public Transition(TransitionGroup group, IonType type, int?offset, int?massIndex, int charge, int?decoyMassShift, CustomIon customIon = null)
{
_group = group;
IonType = type;
CleavageOffset = offset ?? 0;
MassIndex = massIndex ?? 0;
Charge = charge;
DecoyMassShift = decoyMassShift;
// Small molecule precursor transition should have same custom ion as parent
if (IsPrecursor(type) && group.IsCustomIon)
{
CustomIon = group.CustomIon;
}
else
{
CustomIon = customIon;
}
// Derived values
if (!IsCustom(type, group))
{
Peptide peptide = group.Peptide;
Ordinal = OffsetToOrdinal(type, (int)offset, peptide.Length);
AA = (IsNTerminal()
? peptide.Sequence[(int)offset]
: peptide.Sequence[(int)offset + 1]);
}
else
{
// caller may have passed in offset = group.Peptide.Length - 1, which for custom ions gives -1
CleavageOffset = 0;
}
Validate();
}
public static int CompareGroups(TransitionGroup group1, TransitionGroup group2)
{
int chargeDiff = group1.PrecursorCharge - group2.PrecursorCharge;
if (chargeDiff != 0)
{
return(chargeDiff);
}
return(group1.LabelType.CompareTo(group2.LabelType));
}
public PeptideDocNode PermuteModificationsOnPeptide(SrmDocument document, PeptideGroupDocNode peptideGroupDocNode,
PeptideDocNode peptideDocNode, List <IsotopeLabelType> partialLabelTypes)
{
if (SkipPeptide(peptideDocNode))
{
return(peptideDocNode);
}
var potentiallyModifiedResidues = PotentiallyModifiedResidues(peptideDocNode, IsotopeModification);
if (potentiallyModifiedResidues.Count == 0)
{
return(peptideDocNode);
}
// Create a document containing only one peptide so that "ChangePeptideMods" does not have to walk
// over a long list of peptides to see which modifications are in use.
var smallDocument = (SrmDocument)document.ChangeChildren(new DocNode[]
{ peptideGroupDocNode.ChangeChildren(new DocNode[] { peptideDocNode }) });
var newTypedExplicitModifications = PermuteTypedExplicitModifications(partialLabelTypes, peptideDocNode, potentiallyModifiedResidues);
var newExplicitMods = new ExplicitMods(peptideDocNode.Peptide, peptideDocNode.ExplicitMods?.StaticModifications, newTypedExplicitModifications);
var identityPath = new IdentityPath(peptideGroupDocNode.PeptideGroup, peptideDocNode.Peptide);
smallDocument = smallDocument.ChangePeptideMods(identityPath, newExplicitMods, false, GlobalStaticMods,
GlobalIsotopeMods);
peptideDocNode = (PeptideDocNode)smallDocument.FindPeptideGroup(peptideGroupDocNode.PeptideGroup).FindNode(peptideDocNode.Peptide);
var lightChargeStates = peptideDocNode.TransitionGroups.Where(tg => tg.IsLight).Select(tg => tg.PrecursorCharge).Distinct().ToList();
var chargeStatesByLabel =
peptideDocNode.TransitionGroups.ToLookup(tg => tg.LabelType, tg => tg.PrecursorCharge);
var transitionGroupsToAdd = new List <TransitionGroupDocNode>();
foreach (var typedExplicitModifications in newExplicitMods.GetHeavyModifications())
{
