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 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 TestComplexIonGetNeutralFormula()
{
var srmSettings = SrmSettingsList.GetDefault();
var fullTransitionGroup = new TransitionGroupDocNode(
new TransitionGroup(new Peptide("ELVIS"), Adduct.SINGLY_PROTONATED, IsotopeLabelType.light),
Annotations.EMPTY, srmSettings, null, null, ExplicitTransitionGroupValues.EMPTY,
null, null, false);
var fullFormula = fullTransitionGroup.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C25H45N5O9", fullFormula.Molecule.ToString());
var hydrolysisDef = new StaticMod("hydrolysis", null, ModTerminus.C, "-H2O")
.ChangeCrosslinkerSettings(CrosslinkerSettings.EMPTY);
var crossLinkMod = new ExplicitMod(1, hydrolysisDef)
.ChangeLinkedPeptide(new LinkedPeptide(new Peptide("VIS"), 0, null));
var mainPeptide = new Peptide("EL");
var explicitMods = new ExplicitMods(mainPeptide, new[] { crossLinkMod }, new TypedExplicitModifications[0]);
var mainTransitionGroup = new TransitionGroupDocNode(
new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light),
Annotations.EMPTY, srmSettings,
explicitMods, null,
ExplicitTransitionGroupValues.EMPTY,
null, null, false);
var mainFullFormula = mainTransitionGroup.GetNeutralFormula(srmSettings, explicitMods);
Assert.AreEqual(fullFormula, mainFullFormula);
}
public void TestTransitionGroupDocNodeGetNeutralFormula()
{
var peptide = new Peptide("PEPTIDE");
var transitionGroup = new TransitionGroup(peptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var srmSettings = SrmSettingsList.GetDefault();
var transitionGroupDocNode = new TransitionGroupDocNode(transitionGroup, Annotations.EMPTY, srmSettings, null, null, ExplicitTransitionGroupValues.EMPTY, null, null, false);
var moleculeOffset = transitionGroupDocNode.GetNeutralFormula(srmSettings, null);
Assert.AreEqual("C34H53N7O15", moleculeOffset.Molecule.ToString());
}