private static Modification MakeModification(string unmodifiedSequence, ExplicitMod explicitMod)
{
var staticMod = explicitMod.Modification;
int i = explicitMod.IndexAA;
var monoMass = staticMod.MonoisotopicMass ??
SrmSettings.MonoisotopicMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
var avgMass = staticMod.AverageMass ??
SrmSettings.AverageMassCalc.GetAAModMass(unmodifiedSequence[i], i,
unmodifiedSequence.Length);
if (monoMass == 0 && avgMass == 0)
{
char aa = unmodifiedSequence[i];
if ((staticMod.LabelAtoms & LabelAtoms.LabelsAA) != LabelAtoms.None && AminoAcid.IsAA(aa))
{
string heavyFormula = SequenceMassCalc.GetHeavyFormula(aa, staticMod.LabelAtoms);
monoMass = SequenceMassCalc.FormulaMass(BioMassCalc.MONOISOTOPIC, heavyFormula,
SequenceMassCalc.MassPrecision);
avgMass = SequenceMassCalc.FormulaMass(BioMassCalc.AVERAGE, heavyFormula,
SequenceMassCalc.MassPrecision);
}
}
return(new Modification(explicitMod, monoMass, avgMass));
}
public override int GetHashCode()
{
unchecked
{
var hashCode = ExplicitMod.GetHashCode();
hashCode = (hashCode * 397) ^ MonoisotopicMass.GetHashCode();
hashCode = (hashCode * 397) ^ AverageMass.GetHashCode();
return(hashCode);
}
}
public static Modification ResolveModification(SrmSettings settings, IsotopeLabelType labelType, string unmodifiedSequence,
ExplicitMod explicitMod)
{
var modification = MakeModification(unmodifiedSequence, explicitMod);
if (explicitMod?.LinkedPeptide?.Peptide == null)
{
return(modification);
}
return(modification.ChangeLinkedPeptideSequence(GetModifiedSequence(settings,
explicitMod.LinkedPeptide.Peptide.Sequence, explicitMod.LinkedPeptide.ExplicitMods, labelType)));
}
public void TestCrosslinkPrecursorMz()
{
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangePeptideSettings(
srmSettings.PeptideSettings.ChangeModifications(
srmSettings.PeptideSettings.Modifications.ChangeStaticModifications(new StaticMod[0])));
var mainPeptide = new Peptide("WQEGNVFSCSVMHEALHNHYTQK");
var otherPeptide = new Peptide("NQVSLTCLVK");
var linkedPeptide = new LinkedPeptide(otherPeptide, 6, ExplicitMods.EMPTY);
var crosslinkMod = new StaticMod("disulfide", "C", null, "-H2").ChangeCrosslinkerSettings(CrosslinkerSettings.EMPTY);
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.DOUBLY_PROTONATED, IsotopeLabelType.light);
var explicitMod = new ExplicitMod(8, crosslinkMod).ChangeLinkedPeptide(linkedPeptide);
var explicitMods = new ExplicitMods(mainPeptide, new[] { explicitMod }, new List <TypedExplicitModifications>());
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings, explicitMods, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
Assert.AreEqual(1923.9111, transitionGroupDocNode.PrecursorMz, .001);
}
public void TestLooplink()
{
var peptide = new Peptide("PEPTIDE");
var srmSettings = SrmSettingsList.GetDefault();
var transitionFilter = srmSettings.TransitionSettings.Filter;
transitionFilter = transitionFilter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b });
srmSettings = srmSettings.ChangeTransitionSettings(
srmSettings.TransitionSettings.ChangeFilter(transitionFilter));
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var crosslinkerDef = new StaticMod("dss", null, null, "C8H10O2");
var linkedPeptide = new LinkedPeptide(null, 5, null);
var crosslinkMod = new ExplicitMod(2, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(peptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var modifiedSequence = ModifiedSequence.GetModifiedSequence(srmSettings, peptide.Sequence,
explicitModsWithCrosslink, IsotopeLabelType.light);
Assert.AreEqual("PEPTIDE-[dss@3-6]", modifiedSequence.FullNames);
var choices = transitionGroupDocNode.GetPrecursorChoices(srmSettings, explicitModsWithCrosslink, true)
.Cast <TransitionDocNode>().ToArray();
var complexFragmentIons = choices.Select(transition => transition.ComplexFragmentIon.GetName()).ToArray();
// Make sure none of the transitions involve a cleavage in between the two ends of the looplink
// PEpTIdE
var yOrdinals = complexFragmentIons.Where(ion => ion.IonType == IonType.y).Select(ion => ion.Ordinal)
.Distinct().ToList();
var bOrdinals = complexFragmentIons.Where(ion => ion.IonType == IonType.b).Select(ion => ion.Ordinal)
.Distinct().ToList();
CollectionAssert.AreEquivalent(new[] { 6, 5, 1 }, yOrdinals);
CollectionAssert.AreEquivalent(new[] { 1, 2, 6 }, bOrdinals);
}
protected bool Equals(Modification other)
{
return(ExplicitMod.Equals(other.ExplicitMod) && MonoisotopicMass.Equals(other.MonoisotopicMass) &&
AverageMass.Equals(other.AverageMass));
}
public Modification(ExplicitMod explicitMod, double monoMass, double avgMass)
{
ExplicitMod = explicitMod;
MonoisotopicMass = monoMass;
AverageMass = avgMass;
}