Exemple #1
0
        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);
        }
Exemple #2
0
 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();
 }
Exemple #3
0
        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);
            }
        }