private void PopulateChoices()
{
TheList = new ObservableCollection <BoolStringClass>();
var knownProductTypes = Enum.GetValues(typeof(ProductType)).Cast <ProductType>().ToList();
knownProductTypes.Remove(ProductType.D);
knownProductTypes.Remove(ProductType.M);
knownProductTypes.Remove(ProductType.Y);
knownProductTypes.Remove(ProductType.Ycore);
knownProductTypes.Remove(ProductType.zPlusOne);
knownProductTypes.Remove(ProductType.Ycore);
knownProductTypes.Remove(ProductType.Y);
foreach (ProductType productType in knownProductTypes)
{
TheList.Add(new BoolStringClass {
IsSelected = false,
Type = productType,
ToolTip = DissociationTypeCollection.GetMassShiftFromProductType(productType).ToString("F4") + " Da; "
+ TerminusSpecificProductTypes.ProductTypeToFragmentationTerminus[productType] + " terminus"
});
}
ProductTypeList.ItemsSource = TheList;
}
/// <summary>
/// A product is the individual neutral fragment from an MS dissociation. A fragmentation product here contains one of the two termini (N- or C-).
/// The ProductType describes where along the backbone the fragmentaiton occurred (e.g. b-, y-, c-, zdot-). The neutral loss mass (if any) that
/// occurred from a mod on the fragment is listed as a mass. Finally the neutral mass of the whole fragment is provided.
/// </summary>
public Product(ProductType productType, NeutralTerminusFragment terminusFragment, double neutralLoss)
{
TerminusFragment = terminusFragment;
ProductType = productType;
this.NeutralLoss = neutralLoss;
NeutralMass = DissociationTypeCollection.ProductTypeSpecificFragmentNeutralMass(terminusFragment.NeutralMass, productType) - neutralLoss;
}
private static List <MatchedFragmentIon> ReadFragmentIonsFromString(string matchedMzString, string peptideBaseSequence)
{
var peaks = matchedMzString.Split(MzSplit, StringSplitOptions.RemoveEmptyEntries).Select(v => v.Trim())
.ToList();
peaks.RemoveAll(p => p.Contains("\""));
List <MatchedFragmentIon> matchedIons = new List <MatchedFragmentIon>();
foreach (var peak in peaks)
{
var split = peak.Split(new char[] { '+', ':' });
string ionTypeAndNumber = split[0];
Match result = IonParser.Match(ionTypeAndNumber);
ProductType productType = (ProductType)Enum.Parse(typeof(ProductType), result.Groups[1].Value);
int fragmentNumber = int.Parse(result.Groups[2].Value);
int z = int.Parse(split[1]);
double mz = double.Parse(split[2], CultureInfo.InvariantCulture);
double neutralLoss = 0;
// check for neutral loss
if (ionTypeAndNumber.Contains("-"))
{
string temp = ionTypeAndNumber.Replace("(", "");
temp = temp.Replace(")", "");
var split2 = temp.Split('-');
neutralLoss = double.Parse(split2[1], CultureInfo.InvariantCulture);
}
FragmentationTerminus terminus = FragmentationTerminus.None;
if (TerminusSpecificProductTypes.ProductTypeToFragmentationTerminus.ContainsKey(productType))
{
terminus = TerminusSpecificProductTypes.ProductTypeToFragmentationTerminus[productType];
}
int aminoAcidPosition = fragmentNumber;
if (terminus == FragmentationTerminus.C)
{
aminoAcidPosition = peptideBaseSequence.Length - fragmentNumber;
}
Product p = new Product(productType,
terminus,
mz.ToMass(z) - DissociationTypeCollection.GetMassShiftFromProductType(productType),
fragmentNumber,
aminoAcidPosition,
neutralLoss);
matchedIons.Add(new MatchedFragmentIon(ref p, mz, 1.0, z));
}
return(matchedIons);
}
protected override MetaMorpheusEngineResults RunSpecific()
{
bool semiSpecificSearch = CommonParameters.DigestionParams.SearchModeType == CleavageSpecificity.Semi;
