public void TestSingleAminoAcidLinkedPeptide()
{
var srmSettings = SrmSettingsList.GetDefault();
var mainPeptide = new Peptide("A");
var staticMod = new StaticMod("crosslinker", null, null, "-C2");
var linkedPeptide = new LinkedPeptide(new Peptide("D"), 0, null);
var mainTransitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(mainTransitionGroup,
Annotations.EMPTY, srmSettings, null, null,
ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
var modsWithoutLinkedPeptide = new ExplicitMods(mainPeptide, new[] { new ExplicitMod(0, staticMod), }, new TypedExplicitModifications[0]);
Assert.AreEqual("C3H7NO2", AminoAcidFormulas.Default.GetFormula("A").ToString());
Assert.AreEqual("C3H7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null).Molecule.ToString());
Assert.AreEqual("CH7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithoutLinkedPeptide).Molecule.ToString());
Assert.AreEqual("C4H7NO4", AminoAcidFormulas.Default.GetFormula("D").ToString());
var modsWithLinkedPeptide = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(0, staticMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
Assert.AreEqual("C5H14N2O6", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithLinkedPeptide).Molecule.ToString());
var mainComplexFragmentIon = new ComplexFragmentIon(new Transition(mainTransitionGroup, IonType.precursor, mainPeptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, modsWithLinkedPeptide.Crosslinks);
var linkedComplexFragmentIon = new ComplexFragmentIon(
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
var complexFragmentIon =
mainComplexFragmentIon.AddChild(new ModificationSite(0, staticMod.Name), linkedComplexFragmentIon);
var transition = complexFragmentIon.MakeTransitionDocNode(srmSettings, modsWithLinkedPeptide, null);
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var expectedMz = sequenceMassCalc.GetPrecursorMass("A") + sequenceMassCalc.GetPrecursorMass("D") - 24 - BioMassCalc.MassProton;
Assert.AreEqual(expectedMz, transition.Mz, .00001);
}
public void TestComplexIonMz()
{
var srmSettings = SrmSettingsList.GetDefault();
var peptide = new Peptide("DLGEEHFKGLVLIAFSQYLQQCPFDEHVK");
var linkedPeptide = new LinkedPeptide(new Peptide("LVNELTEFAKTCVADESHAGCEK"), 9, null);
var transitionGroup = new TransitionGroup(peptide, Adduct.QUADRUPLY_PROTONATED, IsotopeLabelType.light);
var crosslinkMod = new StaticMod("linker", "K", null, "C8H10O2");
var explicitMod = new ExplicitMod(7, crosslinkMod).ChangeLinkedPeptide(linkedPeptide);
var explicitMods = new ExplicitMods(peptide, new[] { explicitMod }, new List <TypedExplicitModifications>());
var linkedTransition =
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED);
var expectedMzs = new[]
{
Tuple.Create(IonType.b, 2, 1, 229.1183),
Tuple.Create(IonType.b, 10, 3, 1291.2766)
};
foreach (var tuple in expectedMzs)
{
int offset = Transition.OrdinalToOffset(tuple.Item1, tuple.Item2, peptide.Sequence.Length);
var transition = new Transition(transitionGroup, tuple.Item1, offset, 0, Adduct.FromChargeProtonated(tuple.Item3));
var complexFragmentIon = new ComplexFragmentIon(transition, null, explicitMods.Crosslinks);
if (complexFragmentIon.IncludesAaIndex(explicitMod.IndexAA))
{
complexFragmentIon = complexFragmentIon.AddChild(explicitMod.ModificationSite,
new ComplexFragmentIon(linkedTransition, null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE));
}
var complexTransitionDocNode = complexFragmentIon.MakeTransitionDocNode(srmSettings, explicitMods, null);
Assert.AreEqual(tuple.Item4, complexTransitionDocNode.Mz, .0001, "{0}{1}{2}", tuple.Item1, tuple.Item2,
Transition.GetChargeIndicator(Adduct.FromChargeProtonated(tuple.Item3)));
}
}
public void TestIncludesAaIndex()
{
var peptide = new Peptide("AD");
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var precursor =
new ComplexFragmentIon(new Transition(transitionGroup, IonType.precursor, peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
Assert.IsTrue(precursor.IncludesAaIndex(0));
Assert.IsTrue(precursor.IncludesAaIndex(1));
var y1 = new ComplexFragmentIon(new Transition(transitionGroup, IonType.y, Transition.OrdinalToOffset(IonType.y, 1, peptide.Length), 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
Assert.AreEqual(1, y1.Transition.Ordinal);
Assert.IsFalse(y1.IncludesAaIndex(0));
Assert.IsTrue(y1.IncludesAaIndex(1));
var b1 = new ComplexFragmentIon(new Transition(transitionGroup, IonType.b, Transition.OrdinalToOffset(IonType.b, 1, peptide.Length), 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
Assert.AreEqual(1, b1.Transition.Ordinal);
Assert.IsTrue(b1.IncludesAaIndex(0));
Assert.IsFalse(b1.IncludesAaIndex(1));
}
private void WriteLinkedIon(XmlWriter writer, ModificationSite modificationSite, ComplexFragmentIon complexFragmentIon)
{
writer.WriteStartElement(EL.linked_fragment_ion);
if (!complexFragmentIon.IsOrphan)
{
// blank fragment type means orphaned fragment ion
writer.WriteAttribute(ATTR.fragment_type, complexFragmentIon.Transition.IonType);
}
if (complexFragmentIon.Transition.IonType != IonType.precursor)
{
writer.WriteAttribute(ATTR.fragment_ordinal, complexFragmentIon.Transition.Ordinal);
}
writer.WriteAttribute(ATTR.index_aa, modificationSite.IndexAa);
writer.WriteAttribute(ATTR.modification_name, modificationSite.ModName);
WriteTransitionLosses(writer, complexFragmentIon.TransitionLosses);
foreach (var child in complexFragmentIon.Children)
{
WriteLinkedIon(writer, child.Key, child.Value);
}
writer.WriteEndElement();
}
public IEnumerable <IonType> GetAllIonTypes(ComplexFragmentIon complexFragmentIon)
{
return(new[] { complexFragmentIon.Transition.IonType }.Concat(
complexFragmentIon.Children.Values.SelectMany(child => GetAllIonTypes(child))));
}
