private TransitionGroupDocNode MakeTransitionGroupWithAllPossibleChildren(SrmSettings settings, IsotopeLabelType labelType)
{
var peptide = new Peptide(TargetInfoObj.LookupSequence);
var transitionGroup = new TransitionGroup(peptide, TargetInfoObj.TransitionGroupDocNode.PrecursorAdduct, labelType);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings, TargetInfoObj.LookupMods, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var children = transitionGroupDocNode.GetTransitions(settings, TargetInfoObj.LookupMods,
transitionGroupDocNode.PrecursorMz, null, null, null, FragmentFilterObj.UseFilter).Cast <DocNode>().ToList();
return((TransitionGroupDocNode)transitionGroupDocNode.ChangeChildren(children));
}
public void TestTwoAminoAcidLinkedPeptide()
{
const string modName = "crosslinker";
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangeTransitionSettings(srmSettings.TransitionSettings.ChangeFilter(
srmSettings.TransitionSettings.Filter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b })
));
var mainPeptide = new Peptide("AD");
var staticMod = new StaticMod(modName, null, null, "-C2");
var linkedPeptide = new LinkedPeptide(new Peptide("EF"), 1, null);
var mainTransitionGroup = new TransitionGroup(mainPeptide, Adduct.DOUBLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(mainTransitionGroup,
Annotations.EMPTY, srmSettings, null, null, ExplicitTransitionGroupValues.EMPTY, null,
new TransitionDocNode[0], false);
var modsWithLinkedPeptide = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(0, staticMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
Assert.AreEqual(1, srmSettings.PeptideSettings.Modifications.MaxNeutralLosses);
var oneNeutralLossChoices = mainTransitionGroupDocNode.GetTransitions(
srmSettings,
modsWithLinkedPeptide,
mainTransitionGroupDocNode.PrecursorMz,
mainTransitionGroupDocNode.IsotopeDist,
null,
null,
true).Select(transition => transition.ComplexFragmentIon.GetName()).ToList();
var modSite = new ModificationSite(0, modName);
var expectedFragmentIons = new[]
{
ComplexFragmentIonName.PRECURSOR.AddChild(modSite, ComplexFragmentIonName.PRECURSOR),
ComplexFragmentIonName.PRECURSOR.AddChild(modSite, new ComplexFragmentIonName(IonType.y, 1)),
new ComplexFragmentIonName(IonType.y, 1),
new ComplexFragmentIonName(IonType.b, 1).AddChild(modSite, new ComplexFragmentIonName(IonType.precursor, 0)),
ComplexFragmentIonName.ORPHAN.AddChild(modSite, new ComplexFragmentIonName(IonType.b, 1)),
};
CollectionAssert.AreEquivalent(expectedFragmentIons, oneNeutralLossChoices);
}
public static IList <DocNode> GetChoices(TransitionGroupDocNode nodeGroup, SrmSettings settings, ExplicitMods mods, bool useFilter)
{
TransitionGroup group = nodeGroup.TransitionGroup;
SpectrumHeaderInfo libInfo = null;
var transitionRanks = new Dictionary <double, LibraryRankedSpectrumInfo.RankedMI>();
group.GetLibraryInfo(settings, mods, useFilter, ref libInfo, transitionRanks);
var listChoices = new List <DocNode>();
foreach (TransitionDocNode nodeTran in nodeGroup.GetTransitions(settings, mods,
nodeGroup.PrecursorMz, nodeGroup.IsotopeDist, libInfo, transitionRanks, useFilter))
{
listChoices.Add(nodeTran);
}
return(listChoices);
}
public static IList<DocNode> GetChoices(TransitionGroupDocNode nodeGroup, SrmSettings settings, ExplicitMods mods, bool useFilter)
{
TransitionGroup group = nodeGroup.TransitionGroup;
SpectrumHeaderInfo libInfo = null;
var transitionRanks = new Dictionary<double, LibraryRankedSpectrumInfo.RankedMI>();
group.GetLibraryInfo(settings, mods, useFilter, ref libInfo, transitionRanks);
var listChoices = new List<DocNode>();
foreach (TransitionDocNode nodeTran in nodeGroup.GetTransitions(settings, mods,
nodeGroup.PrecursorMz, nodeGroup.IsotopeDist, libInfo, transitionRanks, useFilter))
{
listChoices.Add(nodeTran);
}
return listChoices;
}