double progress = 0;
int oldPercentProgress = 0;
ReportProgress(new ProgressEventArgs(oldPercentProgress, "Performing nonspecific search... " + CurrentPartition + "/" + CommonParameters.TotalPartitions, NestedIds));
byte byteScoreCutoff = (byte)CommonParameters.ScoreCutoff;
int maxThreadsPerFile = CommonParameters.MaxThreadsToUsePerFile;
int[] threads = Enumerable.Range(0, maxThreadsPerFile).ToArray();
Parallel.ForEach(threads, (i) =>
{
byte[] scoringTable = new byte[PeptideIndex.Count];
HashSet <int> idsOfPeptidesPossiblyObserved = new HashSet <int>();
for (; i < ListOfSortedMs2Scans.Length; i += maxThreadsPerFile)
{
// Stop loop if canceled
if (GlobalVariables.StopLoops)
{
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();
Ms2ScanWithSpecificMass scan = ListOfSortedMs2Scans[i];
//get bins to add points to
List <int> allBinsToSearch = GetBinsToSearch(scan, FragmentIndex, CommonParameters.DissociationType);
//the entire indexed scoring is done here
for (int j = 0; j < allBinsToSearch.Count; j++)
{
FragmentIndex[allBinsToSearch[j]].ForEach(id => scoringTable[id]++);
}
//populate ids of possibly observed with those containing allowed precursor masses
List <AllowedIntervalWithNotch> validIntervals = MassDiffAcceptor.GetAllowedPrecursorMassIntervalsFromObservedMass(scan.PrecursorMass).ToList(); //get all valid notches
foreach (AllowedIntervalWithNotch interval in validIntervals)
{
int obsPrecursorFloorMz = (int)Math.Floor(interval.AllowedInterval.Minimum * FragmentBinsPerDalton);
int obsPrecursorCeilingMz = (int)Math.Ceiling(interval.AllowedInterval.Maximum * FragmentBinsPerDalton);
foreach (ProductType pt in ProductTypesToSearch)
{
int dissociationBinShift = (int)Math.Round((WaterMonoisotopicMass - DissociationTypeCollection.GetMassShiftFromProductType(pt)) * FragmentBinsPerDalton);
int lowestBin = obsPrecursorFloorMz - dissociationBinShift;
int highestBin = obsPrecursorCeilingMz - dissociationBinShift;
for (int bin = lowestBin; bin <= highestBin; bin++)
{
if (bin < FragmentIndex.Length && FragmentIndex[bin] != null)
{
FragmentIndex[bin].ForEach(id => idsOfPeptidesPossiblyObserved.Add(id));
}
}
}
for (int bin = obsPrecursorFloorMz; bin <= obsPrecursorCeilingMz; bin++) //no bin shift, since they're precursor masses
{
if (bin < PrecursorIndex.Length && PrecursorIndex[bin] != null)
{
PrecursorIndex[bin].ForEach(id => idsOfPeptidesPossiblyObserved.Add(id));
}
}
}
// done with initial scoring; refine scores and create PSMs
if (idsOfPeptidesPossiblyObserved.Any())
{
int maxInitialScore = idsOfPeptidesPossiblyObserved.Max(id => scoringTable[id]) + 1;
while (maxInitialScore > CommonParameters.ScoreCutoff) //go through all until we hit the end
{
maxInitialScore--;
foreach (int id in idsOfPeptidesPossiblyObserved.Where(id => scoringTable[id] == maxInitialScore))
{
PeptideWithSetModifications peptide = PeptideIndex[id];
List <Product> peptideTheorProducts = peptide.Fragment(CommonParameters.DissociationType, CommonParameters.DigestionParams.FragmentationTerminus).ToList();
Tuple <int, PeptideWithSetModifications> notchAndUpdatedPeptide = Accepts(peptideTheorProducts, scan.PrecursorMass, peptide, CommonParameters.DigestionParams.FragmentationTerminus, MassDiffAcceptor, semiSpecificSearch);
int notch = notchAndUpdatedPeptide.Item1;
if (notch >= 0)
{
peptide = notchAndUpdatedPeptide.Item2;
peptideTheorProducts = peptide.Fragment(CommonParameters.DissociationType, FragmentationTerminus.Both).ToList();
