public static void TestDigestIndices()
{
ModificationMotif.TryGetMotif("X", out ModificationMotif motif);
Modification mod = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
IDictionary <int, List <Modification> > modDict = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
mod
} },
{ 8, new List <Modification> {
mod
} }
};
var prot = new Protein("MNNNNKRRRRR", null, null, null, modDict);
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
DigestionParams digestionParams = new DigestionParams
{
Protease = protease,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
MaxMissedCleavages = 0,
};
var digestList = prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).ToList();
var ok1 = digestList[1];
var ok2 = digestList[3];
Assert.AreEqual(1, ok1.NumMods);
Assert.IsTrue(ok1.allModsOneIsNterminus.ContainsKey(3));
Assert.AreEqual(1, ok2.NumMods);
Assert.IsTrue(ok2.allModsOneIsNterminus.ContainsKey(3));
}
//TO THINK: Is it reasonable to transfer Glycan to Modification the first time Glycan is read in? Which could save time.
//Use glycan index and modification index to reduce space.
public static Modification NGlycanToModification(Glycan glycan)
{
Dictionary <DissociationType, List <double> > neutralLosses = new Dictionary <DissociationType, List <double> >();
if (glycan.Ions != null)
{
List <double> lossMasses = glycan.Ions.Where(p => p.IonMass < 57000000).Select(p => (double)p.LossIonMass / 1E5).OrderBy(p => p).ToList(); //570 is a cutoff for glycan ion size 2N1H, which will generate fragment ions.
neutralLosses.Add(DissociationType.HCD, lossMasses);
neutralLosses.Add(DissociationType.CID, lossMasses);
neutralLosses.Add(DissociationType.EThcD, lossMasses);
}
Dictionary <DissociationType, List <double> > diagnosticIons = new Dictionary <DissociationType, List <double> >();
diagnosticIons.Add(DissociationType.HCD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.CID, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.EThcD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
ModificationMotif.TryGetMotif("N", out ModificationMotif finalMotif); //TO DO: only one motif can be write here.
var id = Glycan.GetKindString(glycan.Kind);
Modification modification = new Modification(
_originalId: id,
_modificationType: "N-Glycosylation",
_monoisotopicMass: (double)glycan.Mass / 1E5,
_locationRestriction: "Anywhere.",
_target: finalMotif,
_neutralLosses: neutralLosses,
_diagnosticIons: diagnosticIons
);
return(modification);
}
public void DoNotWriteSameModTwiceButWriteInHeaderSinceDifferent()
{
Loaders.LoadElements(Path.Combine(TestContext.CurrentContext.TestDirectory, "elements2.dat"));
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "z.txt")).ToList();
Protein protein = new Protein("MCSSSSSSSSSS", "accession", "organism", new List <Tuple <string, string> >(), new Dictionary <int, List <Modification> > {
{ 2, sampleModList.OfType <Modification>().ToList() }
}, null, "name", "full_name", false, false, new List <DatabaseReference>(), new List <SequenceVariation>(), new List <DisulfideBond>());
Assert.AreEqual(1, protein.OneBasedPossibleLocalizedModifications[2].OfType <ModificationWithMass>().Count());
Dictionary <string, HashSet <Tuple <int, Modification> > > dictWithThisMod = new Dictionary <string, HashSet <Tuple <int, Modification> > >();
HashSet <Tuple <int, Modification> > value = new HashSet <Tuple <int, Modification> >();
ModificationMotif.TryGetMotif("C", out ModificationMotif motif);
ModificationWithMass newMod = new ModificationWithMass("Palmitoylation of C", "mt", motif, TerminusLocalization.Any, double.NaN, null, null);
Assert.AreNotEqual(newMod, sampleModList.First());
value.Add(new Tuple <int, Modification>(2, newMod));
dictWithThisMod.Add("accession", value);
var newModResEntries = ProteinDbWriter.WriteXmlDatabase(dictWithThisMod, new List <Protein> {
protein
}, Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins2.xml"));
Assert.AreEqual(0, newModResEntries.Count);