var labelType = typedExplicitModifications.LabelType;
foreach (var chargeState in lightChargeStates.Except(chargeStatesByLabel[labelType]))
{
var tranGroup = new TransitionGroup(peptideDocNode.Peptide, Adduct.FromChargeProtonated(chargeState), labelType);
TransitionDocNode[] transitions = peptideDocNode.GetMatchingTransitions(tranGroup, smallDocument.Settings, newExplicitMods);
var nodeGroup = new TransitionGroupDocNode(tranGroup, transitions);
nodeGroup = nodeGroup.ChangeSettings(smallDocument.Settings, peptideDocNode, newExplicitMods, SrmSettingsDiff.ALL);
transitionGroupsToAdd.Add(nodeGroup);
}
}
if (transitionGroupsToAdd.Any())
{
var newChildren = peptideDocNode.TransitionGroups.Concat(transitionGroupsToAdd).ToList();
newChildren.Sort(Peptide.CompareGroups);
peptideDocNode = (PeptideDocNode)peptideDocNode.ChangeChildren(newChildren.Cast <DocNode>().ToList());
}
return(peptideDocNode);
}
public bool Equals(TransitionGroup obj)
{
if (ReferenceEquals(null, obj))
{
return(false);
}
if (ReferenceEquals(this, obj))
{
return(true);
}
bool equal = Equals(obj._peptide, _peptide) &&
Equals(obj.CustomIon, CustomIon) &&
obj.PrecursorCharge == PrecursorCharge &&
obj.LabelType.Equals(LabelType) &&
obj.DecoyMassShift.Equals(DecoyMassShift);
return(equal); // For debugging convenience
}
public Transition(TransitionGroup group, IonType type, int?offset, int?massIndex, Adduct adduct,
int?decoyMassShift, CustomMolecule customMolecule = null)
{
_group = group;
IonType = type;
CleavageOffset = offset ?? 0;
MassIndex = massIndex ?? 0;
Adduct = adduct;
DecoyMassShift = decoyMassShift;
// Small molecule precursor transition should have same custom molecule as parent
if (IsPrecursor(type) && group.IsCustomIon)
{
CustomIon = new CustomIon(group.CustomMolecule, adduct);
}
else if (customMolecule is CustomIon)
{
// As with reporter ions
CustomIon = (CustomIon)customMolecule;
Assume.IsTrue(Equals(adduct.AdductCharge, CustomIon.Adduct.AdductCharge));
Adduct = CustomIon.Adduct; // Ion mass is part of formula, so use charge only adduct
}
else if (customMolecule != null)
{
CustomIon = new CustomIon(customMolecule, adduct);
}
// Derived values
if (!IsCustom(type, group))
{
Peptide peptide = group.Peptide;
Ordinal = OffsetToOrdinal(type, (int)offset, peptide.Length);
AA = (IsNTerminal()
? peptide.Sequence[(int)offset]
: peptide.Sequence[(int)offset + 1]);
}
else
{
// caller may have passed in offset = group.Peptide.Length - 1, which for custom ions gives -1
CleavageOffset = 0;
}
Validate();
}
public PeptideDocNode CreateDocNodeFromSettings(LibKey key, Peptide peptide, SrmSettingsDiff diff, out TransitionGroupDocNode nodeGroupMatched)
{
if (!key.Target.IsProteomic)
{
// Scan the spectral lib entry for top N ranked (for now, that's just by intensity with high mz as tie breaker) fragments,
// add those as mass-only fragments, or with more detail if peak annotations are present.