List <MatchedFragmentIon> matchedIons = MatchFragmentIons(scan, peptideTheorProducts, ModifiedParametersNoComp);
double thisScore = CalculatePeptideScore(scan.TheScan, matchedIons);
if (thisScore > CommonParameters.ScoreCutoff)
{
PeptideSpectralMatch[] localPeptideSpectralMatches = GlobalCategorySpecificPsms[(int)FdrClassifier.GetCleavageSpecificityCategory(peptide.CleavageSpecificityForFdrCategory)];
if (localPeptideSpectralMatches[i] == null)
{
localPeptideSpectralMatches[i] = new PeptideSpectralMatch(peptide, notch, thisScore, i, scan, CommonParameters.DigestionParams, matchedIons);
}
else
{
localPeptideSpectralMatches[i].AddOrReplace(peptide, thisScore, notch, CommonParameters.ReportAllAmbiguity, matchedIons, 0);
}
}
}
}
}
}
// report search progress
progress++;
int percentProgress = (int)((progress / ListOfSortedMs2Scans.Length) * 100);
if (percentProgress > oldPercentProgress)
{
oldPercentProgress = percentProgress;
ReportProgress(new ProgressEventArgs(percentProgress, "Performing nonspecific search... " + CurrentPartition + "/" + CommonParameters.TotalPartitions, NestedIds));
}
}
});
return(new MetaMorpheusEngineResults(this));
}
private Tuple <int, PeptideWithSetModifications> Accepts(List <Product> fragments, double scanPrecursorMass, PeptideWithSetModifications peptide, FragmentationTerminus fragmentationTerminus, MassDiffAcceptor searchMode, bool semiSpecificSearch)
{
int localminPeptideLength = CommonParameters.DigestionParams.MinPeptideLength;
//Get terminal modifications, if any
Dictionary <int, List <Modification> > databaseAnnotatedMods = semiSpecificSearch ? null : GetTerminalModPositions(peptide, CommonParameters.DigestionParams, VariableTerminalModifications);
for (int i = localminPeptideLength - 1; i < fragments.Count; i++) //minus one start, because fragment 1 is at index 0
{
Product fragment = fragments[i];
double theoMass = fragment.NeutralMass - DissociationTypeCollection.GetMassShiftFromProductType(fragment.ProductType) + WaterMonoisotopicMass;
int notch = searchMode.Accepts(scanPrecursorMass, theoMass);
//check for terminal mods that might reach the observed mass
Modification terminalMod = null;
if (!semiSpecificSearch && notch < 0 && databaseAnnotatedMods.TryGetValue(i + 1, out List <Modification> terminalModsAtThisIndex)) //look for i+1, because the mod might exist at the terminus
{
foreach (Modification mod in terminalModsAtThisIndex)
{
notch = searchMode.Accepts(scanPrecursorMass, theoMass + mod.MonoisotopicMass.Value); //overwrite the notch, since the other notch wasn't accepted
if (notch >= 0)
{
terminalMod = mod;
break;
}
}
}
if (notch >= 0)
{
PeptideWithSetModifications updatedPwsm = null;
if (fragmentationTerminus == FragmentationTerminus.N)
{
int endResidue = peptide.OneBasedStartResidueInProtein + fragment.TerminusFragment.FragmentNumber - 1; //-1 for one based index
Dictionary <int, Modification> updatedMods = new Dictionary <int, Modification>();
foreach (KeyValuePair <int, Modification> mod in peptide.AllModsOneIsNterminus)
{
if (mod.Key < endResidue - peptide.OneBasedStartResidueInProtein + 3) //check if we cleaved it off, +1 for N-terminus being mod 1 and first residue being mod 2, +1 again for the -1 on end residue for one based index, +1 (again) for the one-based start residue
{
updatedMods.Add(mod.Key, mod.Value);
}
}
if (terminalMod != null)
{
updatedMods.Add(endResidue, terminalMod);
}
updatedPwsm = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein, endResidue, CleavageSpecificity.Unknown, "", 0, updatedMods, 0);