List <Protein> new_proteins = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "test_modifications_with_proteins2.xml"), true, DecoyType.None, new List <Modification>(), false, new List <string>(), out Dictionary <string, Modification> um);
Assert.AreEqual(1, new_proteins.Count);
Assert.AreEqual(1, new_proteins[0].OneBasedPossibleLocalizedModifications.Count);
Assert.AreEqual(2, new_proteins[0].OneBasedPossibleLocalizedModifications.SelectMany(kv => kv.Value).Count());
}
public static void TestVeryCloseExperimentalsModern()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var thePep = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First();
var frags = new List <Product>();
thePep.Fragment(DissociationType.HCD, FragmentationTerminus.Both, frags);
var massArray = frags.Select(p => p.NeutralMass).ToArray();
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1), massArray[4].ToMz(1) + 1e-9 };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 600, 1, null, new CommonParameters()) };
CommonParameters CommonParameters = new CommonParameters(productMassTolerance: new PpmTolerance(5), scoreCutoff: 1, digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModificationIsoforms: int.MaxValue, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
var indexEngine = new IndexingEngine(new List <Protein> {
prot
}, new List <Modification>(), new List <Modification>(), null, null, null, 1, DecoyType.Reverse,
CommonParameters, null, 30000, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var cse = new ModernSearchEngine(globalPsms, arrayOfSortedMS2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, null, new OpenSearchMode(), 0, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public void Test_read_xml_write_read_fasta()
{
ModificationMotif.TryGetMotif("X", out ModificationMotif motif);
var nice = new List <Modification>
{
new Modification("fayk", null, "mt", null, motif, "Anywhere.", null, null, null, null, null, null, null, null)
};
List <Protein> ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"xml2.xml"), true, DecoyType.None, nice, false, null,
out Dictionary <string, Modification> un);
ProteinDbWriter.WriteFastaDatabase(ok, Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"rewrite_xml_test.fasta"), "|");
List <Protein> ok2 = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"rewrite_xml_test.fasta"), true, DecoyType.None, false,
ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotNameRegex, ProteinDbLoader.UniprotGeneNameRegex, ProteinDbLoader.UniprotOrganismRegex, out var b);
Assert.AreEqual(ok.Count, ok2.Count);
Assert.True(Enumerable.Range(0, ok.Count).All(i => ok[i].BaseSequence == ok2[i].BaseSequence));
Assert.True(Enumerable.Range(0, ok.Count).All(i => ok[i].Name == ok2[i].Name));
Assert.True(Enumerable.Range(0, ok.Count).All(i => ok[i].Organism == ok2[i].Organism));
Assert.True(Enumerable.Range(0, ok.Count).All(i => ok[i].GeneNames.First().Item2 == ok2[i].GeneNames.First().Item2));
Assert.True(ok.All(p => p.ProteolysisProducts.All(prod => prod.OneBasedBeginPosition == null || prod.OneBasedBeginPosition > 0 && prod.OneBasedBeginPosition <= p.Length)));
Assert.True(ok.All(p => p.ProteolysisProducts.All(prod => prod.OneBasedEndPosition == null || prod.OneBasedEndPosition > 0 && prod.OneBasedEndPosition <= p.Length)));
Assert.True(ok2.All(p => p.ProteolysisProducts.All(prod => prod.OneBasedBeginPosition == null || prod.OneBasedBeginPosition > 0 && prod.OneBasedBeginPosition <= p.Length)));
Assert.True(ok2.All(p => p.ProteolysisProducts.All(prod => prod.OneBasedEndPosition == null || prod.OneBasedEndPosition > 0 && prod.OneBasedEndPosition <= p.Length)));
}
public static void Test_ProteinDigest()
{
DigestionParams d = new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 5,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
ModificationMotif.TryGetMotif("D", out ModificationMotif motif);
Modification mod = new Modification(_originalId: "mod1", _modificationType: "mt", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
IDictionary <int, List <Modification> > oneBasedModification = new Dictionary <int, List <Modification> >
{
{ 3, new List <Modification> {
mod
} }
