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));
}