}
else //if C terminal ions, shave off the n-terminus
{
int startResidue = peptide.OneBasedEndResidueInProtein - fragment.TerminusFragment.FragmentNumber + 1; //plus one for one based index
Dictionary <int, Modification> updatedMods = new Dictionary <int, Modification>(); //updateMods
int indexShift = startResidue - peptide.OneBasedStartResidueInProtein;
foreach (KeyValuePair <int, Modification> mod in peptide.AllModsOneIsNterminus)
{
if (mod.Key > indexShift + 1) //check if we cleaved it off, +1 for N-terminus being mod 1 and first residue being 2
{
int key = mod.Key - indexShift;
updatedMods.Add(key, mod.Value);
}
}
if (terminalMod != null)
{
updatedMods.Add(startResidue - 1, terminalMod);
}
updatedPwsm = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, startResidue, peptide.OneBasedEndResidueInProtein, CleavageSpecificity.Unknown, "", 0, updatedMods, 0);
}
return(new Tuple <int, PeptideWithSetModifications>(notch, updatedPwsm));
}
else if (theoMass > scanPrecursorMass)
{
break;
}
}
//if the theoretical and experimental have the same mass or a terminal mod exists
if (peptide.BaseSequence.Length >= localminPeptideLength)
{
double totalMass = peptide.MonoisotopicMass;// + Constants.ProtonMass;
int notch = searchMode.Accepts(scanPrecursorMass, totalMass);
if (notch >= 0)
{
//need to update so that the cleavage specificity is recorded
PeptideWithSetModifications updatedPwsm = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein, peptide.OneBasedEndResidueInProtein, CleavageSpecificity.Unknown, "", 0, peptide.AllModsOneIsNterminus, peptide.NumFixedMods);
return(new Tuple <int, PeptideWithSetModifications>(notch, updatedPwsm));
}
else //try a terminal mod (if it exists)
{
if (!semiSpecificSearch && databaseAnnotatedMods.TryGetValue(peptide.Length, out List <Modification> terminalModsAtThisIndex))
{
foreach (Modification terminalMod in terminalModsAtThisIndex)
{
notch = searchMode.Accepts(scanPrecursorMass, totalMass + terminalMod.MonoisotopicMass.Value); //overwrite the notch, since the other notch wasn't accepted
if (notch >= 0)
{
//need to update the mod dictionary and don't want to overwrite the peptide incase it's in other scans
Dictionary <int, Modification> updatedMods = new Dictionary <int, Modification>(); //updateMods
foreach (KeyValuePair <int, Modification> mod in peptide.AllModsOneIsNterminus)
{
updatedMods.Add(mod.Key, mod.Value);
}
//add the terminal mod
if (fragmentationTerminus == FragmentationTerminus.N)
{
updatedMods[peptide.OneBasedEndResidueInProtein] = terminalMod;
}
else
{
updatedMods[peptide.OneBasedStartResidueInProtein - 1] = terminalMod;
}
PeptideWithSetModifications updatedPwsm = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein, peptide.OneBasedEndResidueInProtein, CleavageSpecificity.Unknown, "", 0, updatedMods, peptide.NumFixedMods);
return(new Tuple <int, PeptideWithSetModifications>(notch, updatedPwsm));
}
}
}
}
}
return(new Tuple <int, PeptideWithSetModifications>(-1, null));
}
/// <summary>
/// Generates theoretical fragments for given dissociation type for this peptide.
/// The "products" parameter is filled with these fragments.
/// </summary>
public void Fragment(DissociationType dissociationType, FragmentationTerminus fragmentationTerminus, List <Product> products)
{
// This code is specifically written to be memory- and CPU -efficient because it is
// called millions of times for a typical search (i.e., at least once per peptide).