};
Protein prot1 = new Protein("MEDEEK", "prot1", oneBasedModifications: oneBasedModification);
var pep1 = prot1.Digest(d, new List <Modification>(), new List <Modification>()).First();
var pep2 = prot1.Digest(d, new List <Modification>(), new List <Modification>()).Last();
Assert.AreEqual("MEDEEK", pep1.FullSequence);
Assert.AreEqual("MED[mt:mod1 on D]EEK", pep2.FullSequence);
}
public static TheoreticalProteoform make_a_theoretical(string a, double mass, int lysine_count)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("X", out motif);
Modification unmodification = new Modification("Unmodified", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 0);
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("", "")
}, new Dictionary <int, List <Modification> > {
{ 0, new List <Modification> {
unmodification
} }
}, new List <ProteolysisProduct> {
new ProteolysisProduct(1, 12, "")
}, "T2", "T3", true, false, new List <DatabaseReference> {
new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
})
}, new List <GoTerm> {
new GoTerm(new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
}))
});
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm()
});
var t = new TheoreticalProteoform(a, "", p1.BaseSequence, new List <ProteinWithGoTerms> {
p1
}, mass, lysine_count, set, true, false, new Dictionary <InputFile, Protein[]>());
t.modified_mass = mass;
return(t);
}
public static void TestCompactPeptideMasses_cTerminalModifiedPeptide()
{
Protein p = new Protein("PET", "accession");
ModificationMotif.TryGetMotif("T", out ModificationMotif motif);
Modification phosphorylation = new Modification(_originalId: "phospho", _modificationType: "CommonBiological", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H1O3P1"));
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 2);
var aPeptideWithSetModifications = p.Digest(digestionParams, new List <Modification> {
phosphorylation
}, new List <Modification>()).First();
var aCompactPeptide = aPeptideWithSetModifications.CompactPeptide(FragmentationTerminus.Both);
//evaluate N-terminal masses
var nTerminalMasses = aCompactPeptide.TerminalMasses.Where(v => v.Terminus == FragmentationTerminus.N);
HashSet <int> expectedNTerminalMasses = new HashSet <int> {
97, 226
};
Assert.That(expectedNTerminalMasses.SetEquals(nTerminalMasses.Select(v => (int)Math.Round(v.NeutralMass, 1))));
//evaluate C-terminal masses
var cTerminalMasses = aCompactPeptide.TerminalMasses.Where(v => v.Terminus == FragmentationTerminus.C);
HashSet <int> expectedCTerminalMasses = new HashSet <int> {
181, 310, 407
};
Assert.That(expectedCTerminalMasses.SetEquals(cTerminalMasses.Select(v => (int)Math.Round(v.NeutralMass, 1))));
}
public void Test_modification3_hash_set() // numerical tolerance is 1e-9 so these two mods need to evaluate as identical
{
ModificationMotif.TryGetMotif("K", out ModificationMotif motif);
Modification m1 = new Modification(_originalId: "id1", _modificationType: "modificationType", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1.11111d, _databaseReference: new Dictionary <string, IList <string> >(), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ DissociationType.AnyActivationType, new List <double> {
2.222222
} }
}, _diagnosticIons: new Dictionary <DissociationType, List <double> > {
{ DissociationType.AnyActivationType, new List <double> {
1.2233
} }
});
Modification m2 = new Modification(_originalId: "id1", _modificationType: "modificationType", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1.11111d - 1e-10, _databaseReference: new Dictionary <string, IList <string> >(), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ DissociationType.AnyActivationType, new List <double> {
2.222222 + 1e-10
} }
}, _diagnosticIons: new Dictionary <DissociationType, List <double> > {
{ DissociationType.AnyActivationType, new List <double> {
1.2233
} }
});
m1.DatabaseReference.Add("key", new List <string> {
"value"
});
m2.DatabaseReference.Add("key", new List <string> {
"value"
});
HashSet <Modification> mods = new HashSet <Modification>(new Modification[] { m1, m2 });
