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);
}
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();
}
protected override void DoTest()
{
const string crosslinkerName = "Hydrolysis";
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("CrosslinkNeutralLossTest.sky")));
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Modifications;
});
var editModListDlg = ShowEditStaticModsDlg(peptideSettingsUi);
// Define a crosslinker which is a water loss. In this way, two peptides can be joined end to end
// and will have the same chemical formula as a single concatenated peptide
RunDlg <EditStaticModDlg>(editModListDlg.AddItem, editStaticModDlg => {
{
editStaticModDlg.Modification = new StaticMod(crosslinkerName, null, null, "-H2O");
editStaticModDlg.IsCrosslinker = true;
editStaticModDlg.OkDialog();
}
});
RunDlg <EditStaticModDlg>(editModListDlg.AddItem, editStaticModDlg =>
{
editStaticModDlg.Modification = ChangeLossesToIncludeAlways(UniMod.GetModification("Oxidation (M)", true));
editStaticModDlg.OkDialog();
});
RunDlg <EditStaticModDlg>(editModListDlg.AddItem, editStaticModDlg =>
{
editStaticModDlg.Modification = ChangeLossesToIncludeAlways(UniMod.GetModification("Phospho (ST)", true));
editStaticModDlg.OkDialog();
});
OkDialog(editModListDlg, editModListDlg.OkDialog);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
RunDlg <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg, pasteDlg =>
{
// Insert two peptides which are equivalent to each other.
// The first peptide is composed of two short peptides concatenated with the hydrolysis crosslinker.
SetClipboardText(@"AMNFS[Phospho (ST)]GSPGAV-STSPT[Phospho (ST)]QSFM[Oxidation (M)]NTLPR-[Hydrolysis@11,1]
AMNFS[Phospho (ST)]GSPGAVSTSPT[Phospho (ST)]QSFM[Oxidation (M)]NTLPR");
pasteDlg.PastePeptides();
pasteDlg.OkDialog();
});
AssertEx.Serializable(SkylineWindow.Document);
var crosslinkedPeptide = SkylineWindow.Document.Peptides.First();
var flatPeptide = SkylineWindow.Document.Peptides.Skip(1).First();
Assert.IsNotNull(crosslinkedPeptide.ExplicitMods);
Assert.IsNotNull(flatPeptide.ExplicitMods);
Assert.IsTrue(crosslinkedPeptide.ExplicitMods.HasCrosslinks);
Assert.IsFalse(flatPeptide.ExplicitMods.HasCrosslinks);
Assert.AreEqual(1, crosslinkedPeptide.TransitionGroupCount);
Assert.AreEqual(1, flatPeptide.TransitionGroupCount);
var flatPrecursor = flatPeptide.TransitionGroups.First();
var crosslinkedPrecursor = crosslinkedPeptide.TransitionGroups.First();
Assert.AreEqual(flatPrecursor.PrecursorMz, crosslinkedPrecursor.PrecursorMz, DELTA);
ModificationSite crosslinkSite = new ModificationSite(10, crosslinkerName);
var flatTransitionNames = flatPrecursor.Transitions.Select(tran =>
tran.ComplexFragmentIon.GetTargetsTreeLabel() +
Transition.GetChargeIndicator(tran.Transition.Adduct))
.ToList();
Assert.AreEqual(flatPrecursor.TransitionCount, flatTransitionNames.Count);
var crosslinkedTransitionNames = crosslinkedPrecursor.Transitions.Select(tran =>
tran.ComplexFragmentIon.GetTargetsTreeLabel() +
Transition.GetChargeIndicator(tran.Transition.Adduct))
.ToList();
Assert.AreEqual(crosslinkedPrecursor.TransitionCount, crosslinkedTransitionNames.Count);
foreach (var transitionDocNode in flatPrecursor.Transitions)
{
// AMNFSGSPGAV(11)-STSPTQSFMNTLPR(14)
ComplexFragmentIonName complexFragmentIonName = null;
switch (transitionDocNode.Transition.IonType)
{
case IonType.precursor:
complexFragmentIonName = ComplexFragmentIonName.PRECURSOR.AddChild(crosslinkSite, ComplexFragmentIonName.PRECURSOR);
break;
case IonType.b:
if (transitionDocNode.Transition.Ordinal == 11)
{
continue;
}
if (transitionDocNode.Transition.Ordinal <= 11)
{
complexFragmentIonName = new ComplexFragmentIonName(IonType.b, transitionDocNode.Transition.Ordinal);
}
else
{
complexFragmentIonName = ComplexFragmentIonName.PRECURSOR.AddChild(crosslinkSite,
new ComplexFragmentIonName(IonType.b, transitionDocNode.Transition.Ordinal - 11));
}
break;
case IonType.y:
if (transitionDocNode.Transition.Ordinal == 14)
{
continue;
}
if (transitionDocNode.Transition.Ordinal < 14)
{
complexFragmentIonName = ComplexFragmentIonName.ORPHAN.AddChild(crosslinkSite,
new ComplexFragmentIonName(IonType.y, transitionDocNode.Transition.Ordinal));
}
else
{
complexFragmentIonName = new ComplexFragmentIonName(IonType.y, transitionDocNode.Transition.Ordinal - 14)
.AddChild(crosslinkSite, ComplexFragmentIonName.PRECURSOR);
}
break;
}
Assert.IsNotNull(complexFragmentIonName);
if (transitionDocNode.Transition.IonType != IonType.precursor && transitionDocNode.Losses != null &&
transitionDocNode.Losses.Losses.Count > 1)
{
continue;
}
var matchingTransitions = crosslinkedPrecursor.Transitions.Where(tran =>
complexFragmentIonName.Equals(tran.ComplexFragmentIon.GetName()) &&
Equals(transitionDocNode.Losses, tran.Losses) &&
Equals(transitionDocNode.Transition.Adduct, tran.Transition.Adduct)).ToList();
AssertEx.AreEqual(1, matchingTransitions.Count);
AssertEx.AreEqual(transitionDocNode.Mz, matchingTransitions[0].Mz, DELTA);
}
}