// If you modify this code, BE VERY CAREFUL about allocating new memory, especially
// for new collections. This code also deliberately avoids using "yield return", again
// for performance reasons. Be sure to benchmark any changes with a parallelized
// fragmentation of every peptide in a database (i.e., test for speed decreases and
// memory issues).
products.Clear();
var massCaps = DissociationTypeCollection.GetNAndCTerminalMassShiftsForDissociationType(dissociationType);
double cTermMass = 0;
double nTermMass = 0;
List <ProductType> nTermProductTypes = DissociationTypeCollection.GetTerminusSpecificProductTypesFromDissociation(dissociationType, FragmentationTerminus.N);
List <ProductType> cTermProductTypes = DissociationTypeCollection.GetTerminusSpecificProductTypesFromDissociation(dissociationType, FragmentationTerminus.C);
bool calculateNTermFragments = fragmentationTerminus == FragmentationTerminus.N ||
fragmentationTerminus == FragmentationTerminus.Both;
bool calculateCTermFragments = fragmentationTerminus == FragmentationTerminus.C ||
fragmentationTerminus == FragmentationTerminus.Both;
//From http://www.matrixscience.com/help/fragmentation_help.html
//Low Energy CID -- In low energy CID(i.e.collision induced dissociation in a triple quadrupole or an ion trap) a peptide carrying a positive charge fragments mainly along its backbone,
//generating predominantly b and y ions. In addition, for fragments containing RKNQ, peaks are seen for ions that have lost ammonia (-17 Da) denoted a*, b* and y*. For fragments containing
//STED, loss of water(-18 Da) is denoted a°, b° and y°. Satellite ions from side chain cleavage are not observed.
bool haveSeenNTermDegreeIon = false;
bool haveSeenNTermStarIon = false;
bool haveSeenCTermDegreeIon = false;
bool haveSeenCTermStarIon = false;
// these two collections keep track of the neutral losses observed so far on the n-term or c-term.
// they are apparently necessary, but allocating memory for collections in this function results in
// inefficient memory usage and thus frequent garbage collection.
// TODO: If you can think of a way to remove these collections and still maintain correct
// fragmentation, please do so.
HashSet <double> nTermNeutralLosses = null;
HashSet <double> cTermNeutralLosses = null;
// n-terminus mod
if (calculateNTermFragments)
{
if (AllModsOneIsNterminus.TryGetValue(1, out Modification mod))
{
nTermMass += mod.MonoisotopicMass.Value;
}
}
// c-terminus mod
if (calculateCTermFragments)
{
if (AllModsOneIsNterminus.TryGetValue(BaseSequence.Length + 2, out Modification mod))
{
cTermMass += mod.MonoisotopicMass.Value;
}
}
for (int r = 0; r < BaseSequence.Length - 1; r++)
{
// n-term fragments
if (calculateNTermFragments)
{
char nTermResidue = BaseSequence[r];
// get n-term residue mass
if (Residue.TryGetResidue(nTermResidue, out Residue residue))
{
nTermMass += residue.MonoisotopicMass;
}
else
{
nTermMass = double.NaN;
}
// add side-chain mod
if (AllModsOneIsNterminus.TryGetValue(r + 2, out Modification mod))
{
nTermMass += mod.MonoisotopicMass.Value;
}
// handle star and degree ions for low-res CID
if (dissociationType == DissociationType.LowCID)
{
if (nTermResidue == 'R' || nTermResidue == 'K' || nTermResidue == 'N' || nTermResidue == 'Q')
{
haveSeenNTermStarIon = true;
}
if (nTermResidue == 'S' || nTermResidue == 'T' || nTermResidue == 'E' || nTermResidue == 'D')
{
haveSeenNTermDegreeIon = true;
}
}