foreach (var nodePep in peptide.CreateDocNodes(Settings, new MaxModFilter(0)))
{
SpectrumHeaderInfo libInfo;
if (nodePep != null && Settings.PeptideSettings.Libraries.TryGetLibInfo(key, out libInfo))
{
var isotopeLabelType = key.Adduct.HasIsotopeLabels ? IsotopeLabelType.heavy : IsotopeLabelType.light;
var group = new TransitionGroup(peptide, key.Adduct, isotopeLabelType);
nodeGroupMatched = new TransitionGroupDocNode(group, Annotations.EMPTY, Settings, null, libInfo, ExplicitTransitionGroupValues.EMPTY, null, null, false);
SpectrumPeaksInfo spectrum;
if (Settings.PeptideSettings.Libraries.TryLoadSpectrum(key, out spectrum))
{
// Add fragment and precursor transitions as needed
var transitionDocNodes =
Settings.TransitionSettings.Filter.SmallMoleculeIonTypes.Contains(IonType.precursor)
? nodeGroupMatched.GetPrecursorChoices(Settings, null, true) // Gives list of precursors
: new List <DocNode>();
if (Settings.TransitionSettings.Filter.SmallMoleculeIonTypes.Contains(IonType.custom))
{
GetSmallMoleculeFragments(key, nodeGroupMatched, spectrum, transitionDocNodes);
}
nodeGroupMatched = (TransitionGroupDocNode)nodeGroupMatched.ChangeChildren(transitionDocNodes);
return((PeptideDocNode)nodePep.ChangeChildren(new List <DocNode>()
{
nodeGroupMatched
}));
}
}
}
nodeGroupMatched = null;
return(null);
}
return(CreateDocNodeFromSettings(key.Target, peptide, diff, out nodeGroupMatched));
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
int?productZ,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double?minDelta = null;
double?minFragmentMass = null, maxFragmentMass = null, maxLoss = null;
if (massShiftType == MassShiftType.none)
{
if (!productZ.HasValue)
{
minFragmentMass = productMz - tolerance;
}
else
{
minFragmentMass = SequenceMassCalc.GetMH(productMz - tolerance, productZ.Value);
maxFragmentMass = SequenceMassCalc.GetMH(productMz + tolerance, productZ.Value);
}
}
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
maxLoss = Math.Max(maxLoss ?? 0, lossesTrial.Mass);
}
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
if (maxLoss.HasValue)
{
maxFragmentMass += maxLoss.Value;
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
// The peptide length is 1 longer than the mass array
for (int ord = len; ord > 0; ord--)
{
int offset = Transition.OrdinalToOffset(type, ord, len + 1);
var productMassBase = productMasses[type, offset];
// Until below the maximum fragment mass no possible matches
if (maxFragmentMass.HasValue && productMassBase > maxFragmentMass.Value)
{
continue;
}
// Once below the minimum fragment mass no more possible matches, so stop
if (minFragmentMass.HasValue && productMassBase < minFragmentMass.Value)
{
break;
}
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMassBase;
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productZ, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
bestOrdinal = ord;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
public Transition(TransitionGroup group, Adduct charge, int?massIndex, CustomMolecule customMolecule, IonType type = IonType.custom)
: this(group, type, null, massIndex, charge, null, customMolecule)
{
}
public Transition(TransitionGroup group, IonType type, int offset, int massIndex, Adduct charge)
: this(group, type, offset, massIndex, charge, null)
{
}
/// <summary>
/// Creates a precursor transition
/// </summary>
/// <param name="group">The <see cref="TransitionGroup"/> which the transition represents</param>
/// <param name="massIndex">Isotope mass shift</param>
/// <param name="productAdduct">Adduct on the transition</param>
/// <param name="customMolecule">Non-null if this is a custom transition</param>
public Transition(TransitionGroup group, int massIndex, Adduct productAdduct, CustomMolecule customMolecule = null)
: this(group, IonType.precursor, group.Peptide.Length - 1, massIndex, productAdduct, null, customMolecule)
{
}
public static bool IsCustom(IonType type, TransitionGroup parent)
{
return(type == IonType.custom || (type == IonType.precursor && parent.IsCustomIon));
}
public static int CalcProductCharge(double productPrecursorMass,
int precursorCharge,
double[,] productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double minDelta = double.MaxValue, minDeltaNs = double.MaxValue;
int bestCharge = 0, bestChargeNs = 0;
IonType? bestIonType = null, bestIonTypeNs = null;
int? bestOrdinal = null, bestOrdinalNs = null;
TransitionLosses bestLosses = null, bestLossesNs = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
double productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
int? charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (charge.HasValue && charge.Value == precursorCharge)
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge.Value) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge.Value;
bestIonTypeNs = IonType.precursor;
bestOrdinalNs = len + 1;
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge.Value;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
foreach (IonType type in Transition.ALL_TYPES)
{
// Types have priorities. If moving to a lower priority type, and there is already a
// suitable answer stop looking.
