedScore)
{
bestBetaLocalizedScore = score;
bestBetaSite = possibleSite;
bestMatchedBetaIons = matchedIons;
bestMatchedChildBetaIons = matchedChildBetaIons;
}
}
}
if (bestAlphaLocalizedScore < CommonParameters.ScoreCutoff ||
bestBetaLocalizedScore < CommonParameters.ScoreCutoff)
{
return(null);
}
var localizedAlpha = new CrosslinkSpectralMatch(alphaPeptide.BestPeptide, alphaPeptide.BestNotch, bestAlphaLocalizedScore, 0, theScan, alphaPeptide.BestPeptide.DigestionParams, bestMatchedAlphaIons);
var localizedBeta = new CrosslinkSpectralMatch(betaPeptide.BestPeptide, betaPeptide.BestNotch, bestBetaLocalizedScore, 0, theScan, betaPeptide.BestPeptide.DigestionParams, bestMatchedBetaIons);
localizedAlpha.XlRank = new List <int> {
ind, inx
};
localizedAlpha.XLTotalScore = localizedAlpha.Score + localizedBeta.Score;
localizedAlpha.BetaPeptide = localizedBeta;
localizedAlpha.ChildMatchedFragmentIons = bestMatchedChildAlphaIons;
localizedBeta.ChildMatchedFragmentIons = bestMatchedChildBetaIons;
if (crosslinker.Cleavable)
{
//TODO: re-enable intensity ranks
//psmCrossAlpha.ParentIonMaxIntensityRanks = psmCrossAlpha.MatchedFragmentIons.Where(p => p.NeutralTheoreticalProduct.ProductType == ProductType.M).Select(p => p.IntensityRank).ToList();
//localizedAlpha.ParentIonMaxIntensityRanks = new List<int>();
//localizedAlpha.ParentIonExistNum = psmCrossAlpha.ParentIonMaxIntensityRanks.Count;
}
localizedAlpha.CrossType = PsmCrossType.Cross;
localizedCrosslinkedSpectralMatch = localizedAlpha;
localizedCrosslinkedSpectralMatch.LinkPositions = new List <int> {
bestAlphaSite
};
localizedCrosslinkedSpectralMatch.BetaPeptide.LinkPositions = new List <int> {
bestBetaSite
};
}
}
return(localizedCrosslinkedSpectralMatch);
}
/// <summary>
///
/// </summary>
private List <CrosslinkSpectralMatch> FindCrosslinkedPeptide(Ms2ScanWithSpecificMass theScan, List <BestPeptideScoreNotch> theScanBestPeptide, int scanIndex)
{
List <CrosslinkSpectralMatch> possibleMatches = new List <CrosslinkSpectralMatch>();
for (int alphaIndex = 0; alphaIndex < theScanBestPeptide.Count; alphaIndex++)
{
PeptideWithSetModifications bestPeptide = theScanBestPeptide[alphaIndex].BestPeptide;
//Single Peptide
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass) >= 0)
{
List <Product> products = bestPeptide.Fragment(CommonParameters.DissociationType, FragmentationTerminus.Both).ToList();
var matchedFragmentIons = MatchFragmentIons(theScan, products, CommonParameters);
double score = CalculatePeptideScore(theScan.TheScan, matchedFragmentIons);
var psmCrossSingle = new CrosslinkSpectralMatch(bestPeptide, theScanBestPeptide[alphaIndex].BestNotch, score, scanIndex, theScan, CommonParameters.DigestionParams, matchedFragmentIons)
{
CrossType = PsmCrossType.Single,
XlRank = new List <int> {
alphaIndex
}
};
possibleMatches.Add(psmCrossSingle);
}
// Deadend Peptide
else if (QuenchTris && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.DeadendMassTris) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Any())
{
// tris deadend
possibleMatches.Add(LocalizeDeadEndSite(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, TrisDeadEnd, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
else if (QuenchH2O && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.DeadendMassH2O) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Any())
{
// H2O deadend
possibleMatches.Add(LocalizeDeadEndSite(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, H2ODeadEnd, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
else if (QuenchNH2 && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.DeadendMassNH2) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Any())
{
// NH2 deadend
possibleMatches.Add(LocalizeDeadEndSite(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, NH2DeadEnd, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
// loop peptide
else if (Crosslinker.LoopMass != 0 && XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, bestPeptide.MonoisotopicMass + Crosslinker.LoopMass) >= 0)
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (possibleCrosslinkLocations.Count >= 2)
{
possibleMatches.Add(LocalizeLoopSites(bestPeptide, theScan, CommonParameters, possibleCrosslinkLocations, Loop, theScanBestPeptide[alphaIndex].BestNotch, scanIndex, alphaIndex));
}
}
// Cross-linked peptide
else if (theScan.PrecursorMass - bestPeptide.MonoisotopicMass >= (CommonParameters.DigestionParams.MinPeptideLength * 50))
{
List <int> possibleCrosslinkLocations = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, bestPeptide);
if (!possibleCrosslinkLocations.Any())
{
continue;
}
PeptideWithSetModifications alphaPeptide = bestPeptide;
for (int betaIndex = 0; betaIndex < theScanBestPeptide.Count; betaIndex++)
{
PeptideWithSetModifications betaPeptide = theScanBestPeptide[betaIndex].BestPeptide;
if (XLPrecusorSearchMode.Accepts(theScan.PrecursorMass, alphaPeptide.MonoisotopicMass + betaPeptide.MonoisotopicMass + Crosslinker.TotalMass) >= 0)
{
List <int> possibleBetaCrosslinkSites = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(AllCrosslinkerSites, betaPeptide);
if (!possibleBetaCrosslinkSites.Any())
{
continue;
}
CrosslinkSpectralMatch csm = LocalizeCrosslinkSites(theScan, theScanBestPeptide[alphaIndex], theScanBestPeptide[betaIndex], Crosslinker, alphaIndex, betaIndex);
possibleMatches.Add(csm);
}
}
}
}
return(possibleMatches);
}