// skip first N-terminal fragment (b1, aDegree1, ...) for CID
if (r == 0 && (dissociationType == DissociationType.CID || dissociationType == DissociationType.LowCID))
{
goto CTerminusFragments;
}
// generate products
for (int i = 0; i < nTermProductTypes.Count; i++)
{
if (dissociationType == DissociationType.LowCID)
{
if (!haveSeenNTermStarIon && (nTermProductTypes[i] == ProductType.aStar || nTermProductTypes[i] == ProductType.bStar))
{
continue;
}
if (!haveSeenNTermDegreeIon && (nTermProductTypes[i] == ProductType.aDegree || nTermProductTypes[i] == ProductType.bDegree))
{
continue;
}
}
products.Add(new Product(
nTermProductTypes[i],
FragmentationTerminus.N,
nTermMass + massCaps.Item1[i],
r + 1,
r + 1,
0));
if (mod != null && mod.NeutralLosses != null &&
mod.NeutralLosses.TryGetValue(dissociationType, out List <double> neutralLosses))
{
foreach (double neutralLoss in neutralLosses.Where(p => p != 0))
{
if (nTermNeutralLosses == null)
{
nTermNeutralLosses = new HashSet <double>();
}
nTermNeutralLosses.Add(neutralLoss);
}
}
if (nTermNeutralLosses != null)
{
foreach (double neutralLoss in nTermNeutralLosses)
{
products.Add(new Product(
nTermProductTypes[i],
FragmentationTerminus.N,
nTermMass + massCaps.Item1[i] - neutralLoss,
r + 1,
r + 1,
neutralLoss));
}
}
}
}
// c-term fragments
CTerminusFragments:
if (calculateCTermFragments)
{
char cTermResidue = BaseSequence[BaseSequence.Length - r - 1];
// get c-term residue mass
if (Residue.TryGetResidue(cTermResidue, out Residue residue))
{
cTermMass += residue.MonoisotopicMass;
}
else
{
cTermMass = double.NaN;
}
// add side-chain mod
if (AllModsOneIsNterminus.TryGetValue(BaseSequence.Length - r + 1, out Modification mod))
{
cTermMass += mod.MonoisotopicMass.Value;
}
// handle star and degree ions for low-res CID
if (dissociationType == DissociationType.LowCID)
{
if (cTermResidue == 'R' || cTermResidue == 'K' || cTermResidue == 'N' || cTermResidue == 'Q')
{
haveSeenCTermStarIon = true;
}
if (cTermResidue == 'S' || cTermResidue == 'T' || cTermResidue == 'E' || cTermResidue == 'D')
{
haveSeenCTermDegreeIon = true;
}
}
// generate products
for (int i = 0; i < cTermProductTypes.Count; i++)
{
// skip zDot ions for proline residues for ETD/ECD/EThcD
if (cTermResidue == 'P' &&
(dissociationType == DissociationType.ECD || dissociationType == DissociationType.ETD || dissociationType == DissociationType.EThcD) &&
cTermProductTypes[i] == ProductType.zDot)
{
continue;
}
if (dissociationType == DissociationType.LowCID)
{
if (!haveSeenCTermStarIon && cTermProductTypes[i] == ProductType.yStar)
{
continue;
}
if (!haveSeenCTermDegreeIon && cTermProductTypes[i] == ProductType.yDegree)
{
continue;
}
}
products.Add(new Product(
cTermProductTypes[i],
FragmentationTerminus.C,
cTermMass + massCaps.Item2[i],
r + 1,
BaseSequence.Length - r,
0));
if (mod != null && mod.NeutralLosses != null &&
mod.NeutralLosses.TryGetValue(dissociationType, out List <double> neutralLosses))
{
foreach (double neutralLoss in neutralLosses.Where(p => p != 0))
{
if (cTermNeutralLosses == null)
{
cTermNeutralLosses = new HashSet <double>();
}
cTermNeutralLosses.Add(neutralLoss);
}
}
if (cTermNeutralLosses != null)
{
foreach (double neutralLoss in cTermNeutralLosses)
{
products.Add(new Product(
cTermProductTypes[i],
FragmentationTerminus.C,
cTermMass + massCaps.Item2[i] - neutralLoss,
r + 1,
BaseSequence.Length - r,
neutralLoss));
}
}
}
}
}
// zDot generates one more ion...
