public void TestCrosslinkGetNeutralFormula()
{
var mainPeptide = new Peptide("MERCURY");
var srmSettings = SrmSettingsList.GetDefault();
srmSettings = srmSettings.ChangePeptideSettings(
srmSettings.PeptideSettings.ChangeModifications(srmSettings.PeptideSettings.Modifications
.ChangeStaticModifications(new StaticMod[0])));
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
null, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var unlinkedFormula = mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C37H61N13O11S2Se", unlinkedFormula.ToString());
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 2, null);
var linkedPeptideFormula = linkedPeptide.GetNeutralFormula(srmSettings, IsotopeLabelType.light);
Assert.AreEqual("C30H53N11O12S", linkedPeptideFormula.ToString());
var crosslinkMod = new StaticMod("disulfide", null, null, "-H2");
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(3, crosslinkMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
var crosslinkedFormula =
mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, explicitModsWithCrosslink);
Assert.AreEqual("C67H112N24O23S3Se", crosslinkedFormula.Molecule.ToString());
}
public void TestSingleAminoAcidLinkedPeptide()
{
var srmSettings = SrmSettingsList.GetDefault();
var mainPeptide = new Peptide("A");
var staticMod = new StaticMod("crosslinker", null, null, "-C2");
var linkedPeptide = new LinkedPeptide(new Peptide("D"), 0, null);
var mainTransitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(mainTransitionGroup,
Annotations.EMPTY, srmSettings, null, null,
ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
var modsWithoutLinkedPeptide = new ExplicitMods(mainPeptide, new[] { new ExplicitMod(0, staticMod), }, new TypedExplicitModifications[0]);
Assert.AreEqual("C3H7NO2", AminoAcidFormulas.Default.GetFormula("A").ToString());
Assert.AreEqual("C3H7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null).Molecule.ToString());
Assert.AreEqual("CH7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithoutLinkedPeptide).Molecule.ToString());
Assert.AreEqual("C4H7NO4", AminoAcidFormulas.Default.GetFormula("D").ToString());
var modsWithLinkedPeptide = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(0, staticMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
Assert.AreEqual("C5H14N2O6", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithLinkedPeptide).Molecule.ToString());
var mainComplexFragmentIon = new ComplexFragmentIon(new Transition(mainTransitionGroup, IonType.precursor, mainPeptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, modsWithLinkedPeptide.Crosslinks);
var linkedComplexFragmentIon = new ComplexFragmentIon(
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
var complexFragmentIon =
mainComplexFragmentIon.AddChild(new ModificationSite(0, staticMod.Name), linkedComplexFragmentIon);
var transition = complexFragmentIon.MakeTransitionDocNode(srmSettings, modsWithLinkedPeptide, null);
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var expectedMz = sequenceMassCalc.GetPrecursorMass("A") + sequenceMassCalc.GetPrecursorMass("D") - 24 - BioMassCalc.MassProton;
Assert.AreEqual(expectedMz, transition.Mz, .00001);
}
public void TestCrosslinkModSerialization()
{
var settings = SrmSettingsList.GetDefault();
var crosslinkerDef = new StaticMod("disulfide", null, null, "-H2")
.ChangeCrosslinkerSettings(CrosslinkerSettings.EMPTY);
settings = settings.ChangePeptideSettings(settings.PeptideSettings.ChangeModifications(
settings.PeptideSettings.Modifications.ChangeStaticModifications(new[] { crosslinkerDef })));
settings = settings.ChangeTransitionSettings(settings.TransitionSettings.ChangeFilter(
settings.TransitionSettings.Filter
.ChangeFragmentRangeFirstName(TransitionFilter.StartFragmentFinder.ION_1.Name)
.ChangeFragmentRangeLastName(@"last ion")
.ChangePeptideIonTypes(new[] { IonType.precursor, IonType.y, IonType.b })
)); var mainPeptide = new Peptide("MERCURY");
var transitionGroup = new TransitionGroup(mainPeptide, Adduct.DOUBLY_PROTONATED, IsotopeLabelType.light);
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 2, null);