if ((type == Transition.ALL_TYPES[2] || type == Transition.ALL_TYPES[2]) &&
(MatchMz(minDelta, tolerance) || MatchMz(minDeltaNs, tolerance)))
{
break;
}
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
double productMass = productMasses[(int)type, offset];
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
int?chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (chargeFound.HasValue)
{
int charge = chargeFound.Value;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (potentialMassShift == 0 && minDeltaNs > delta)
{
bestChargeNs = charge;
bestIonTypeNs = type;
// The peptide length is 1 longer than the mass array
bestOrdinalNs = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLossesNs = lossesTrial;
minDeltaNs = delta;
}
else if (potentialMassShift != 0 && minDelta > delta)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
// Pefer no-shift to shift, even if the shift value is closer
if (MatchMz(minDelta, tolerance) && !MatchMz(minDeltaNs, tolerance))
{
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
ionType = bestIonTypeNs;
ordinal = bestOrdinalNs;
losses = bestLossesNs;
massShift = 0;
return(bestChargeNs);
}
public static Adduct CalcProductCharge(TypedMass productPrecursorMass,
Adduct precursorCharge,
IList <IonType> acceptedIonTypes,
IonTable <TypedMass> productMasses,
IList <IList <ExplicitLoss> > potentialLosses,
double productMz,
double tolerance,
MassType massType,
MassShiftType massShiftType,
out IonType?ionType,
out int?ordinal,
out TransitionLosses losses,
out int massShift)
{
// Get length of fragment ion mass array
int len = productMasses.GetLength(1);
// Check all possible ion types and offsets
double? minDelta = null;
var bestCharge = Adduct.EMPTY;
IonType? bestIonType = null;
int? bestOrdinal = null;
TransitionLosses bestLosses = null;
int bestMassShift = 0;
// Check to see if it is the precursor
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(IonType.precursor, 0, massType, potentialLosses))
{
var productMass = productPrecursorMass - (lossesTrial != null ? lossesTrial.Mass : 0);
int potentialMassShift;
int nearestCharge;
var charge = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (Equals(charge, precursorCharge))
{
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = IonType.precursor;
bestOrdinal = len + 1;
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
var categoryLast = -1;
foreach (var typeAccepted in GetIonTypes(acceptedIonTypes))
{
var type = typeAccepted.IonType;
var category = typeAccepted.IonCategory;
// Types have priorities. If changing type category, and there is already a
// suitable answer stop looking.
if (category != categoryLast && minDelta.HasValue && MatchMz(minDelta.Value, tolerance))
{
break;
}
categoryLast = category;
for (int offset = 0; offset < len; offset++)
{
foreach (var lossesTrial in TransitionGroup.CalcTransitionLosses(type, offset, massType, potentialLosses))
{
// Look for the closest match.
var productMass = productMasses[type, offset];
if (lossesTrial != null)
{
productMass -= lossesTrial.Mass;
}
int potentialMassShift;
int nearestCharge;
var chargeFound = CalcProductCharge(productMass, productMz, tolerance, false, precursorCharge,
massShiftType, out potentialMassShift, out nearestCharge);
if (!chargeFound.IsEmpty)
{
var charge = chargeFound;
double potentialMz = SequenceMassCalc.GetMZ(productMass, charge) + potentialMassShift;
double delta = Math.Abs(productMz - potentialMz);
if (CompareIonMatch(delta, lossesTrial, potentialMassShift, minDelta, bestLosses, bestMassShift) < 0)
{
bestCharge = charge;
bestIonType = type;
// The peptide length is 1 longer than the mass array
bestOrdinal = Transition.OffsetToOrdinal(type, offset, len + 1);
bestLosses = lossesTrial;
bestMassShift = potentialMassShift;
minDelta = delta;
}
}
}
}
}
ionType = bestIonType;
ordinal = bestOrdinal;
losses = bestLosses;
massShift = bestMassShift;
return(bestCharge);
}
public IEnumerable <TransitionDocNode> GetTransitions(SrmSettings settings,
TransitionGroupDocNode groupDocNode,
ExplicitMods mods,
double precursorMz,
IsotopeDistInfo isotopeDist,
SpectrumHeaderInfo libInfo,
IDictionary <double, LibraryRankedSpectrumInfo.RankedMI> transitionRanks,
bool useFilter)
{
Assume.IsTrue(ReferenceEquals(groupDocNode.TransitionGroup, this));
// Get necessary mass calculators and masses
var calcFilterPre = settings.GetPrecursorCalc(IsotopeLabelType.light, mods);
var calcFilter = settings.GetFragmentCalc(IsotopeLabelType.light, mods);
var calcPredict = settings.GetFragmentCalc(LabelType, mods);
string sequence = Peptide.Sequence;
// Save the true precursor m/z for TranstionSettings.Accept() now that all isotope types are
// checked. This is more correct than just using the light precursor m/z for precursor window
// exclusion.