if (cTermProductTypes.Contains(ProductType.zDot) && BaseSequence[0] != 'P')
{
// get c-term residue mass
if (Residue.TryGetResidue(BaseSequence[0], out Residue residue))
{
cTermMass += residue.MonoisotopicMass;
}
else
{
cTermMass = double.NaN;
}
// add side-chain mod
if (AllModsOneIsNterminus.TryGetValue(1, out Modification mod))
{
cTermMass += mod.MonoisotopicMass.Value;
}
// generate zDot product
products.Add(new Product(
ProductType.zDot,
FragmentationTerminus.C,
cTermMass + DissociationTypeCollection.GetMassShiftFromProductType(ProductType.zDot),
BaseSequence.Length,
1,
0));
if (mod != null && mod.NeutralLosses != null &&
mod.NeutralLosses.TryGetValue(dissociationType, out List <double> neutralLosses))
{
foreach (double neutralLoss in neutralLosses.Where(p => p != 0))
{
products.Add(new Product(
ProductType.zDot,
FragmentationTerminus.C,
cTermMass + DissociationTypeCollection.GetMassShiftFromProductType(ProductType.zDot) - neutralLoss,
BaseSequence.Length,
1,
neutralLoss));
}
}
}
foreach (var mod in AllModsOneIsNterminus.Where(p => p.Value.NeutralLosses != null))
{
// molecular ion minus neutral losses
if (mod.Value.NeutralLosses.TryGetValue(dissociationType, out List <double> losses))
{
foreach (double neutralLoss in losses.Where(p => p != 0))
{
if (neutralLoss != 0)
{
products.Add(new Product(ProductType.M, FragmentationTerminus.Both, MonoisotopicMass - neutralLoss, 0, 0, neutralLoss));
}
}
}
}
// generate diagnostic ions
// TODO: this code is memory-efficient but sort of CPU inefficient; it can be further optimized.
// however, diagnostic ions are fairly rare so it's probably OK for now
foreach (double diagnosticIon in AllModsOneIsNterminus.Where(p => p.Value.DiagnosticIons != null &&
p.Value.DiagnosticIons.ContainsKey(dissociationType)).SelectMany(p => p.Value.DiagnosticIons[dissociationType]).Distinct())
{
int diagnosticIonLabel = (int)Math.Round(diagnosticIon.ToMz(1), 0);
// the diagnostic ion is assumed to be annotated in the mod info as the *neutral mass* of the diagnostic ion, not the ionized species
products.Add(new Product(ProductType.D, FragmentationTerminus.Both, diagnosticIon, diagnosticIonLabel, 0, 0));
}
}
private Tuple <int, PeptideWithSetModifications> Accepts(List <Product> fragments, double scanPrecursorMass, PeptideWithSetModifications peptide, FragmentationTerminus fragmentationTerminus, MassDiffAcceptor searchMode)
{
//all masses in N and CTerminalMasses are b-ion masses, which are one water away from a full peptide
int localminPeptideLength = commonParameters.DigestionParams.MinPeptideLength;
for (int i = localminPeptideLength - 1; i < fragments.Count; i++) //minus one start, because fragment 1 is at index 0
{
Product fragment = fragments[i];
double theoMass = fragment.NeutralMass - DissociationTypeCollection.GetMassShiftFromProductType(fragment.ProductType) + WaterMonoisotopicMass;
int notch = searchMode.Accepts(scanPrecursorMass, theoMass);
if (notch >= 0)
{
PeptideWithSetModifications updatedPwsm = null;
if (fragmentationTerminus == FragmentationTerminus.N)
{
int endResidue = peptide.OneBasedStartResidueInProtein + fragment.TerminusFragment.FragmentNumber - 1; //-1 for one based index
Dictionary <int, Modification> updatedMods = new Dictionary <int, Modification>();
foreach (KeyValuePair <int, Modification> mod in peptide.AllModsOneIsNterminus)
{
if (mod.Key < endResidue - peptide.OneBasedStartResidueInProtein + 3) //check if we cleaved it off, +1 for N-terminus being mod 1 and first residue being mod 2, +1 again for the -1 on end residue for one based index, +1 (again) for the one-based start residue