var crosslinkMod = new ExplicitMod(3, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, settings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, true);
var peptideDocNode = new PeptideDocNode(mainPeptide, settings, explicitModsWithCrosslink, null, ExplicitRetentionTimeInfo.EMPTY, new [] { transitionGroupDocNode }, false);
peptideDocNode = peptideDocNode.ChangeSettings(settings, SrmSettingsDiff.ALL);
Assert.AreNotEqual(0, peptideDocNode.TransitionCount);
var peptideGroupDocNode = new PeptideGroupDocNode(new PeptideGroup(), Annotations.EMPTY, "Peptides", null, new [] { peptideDocNode });
var srmDocument = (SrmDocument) new SrmDocument(settings).ChangeChildren(new[] { peptideGroupDocNode });
AssertEx.Serializable(srmDocument);
string docXML = null;
AssertEx.RoundTrip(srmDocument, ref docXML);
Assert.IsNotNull(docXML);
}
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 TestPermuteComplexIons()
{
var mainPeptide = new Peptide("MERCURY");
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(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var crosslinkerDef = new StaticMod("disulfide", "C", null, "-H2");
var linkedPeptide = new LinkedPeptide(new Peptide("ARSENIC"), 6, null);
var crosslinkMod = new ExplicitMod(3, crosslinkerDef).ChangeLinkedPeptide(linkedPeptide);
var explicitModsWithCrosslink = new ExplicitMods(mainPeptide, new[] { crosslinkMod }, new TypedExplicitModifications[0]);
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings,
explicitModsWithCrosslink, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var choices = transitionGroupDocNode.GetPrecursorChoices(srmSettings, explicitModsWithCrosslink, true)
.Cast <TransitionDocNode>().ToArray();
var complexFragmentIons = choices.Select(transition => transition.ComplexFragmentIon.GetName()).ToArray();
Assert.AreNotEqual(0, complexFragmentIons.Length);
}
private bool TryMakeLinkedPeptide(out LinkedPeptide linkedPeptide)
{
linkedPeptide = null;
Peptide peptide;
if (!TryMakePeptide(out peptide))
{
return(false);
}
string peptideSequence = peptide == null ? ParentPeptide.Peptide.Sequence : peptide.Sequence;
var messageBoxHelper = new MessageBoxHelper(this);
int aaOrdinal;
if (!messageBoxHelper.ValidateNumberTextBox(tbxAttachmentOrdinal, 1, peptideSequence.Length, out aaOrdinal))
{
return(false);
}
string validAminoAcids = _crosslinkMod?.AAs;
if (!string.IsNullOrEmpty(validAminoAcids))
{
char aa = peptideSequence[aaOrdinal - 1];
if (!validAminoAcids.Contains(aa))
{
string message = string.Format(Resources.EditLinkedPeptideDlg_TryMakeLinkedPeptide_The_crosslinker___0___cannot_attach_to_the_amino_acid___1___,
_crosslinkMod.Name, aa);
messageBoxHelper.ShowTextBoxError(tbxAttachmentOrdinal, message);
return(false);
}
}
linkedPeptide = new LinkedPeptide(peptide, aaOrdinal - 1, MakeExplicitMods(peptide, _explicitMods));
return(true);
}
public void OkDialog()
{
LinkedPeptide linkedPeptide;
if (!TryMakeLinkedPeptide(out linkedPeptide))
{
return;
}
LinkedPeptide = linkedPeptide;
DialogResult = DialogResult.OK;
}
private void WriteLinkedPeptide(XmlWriter writer, LinkedPeptide linkedPeptide)
{
writer.WriteStartElement(EL.linked_peptide);
writer.WriteAttribute(ATTR.index_aa, linkedPeptide.IndexAa);
if (linkedPeptide.Peptide != null)
{
writer.WriteAttributeIfString(ATTR.sequence, linkedPeptide.Peptide.Sequence);
if (null != linkedPeptide.ExplicitMods)
{
WriteExplicitMods(writer, linkedPeptide.Peptide.Sequence, linkedPeptide.ExplicitMods);
}
}
writer.WriteEndElement();
}
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);
}
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);
}
public EditLinkedPeptideDlg(SrmSettings settings, PeptideDocNode parentPeptide, LinkedPeptide linkedPeptide, StaticMod crosslinkMod)
{
InitializeComponent();
_settings = settings;
ParentPeptide = parentPeptide;
_crosslinkMod = crosslinkMod;
if (linkedPeptide != null)
{
if (linkedPeptide.Peptide != null)
{
tbxPeptideSequence.Text = linkedPeptide.Peptide.Sequence;
}
else
{
cbxLooplink.Checked = true;
}
tbxAttachmentOrdinal.Text = (linkedPeptide.IndexAa + 1).ToString();
_explicitMods = linkedPeptide.ExplicitMods;
}
}