double precursorMzAccept = precursorMz;
if (!ReferenceEquals(calcFilter, calcPredict))
{
// Get the normal precursor m/z for filtering, so that light and heavy ion picks will match.
precursorMz = IsCustomIon ?
BioMassCalc.CalculateIonMz(calcFilterPre.GetPrecursorMass(groupDocNode.CustomIon), groupDocNode.TransitionGroup.PrecursorCharge) :
SequenceMassCalc.GetMZ(calcFilterPre.GetPrecursorMass(sequence), groupDocNode.TransitionGroup.PrecursorCharge);
}
if (!IsAvoidMismatchedIsotopeTransitions)
{
precursorMzAccept = precursorMz;
}
var tranSettings = settings.TransitionSettings;
var filter = tranSettings.Filter;
var charges = filter.ProductCharges;
var startFinder = filter.FragmentRangeFirst;
var endFinder = filter.FragmentRangeLast;
double precursorMzWindow = filter.PrecursorMzWindow;
var types = filter.IonTypes;
MassType massType = tranSettings.Prediction.FragmentMassType;
int minMz = tranSettings.Instrument.GetMinMz(precursorMzAccept);
int maxMz = tranSettings.Instrument.MaxMz;
var pepMods = settings.PeptideSettings.Modifications;
var potentialLosses = CalcPotentialLosses(sequence, pepMods, mods, massType);
// A start m/z will need to be calculated if the start fragment
// finder uses m/z and their are losses to consider. If the filter
// is set to only consider fragments with m/z greater than the
// precursor, the code below needs to also prevent loss fragments
// from being under that m/z.
double startMz = 0;
// Get library settings
var pick = tranSettings.Libraries.Pick;
if (!useFilter)
{
pick = TransitionLibraryPick.all;
var listAll = Transition.ALL_CHARGES.ToList();
listAll.AddRange(charges.Where(c => !Transition.ALL_CHARGES.Contains(c)));
listAll.Sort();
charges = listAll.ToArray();
types = Transition.ALL_TYPES;
}
// If there are no libraries or no library information, then
// picking cannot use library information
else if (!settings.PeptideSettings.Libraries.HasLibraries || libInfo == null)
{
pick = TransitionLibraryPick.none;
}
// If filtering without library picking
if (potentialLosses != null)
{
if (pick == TransitionLibraryPick.none)
{
// Only include loss combinations where all losses are included always
potentialLosses = potentialLosses.Where(losses =>
losses.All(loss => loss.TransitionLoss.Loss.Inclusion == LossInclusion.Always)).ToArray();
}
else if (useFilter)
{
// Exclude all losses which should never be included by default
potentialLosses = potentialLosses.Where(losses =>
losses.All(loss => loss.TransitionLoss.Loss.Inclusion != LossInclusion.Never)).ToArray();
}
if (!potentialLosses.Any())
{
potentialLosses = null;
}
}
// Return precursor ions
if (!useFilter || types.Contains(IonType.precursor))
{
bool libraryFilter = (pick == TransitionLibraryPick.all || pick == TransitionLibraryPick.filter);
foreach (var nodeTran in GetPrecursorTransitions(settings, mods, calcFilterPre, calcPredict,
precursorMz, isotopeDist, potentialLosses, transitionRanks, libraryFilter, useFilter))
{
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
}
// Return special ions from settings, if this is a peptide
if (!IsCustomIon)
{
// This is a peptide, but it may have custom transitions (reporter ions), check those
