private List <MatchedFragmentIon> ScoreChildScan(Ms2ScanWithSpecificMass parentScan, Ms2ScanWithSpecificMass childScan, int possibleSite, BestPeptideScoreNotch mainPeptide, BestPeptideScoreNotch otherPeptide)
{
bool shortMassAlphaMs3 = XLPrecusorSearchMode.Accepts(childScan.PrecursorMass, mainPeptide.BestPeptide.MonoisotopicMass + Crosslinker.CleaveMassShort) >= 0;
bool longMassAlphaMs3 = XLPrecusorSearchMode.Accepts(childScan.PrecursorMass, mainPeptide.BestPeptide.MonoisotopicMass + Crosslinker.CleaveMassLong) >= 0;
List <Product> childProducts;
if (Crosslinker.Cleavable && (shortMassAlphaMs3 || longMassAlphaMs3))
{
double massToLocalize = shortMassAlphaMs3 ? Crosslinker.CleaveMassShort : Crosslinker.CleaveMassLong;
if (mainPeptide.BestPeptide.AllModsOneIsNterminus.TryGetValue(possibleSite + 1, out var existingMod))
{
massToLocalize += existingMod.MonoisotopicMass.Value;
}
Dictionary <int, Modification> mod = new Dictionary <int, Modification> {
{ possibleSite + 1, new Modification(_monoisotopicMass: massToLocalize) }
};
foreach (var otherExistingMod in mainPeptide.BestPeptide.AllModsOneIsNterminus.Where(p => p.Key != possibleSite + 1))
{
mod.Add(otherExistingMod.Key, otherExistingMod.Value);
}
var peptideWithMod = new PeptideWithSetModifications(mainPeptide.BestPeptide.Protein, mainPeptide.BestPeptide.DigestionParams,
mainPeptide.BestPeptide.OneBasedStartResidueInProtein, mainPeptide.BestPeptide.OneBasedEndResidueInProtein,
mainPeptide.BestPeptide.CleavageSpecificityForFdrCategory, mainPeptide.BestPeptide.PeptideDescription,
mainPeptide.BestPeptide.MissedCleavages, mod, mainPeptide.BestPeptide.NumFixedMods);
childProducts = peptideWithMod.Fragment(CommonParameters.ChildScanDissociationType, FragmentationTerminus.Both).ToList();
}
else if (Math.Abs(childScan.PrecursorMass - parentScan.PrecursorMass) < 0.01 && CommonParameters.DissociationType != CommonParameters.ChildScanDissociationType)
{
// same species got fragmented twice, the second time with a different dissociation type
childProducts = CrosslinkedPeptide.XlGetTheoreticalFragments(CommonParameters.ChildScanDissociationType,
Crosslinker, new List <int> {
possibleSite
}, otherPeptide.BestPeptide.MonoisotopicMass, mainPeptide.BestPeptide).First().Item2;
}
else
{
return(null);
}
var matchedChildIons = MatchFragmentIons(childScan, childProducts, CommonParameters);
return(matchedChildIons);
}
protected override MetaMorpheusEngineResults RunSpecific()
{
double progress = 0;
int oldPercentProgress = 0;
ReportProgress(new ProgressEventArgs(oldPercentProgress, "Performing crosslink search... " + CurrentPartition + "/" + commonParameters.TotalPartitions, nestedIds));
byte byteScoreCutoff = (byte)commonParameters.ScoreCutoff;
Parallel.ForEach(Partitioner.Create(0, ListOfSortedms2Scans.Length), new ParallelOptions {
MaxDegreeOfParallelism = commonParameters.MaxThreadsToUsePerFile
}, (range, loopState) =>
{
byte[] scoringTable = new byte[PeptideIndex.Count];
List <int> idsOfPeptidesPossiblyObserved = new List <int>();
for (int i = range.Item1; i < range.Item2; i++)
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
loopState.Stop();
return;
}
// empty the scoring table to score the new scan (conserves memory compared to allocating a new array)
