public ComplexFragmentIon MakeComplexFragmentIon(SrmSettings settings, IsotopeLabelType labelType, ComplexFragmentIonName complexFragmentIonName)
{
var transitionGroup = GetTransitionGroup(labelType, Adduct.SINGLY_PROTONATED);
Transition transition;
if (complexFragmentIonName.IonType == IonType.precursor || complexFragmentIonName.IonType == IonType.custom)
{
transition = new Transition(transitionGroup, IonType.precursor, Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED);
}
else
{
transition = new Transition(transitionGroup, complexFragmentIonName.IonType,
Transition.OrdinalToOffset(complexFragmentIonName.IonType, complexFragmentIonName.Ordinal, Peptide.Length),
0, Adduct.SINGLY_PROTONATED);
}
var result = new ComplexFragmentIon(transition, null, CrosslinkStructure, complexFragmentIonName.IsOrphan);
if (ExplicitMods != null)
{
foreach (var child in complexFragmentIonName.Children)
{
LinkedPeptide linkedPeptide;
if (!ExplicitMods.Crosslinks.TryGetValue(child.Item1, out linkedPeptide))
{
throw new InvalidOperationException(@"No crosslink at " + child.Item1);
}
result = result.AddChild(child.Item1,
linkedPeptide.MakeComplexFragmentIon(settings, labelType, child.Item2));
}
}
return(result);
}
public MoleculeMassOffset GetNeutralFormula(ComplexFragmentIon complexFragmentIon)
{
var result = GetSimpleFragmentFormula(complexFragmentIon);
foreach (var child in complexFragmentIon.Children)
{
var childBuilder = GetChildBuilder(child.Key);
result = result.Plus(childBuilder.GetNeutralFormula(child.Value));
}
result = SubtractLosses(result, complexFragmentIon.TransitionLosses);
return(result);
}
public IEnumerable <ComplexFragmentIon> ListSimpleFragmentIons(SrmSettings settings, bool useFilter)
{
var transitionGroupDocNode =
GetTransitionGroupDocNode(settings, IsotopeLabelType.light, Adduct.SINGLY_PROTONATED);
yield return(ComplexFragmentIon.NewOrphanFragmentIon(transitionGroupDocNode.TransitionGroup, ExplicitMods, Adduct.SINGLY_PROTONATED));
foreach (var transitionDocNode in transitionGroupDocNode.TransitionGroup.GetTransitions(settings,
transitionGroupDocNode, ExplicitMods, transitionGroupDocNode.PrecursorMz,
transitionGroupDocNode.IsotopeDist, null, null, useFilter, false))
{
if (transitionDocNode.Transition.MassIndex != 0)
{
continue;
}
yield return(new ComplexFragmentIon(transitionDocNode.Transition, transitionDocNode.Losses, CrosslinkStructure));
}
}
/// <summary>
/// Returns the chemical formula for this fragment and none of its children.
/// </summary>
private MoleculeMassOffset GetSimpleFragmentFormula(ComplexFragmentIon complexFragmentIon)
{
if (complexFragmentIon.IsOrphan)
{
return(MoleculeMassOffset.EMPTY);
}
var key = Tuple.Create(complexFragmentIon.Transition.IonType, complexFragmentIon.Transition.CleavageOffset);
MoleculeMassOffset moleculeMassOffset;
if (_fragmentedMolecules.TryGetValue(key, out moleculeMassOffset))
{
return(moleculeMassOffset);
}
var fragmentedMolecule = GetSimplePrecursorMolecule().ChangeFragmentIon(complexFragmentIon.Transition.IonType, complexFragmentIon.Transition.Ordinal);
moleculeMassOffset = new MoleculeMassOffset(fragmentedMolecule.FragmentFormula, 0, 0);
_fragmentedMolecules.Add(key, moleculeMassOffset);
return(moleculeMassOffset);
}
private IEnumerable <ComplexFragmentIon> PermuteFragmentIon(SrmSettings settings,
int maxFragmentationCount,
ComplexFragmentIon fragmentIon,
ModificationSite modificationSite,
IList <ComplexFragmentIon> linkedFragmentIons)
{
if (fragmentIon.IsOrphan && !fragmentIon.IsEmptyOrphan ||
!fragmentIon.IncludesAaIndex(modificationSite.IndexAa))
{
yield return(fragmentIon);
yield break;
}
int fragmentCountRemaining = maxFragmentationCount - fragmentIon.GetFragmentationEventCount();
foreach (var linkedFragmentIon in linkedFragmentIons)
{
if (linkedFragmentIon.GetFragmentationEventCount() > fragmentCountRemaining)
{
continue;
}
if (fragmentIon.IsOrphan)
{
if (linkedFragmentIon.IncludesAaIndex(IndexAa))
{
continue;
}
}
else
{
if (!linkedFragmentIon.IncludesAaIndex(IndexAa))
{
continue;
}
}
yield return(fragmentIon.AddChild(modificationSite, linkedFragmentIon));
}
}
public TransitionDocNode MakeTransitionDocNode(ComplexFragmentIon complexFragmentIon,
IsotopeDistInfo isotopeDist,
Annotations annotations,
TransitionDocNode.TransitionQuantInfo transitionQuantInfo,
ExplicitTransitionValues explicitTransitionValues,
Results <TransitionChromInfo> results)
{
var neutralFormula = GetNeutralFormula(complexFragmentIon);
var productMass = GetFragmentMassFromFormula(Settings, neutralFormula);
if (complexFragmentIon.Children.Count > 0)
{
complexFragmentIon = complexFragmentIon.CloneTransition();
}
if (complexFragmentIon.IsMs1 && Settings.TransitionSettings.FullScan.IsHighResPrecursor)
{
isotopeDist = isotopeDist ?? GetPrecursorIsotopeDistInfo(complexFragmentIon.Transition.Adduct, 0);
productMass = isotopeDist.GetMassI(complexFragmentIon.Transition.MassIndex, complexFragmentIon.Transition.DecoyMassShift);
transitionQuantInfo = transitionQuantInfo.ChangeIsotopeDistInfo(new TransitionIsotopeDistInfo(
isotopeDist.GetRankI(complexFragmentIon.Transition.MassIndex), isotopeDist.GetProportionI(complexFragmentIon.Transition.MassIndex)));
}
return(new TransitionDocNode(complexFragmentIon, annotations, productMass, transitionQuantInfo, explicitTransitionValues, results));
}
public TransitionDocNode MakeTransitionDocNode(ComplexFragmentIon complexFragmentIon, IsotopeDistInfo isotopeDist = null)
{
return(MakeTransitionDocNode(complexFragmentIon, isotopeDist, Annotations.EMPTY,
TransitionDocNode.TransitionQuantInfo.DEFAULT, ExplicitTransitionValues.EMPTY, null));
}
public TypedMass GetFragmentMass(ComplexFragmentIon complexFragmentIon)
{
var neutralFormula = GetNeutralFormula(complexFragmentIon);
return(GetFragmentMassFromFormula(Settings, neutralFormula));
}