foreach (var measuredIon in tranSettings.Filter.MeasuredIons.Where(m => m.IsCustom))
{
if (useFilter && measuredIon.IsOptional)
{
continue;
}
var tran = new Transition(this, measuredIon.Charge, null, measuredIon.CustomIon);
double mass = settings.GetFragmentMass(IsotopeLabelType.light, null, tran, null);
var nodeTran = new TransitionDocNode(tran, null, mass, null, null);
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
}
// For small molecules we can't generate new nodes, so just mz filter those we have
foreach (var nodeTran in groupDocNode.Transitions.Where(tran => tran.Transition.IsNonPrecursorNonReporterCustomIon()))
{
if (minMz <= nodeTran.Mz && nodeTran.Mz <= maxMz)
{
yield return(nodeTran);
}
}
if (sequence == null) // Completely custom
{
yield break;
}
// If picking relies on library information
if (useFilter && pick != TransitionLibraryPick.none)
{
// If it is not yet loaded, or nothing got ranked, return an empty enumeration
if (!settings.PeptideSettings.Libraries.IsLoaded ||
(transitionRanks != null && transitionRanks.Count == 0))
{
yield break;
}
}
double[,] massesPredict = calcPredict.GetFragmentIonMasses(sequence);
int len = massesPredict.GetLength(1);
if (len == 0)
{
yield break;
}
double[,] massesFilter = massesPredict;
if (!ReferenceEquals(calcFilter, calcPredict))
{
// Get the normal m/z values for filtering, so that light and heavy
// ion picks will match.
massesFilter = calcFilter.GetFragmentIonMasses(sequence);
}
// Get types other than this to make sure matches are possible for all types
var listOtherTypes = new List <Tuple <TransitionGroupDocNode, IFragmentMassCalc> >();
foreach (var labelType in settings.PeptideSettings.Modifications.GetModificationTypes())
{
if (Equals(labelType, LabelType))
{
continue;
}
var calc = settings.GetFragmentCalc(labelType, mods);
if (calc == null)
{
continue;
}
var tranGroupOther = new TransitionGroup(Peptide, PrecursorCharge, labelType, false, DecoyMassShift);
var nodeGroupOther = new TransitionGroupDocNode(tranGroupOther, Annotations.EMPTY, settings, mods,
libInfo, ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
listOtherTypes.Add(new Tuple <TransitionGroupDocNode, IFragmentMassCalc>(nodeGroupOther, calc));
}
// Loop over potential product ions picking transitions
foreach (IonType type in types)
{
// Precursor type is handled above.
if (type == IonType.precursor)
{
continue;
}
foreach (int charge in charges)
{
// Precursor charge can never be lower than product ion charge.
if (Math.Abs(PrecursorCharge) < Math.Abs(charge))
{
continue;
}
int start = 0, end = 0;
if (pick != TransitionLibraryPick.all)
{
start = startFinder.FindStartFragment(massesFilter, type, charge,
precursorMz, precursorMzWindow, out startMz);
end = endFinder.FindEndFragment(type, start, len);
if (Transition.IsCTerminal(type))
{
Helpers.Swap(ref start, ref end);
}
}
for (int i = 0; i < len; i++)
{
// Get the predicted m/z that would be used in the transition
double massH = massesPredict[(int)type, i];
foreach (var losses in CalcTransitionLosses(type, i, massType, potentialLosses))
{
double ionMz = SequenceMassCalc.GetMZ(Transition.CalcMass(massH, losses), charge);
// Make sure the fragment m/z value falls within the valid instrument range.