Array.Clear(scoringTable, 0, scoringTable.Length);
idsOfPeptidesPossiblyObserved.Clear();
var scan = ListOfSortedms2Scans[i];
// get fragment bins for this scan
List <int> allBinsToSearch = GetBinsToSearch(scan);
List <BestPeptideScoreNotch> bestPeptideScoreNotchList = new List <BestPeptideScoreNotch>();
// get allowed theoretical masses from the known experimental mass
// note that this is the OPPOSITE of the classic search (which calculates experimental masses from theoretical values)
// this is just PRELIMINARY precursor-mass filtering
// additional checks are made later to ensure that the theoretical precursor mass is acceptable
var notches = MassDiffAcceptor.GetAllowedPrecursorMassIntervals(scan.PrecursorMass);
double lowestMassPeptideToLookFor = Double.NegativeInfinity;
double highestMassPeptideToLookFor = Double.PositiveInfinity;
double largestMassDiff = notches.Max(p => p.AllowedInterval.Maximum);
double smallestMassDiff = notches.Min(p => p.AllowedInterval.Minimum);
if (!Double.IsInfinity(largestMassDiff))
{
double largestOppositeMassDiff = -1 * (notches.Max(p => p.AllowedInterval.Maximum) - scan.PrecursorMass);
lowestMassPeptideToLookFor = scan.PrecursorMass + largestOppositeMassDiff;
}
if (!Double.IsNegativeInfinity(smallestMassDiff))
{
double smallestOppositeMassDiff = -1 * (notches.Min(p => p.AllowedInterval.Minimum) - scan.PrecursorMass);
highestMassPeptideToLookFor = scan.PrecursorMass + smallestOppositeMassDiff;
}
// first-pass scoring
IndexedScoring(allBinsToSearch, scoringTable, byteScoreCutoff, idsOfPeptidesPossiblyObserved, scan.PrecursorMass, lowestMassPeptideToLookFor, highestMassPeptideToLookFor);
// done with indexed scoring; refine scores and create PSMs
if (idsOfPeptidesPossiblyObserved.Any())
{
List <int> idsRankedByScore = new List <int>();
foreach (var id in idsOfPeptidesPossiblyObserved)
{
idsRankedByScore.Add(id);
}
idsRankedByScore = idsRankedByScore.OrderByDescending(p => scoringTable[p]).ToList();
idsRankedByScore = idsRankedByScore.Take(CrosslinkSearchTopNum).ToList();
if (CrosslinkSearchTop)
{
idsOfPeptidesPossiblyObserved = idsRankedByScore;
}
foreach (var id in idsOfPeptidesPossiblyObserved)
{
var peptide = PeptideIndex[id];
double thePrecursorMass = scan.PrecursorMass;
int notch = MassDiffAcceptor.Accepts(scan.PrecursorMass, peptide.MonoisotopicMassIncludingFixedMods);
BestPeptideScoreNotch bestPeptideScoreNotch = new BestPeptideScoreNotch(peptide, scoringTable[id], notch);
bestPeptideScoreNotchList.Add(bestPeptideScoreNotch);
}
var possiblePsmCross = FindCrosslinkedPeptide(scan, bestPeptideScoreNotchList, i);
if (possiblePsmCross != null)
{
lock (GlobalPsmsCross)
GlobalPsmsCross.Add(possiblePsmCross);
}
}
// report search progress
progress++;
var percentProgress = (int)((progress / ListOfSortedms2Scans.Length) * 100);
if (percentProgress > oldPercentProgress)
{
oldPercentProgress = percentProgress;
ReportProgress(new ProgressEventArgs(percentProgress, "Performing crosslink search... " + CurrentPartition + "/" + commonParameters.TotalPartitions, nestedIds));
}
}
});
return(new MetaMorpheusEngineResults(this));
}
/// <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);
}