public void TestGetFragmentFormula()
{
var pepseq = "PEPTIDE";
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var precursor = FragmentedMolecule.EMPTY.ChangeModifiedSequence(
new ModifiedSequence(pepseq, new ModifiedSequence.Modification[0], MassType.Monoisotopic));
var peptide = new Peptide(precursor.UnmodifiedSequence);
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var settings = SrmSettingsList.GetDefault();
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings,
ExplicitMods.EMPTY, null, null, null, new TransitionDocNode[0], false);
foreach (var ionType in new[] { IonType.a, IonType.b, IonType.c, IonType.x, IonType.y, IonType.z })
{
for (int ordinal = 1; ordinal < pepseq.Length; ordinal++)
{
var transition = new Transition(transitionGroup, ionType, Transition.OrdinalToOffset(ionType, ordinal, pepseq.Length), 0, Adduct.SINGLY_PROTONATED);
var fragment = precursor.ChangeFragmentIon(ionType, ordinal);
var actualMassDistribution = FragmentedMolecule.Settings.DEFAULT.GetMassDistribution(
fragment.FragmentFormula, 0, 0);
var expectedMz = sequenceMassCalc.GetFragmentMass(transition, transitionGroupDocNode.IsotopeDist);
if (expectedMz.IsMassH())
{
expectedMz = new TypedMass(expectedMz.Value - BioMassCalc.MassProton, expectedMz.MassType & ~MassType.bMassH);
}
var actualMz = actualMassDistribution.MostAbundanceMass;
if (Math.Abs(expectedMz - actualMz) > .001)
{
Assert.AreEqual(expectedMz, actualMz, .001, "Ion type {0} Ordinal {1}", ionType, ordinal);
}
}
}
}