// CONSIDER: This means that a heavy transition might excede the instrument
// range where a light one is accepted, leading to a disparity
// between heavy and light transtions picked.
if (minMz > ionMz || ionMz > maxMz)
{
continue;
}
TransitionDocNode nodeTranReturn = null;
bool accept = true;
if (pick == TransitionLibraryPick.all || pick == TransitionLibraryPick.all_plus)
{
if (!useFilter)
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
accept = false;
}
else
{
if (IsMatched(transitionRanks, ionMz, type, charge, losses))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
accept = false;
}
// If allowing library or filter, check the filter to decide whether to accept
else if (pick == TransitionLibraryPick.all_plus &&
tranSettings.Accept(sequence, precursorMzAccept, type, i, ionMz, start, end, startMz))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
}
}
else if (tranSettings.Accept(sequence, precursorMzAccept, type, i, ionMz, start, end, startMz))
{
if (pick == TransitionLibraryPick.none)
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
else
{
if (IsMatched(transitionRanks, ionMz, type, charge, losses))
{
nodeTranReturn = CreateTransitionNode(type, i, charge, massH, losses, transitionRanks);
}
}
}
if (nodeTranReturn != null)
{
if (IsAvoidMismatchedIsotopeTransitions &&
!OtherLabelTypesAllowed(settings, minMz, maxMz, start, end, startMz, accept,
groupDocNode, nodeTranReturn, listOtherTypes))
{
continue;
}
Assume.IsTrue(minMz <= nodeTranReturn.Mz && nodeTranReturn.Mz <= maxMz);
yield return(nodeTranReturn);
}
}
}
}
}
}
public static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings,
TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues,
SkylineDocumentProto.Types.Transition transitionProto)
{
var stringPool = scrubber.StringPool;
IonType ionType = DataValues.FromIonType(transitionProto.FragmentType);
MeasuredIon measuredIon = null;
if (transitionProto.MeasuredIonName != null)
{
measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault(
i => i.Name.Equals(transitionProto.MeasuredIonName.Value));
if (measuredIon == null)
{
throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName));
}
ionType = IonType.custom;
}
bool isCustom = Transition.IsCustom(ionType, group);
bool isPrecursor = Transition.IsPrecursor(ionType);
CustomMolecule customIon = null;
if (isCustom)
{
if (measuredIon != null)
{
customIon = measuredIon.SettingsCustomIon;
}
else if (isPrecursor)
{
customIon = group.CustomMolecule;
}
else
{
var formula = DataValues.FromOptional(transitionProto.Formula);
var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc
var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH);
var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH);
var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH;
var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH;
customIon = new CustomMolecule(formula,
new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic),
new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average),
DataValues.FromOptional(transitionProto.CustomIonName), moleculeID);
}
}
Transition transition;
var adductString = DataValues.FromOptional(transitionProto.Adduct);
var adduct = string.IsNullOrEmpty(adductString)
? Adduct.FromChargeProtonated(transitionProto.Charge)
: Adduct.FromStringAssumeChargeOnly(adductString);
if (isCustom)
{
transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType);
}
else if (isPrecursor)
{
transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex,
group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
else
{
int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal,
group.Peptide.Length);
transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift));
}
var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses);
var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist);
var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist);
if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null)
{
throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift);
}
TransitionLibInfo libInfo = null;
if (transitionProto.LibInfo != null)
{
libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity);
}
var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition);
var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results);
var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create(
DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy),
DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset),
DataValues.FromOptional(transitionProto.ExplicitSLens),
DataValues.FromOptional(transitionProto.ExplicitConeVoltage),
DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential));
return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results));
}
public Transition(TransitionGroup group, int charge, int?massIndex, CustomIon customIon, IonType type = IonType.custom)
: this(group, type, null, massIndex, charge, null, customIon)
{
}
/// <summary>
/// Creates a precursor transition
/// </summary>
/// <param name="group">The <see cref="TransitionGroup"/> which the transition represents</param>
/// <param name="massIndex">Isotope mass shift</param>
/// <param name="customIon">Non-null if this is a custom transition</param>
public Transition(TransitionGroup group, int massIndex, CustomIon customIon = null)
: this(group, IonType.precursor, group.Peptide.Length - 1, massIndex, group.PrecursorCharge, null, customIon)
{
}