{
updatedMods.Add(mod.Key, mod.Value);
}
}
updatedPwsm = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein, endResidue, CleavageSpecificity.Unknown, "", 0, updatedMods, 0);
}
else
{
int startResidue = peptide.OneBasedEndResidueInProtein - fragment.TerminusFragment.FragmentNumber + 1; //plus one for one based index
Dictionary <int, Modification> updatedMods = new Dictionary <int, Modification>(); //updateMods
int indexShift = startResidue - peptide.OneBasedStartResidueInProtein;
foreach (KeyValuePair <int, Modification> mod in peptide.AllModsOneIsNterminus)
{
if (mod.Key > indexShift + 1) //check if we cleaved it off, +1 for N-terminus being mod 1 and first residue being 2
{
int key = mod.Key - indexShift;
updatedMods.Add(key, mod.Value);
}
}
updatedPwsm = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, startResidue, peptide.OneBasedEndResidueInProtein, CleavageSpecificity.Unknown, "", 0, updatedMods, 0);
}
return(new Tuple <int, PeptideWithSetModifications>(notch, updatedPwsm));
}
else if (theoMass > scanPrecursorMass)
{
break;
}
}
//if the theoretical and experimental have the same mass
if (fragments.Count > localminPeptideLength)
{
double totalMass = peptide.MonoisotopicMass;// + Constants.ProtonMass;
int notch = searchMode.Accepts(scanPrecursorMass, totalMass);
if (notch >= 0)
{
//need to update so that the cleavage specificity is recorded
PeptideWithSetModifications updatedPwsm = new PeptideWithSetModifications(peptide.Protein, peptide.DigestionParams, peptide.OneBasedStartResidueInProtein, peptide.OneBasedEndResidueInProtein, CleavageSpecificity.Unknown, "", 0, peptide.AllModsOneIsNterminus, peptide.NumFixedMods);
return(new Tuple <int, PeptideWithSetModifications>(notch, updatedPwsm));
}
}
return(new Tuple <int, PeptideWithSetModifications>(-1, null));
}
//add possible protein/peptide terminal modifications that aren't on the terminal amino acids
//The purpose is for terminal mods that are contained WITHIN the Single peptide
private void AddInteriorTerminalModsToPrecursorIndex(List <int>[] precursorIndex, List <Product> fragmentMasses, PeptideWithSetModifications peptide, int peptideId, List <Modification> variableModifications)
{
//Get database annotated mods
Dictionary <int, List <Modification> > databaseAnnotatedMods = NonSpecificEnzymeSearchEngine.GetTerminalModPositions(peptide, CommonParameters.DigestionParams, variableModifications);
foreach (KeyValuePair <int, List <Modification> > relevantDatabaseMod in databaseAnnotatedMods)
{
int fragmentNumber = relevantDatabaseMod.Key;
Product fragmentAtIndex = fragmentMasses.Where(x => x.TerminusFragment.FragmentNumber == fragmentNumber).FirstOrDefault();
double basePrecursorMass = fragmentAtIndex == null ? peptide.MonoisotopicMass : fragmentAtIndex.NeutralMass - DissociationTypeCollection.GetMassShiftFromProductType(fragmentAtIndex.ProductType) + WaterMonoisotopicMass;
foreach (Modification mod in relevantDatabaseMod.Value)
{
double modifiedMass = basePrecursorMass + mod.MonoisotopicMass.Value;
if (modifiedMass <= MaxFragmentSize) //if the precursor is larger than the index allows, then don't add it
{
int precursorBin = (int)Math.Round(modifiedMass * FragmentBinsPerDalton);
if (precursorIndex[precursorBin] == null)
{
precursorIndex[precursorBin] = new List <int> {
peptideId
};
}
else
{
precursorIndex[precursorBin].Add(peptideId);
}
}
}
}
}