Assert.AreEqual(1, mods.Count);
Assert.IsTrue(m1.Equals(m2));
}
public static void TestCompactPeptideMasses_internallyModifiedPeptide_NeutralLoss()
{
Protein p = new Protein("PET", "accession");
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
Modification phosphorylation = new Modification(_originalId: "phospho", _modificationType: "CommonBiological", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H1O3P1"), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ MassSpectrometry.DissociationType.HCD, new List <double> {
0, ChemicalFormula.ParseFormula("H3O4P1").MonoisotopicMass
} }
});
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 2);
var aPeptideWithSetModifications = p.Digest(digestionParams, new List <Modification> {
phosphorylation
}, new List <Modification>()).First();
var aCompactPeptide = aPeptideWithSetModifications.CompactPeptide(FragmentationTerminus.Both);
var allFragmentNeutralMasses = aPeptideWithSetModifications.Fragment(DissociationType.HCD, FragmentationTerminus.Both);
//evaluate N-terminal masses
var n = allFragmentNeutralMasses.Where(f => f.TerminusFragment.Terminus == FragmentationTerminus.N).ToList();
HashSet <int> expectedNTerminalMasses = new HashSet <int> {
97, 306, 208
};
Assert.That(expectedNTerminalMasses.SetEquals(n.Select(v => (int)Math.Round(v.NeutralMass, 1))));
//evaluate C-terminal masses
var c = allFragmentNeutralMasses.Where(f => f.TerminusFragment.Terminus == FragmentationTerminus.C).ToList();
HashSet <int> expectedCTerminalMasses = new HashSet <int> {
119, 328, 230
};
Assert.That(expectedCTerminalMasses.SetEquals(c.Select(v => (int)Math.Round(v.NeutralMass, 1))));
}
public static void TestCompactPeptideMasses_nTerminalModifiedPeptide_NeutralLoss_DissociationTypes_CID_and_HCD()//there should be no added neutral losses in this case becuase the allowed dissociation type doesn't match the dissociation type used in the experiment
{
Protein p = new Protein("PET", "accession");
ModificationMotif.TryGetMotif("P", out ModificationMotif motif);
Modification phosphorylation = new Modification(_originalId: "phospho", _modificationType: "CommonBiological", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H1O3P1"), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ MassSpectrometry.DissociationType.CID, new List <double> {
0, ChemicalFormula.ParseFormula("H3O4P1").MonoisotopicMass
} }
});
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 2);
var aPeptideWithSetModifications = p.Digest(digestionParams, new List <Modification> {
phosphorylation
}, new List <Modification>()).First();
var aCompactPeptide = aPeptideWithSetModifications.CompactPeptide(FragmentationTerminus.Both);
//evaluate N-terminal masses
var nTerminalMasses = aCompactPeptide.TerminalMasses.Where(v => v.Terminus == FragmentationTerminus.N);
HashSet <int> expectedNTerminalMasses = new HashSet <int> {
177, 306
};
Assert.That(expectedNTerminalMasses.SetEquals(nTerminalMasses.Select(v => (int)Math.Round(v.NeutralMass, 1))));
//evaluate C-terminal masses
var cTerminalMasses = aCompactPeptide.TerminalMasses.Where(v => v.Terminus == FragmentationTerminus.C);
HashSet <int> expectedCTerminalMasses = new HashSet <int> {
101, 230, 407
};
Assert.That(expectedCTerminalMasses.SetEquals(cTerminalMasses.Select(v => (int)Math.Round(v.NeutralMass, 1))));
}
//Motif should be writen with required form
public static List <int> GetPossibleModSites(PeptideWithSetModifications peptide, string[] motifs)
{
List <int> possibleModSites = new List <int>();
List <Modification> modifications = new List <Modification>();
foreach (var mtf in motifs)
{
if (ModificationMotif.TryGetMotif(mtf, out ModificationMotif aMotif))
{
Modification modWithMotif = new Modification(_target: aMotif, _locationRestriction: "Anywhere.");
modifications.Add(modWithMotif);
}
}
foreach (var modWithMotif in modifications)
{
for (int r = 0; r < peptide.Length; r++)
{
if (peptide.AllModsOneIsNterminus.Keys.Contains(r + 2))
{
continue;
}
//FullSequence is used here to avoid duplicated modification on same sites?
if (ModificationLocalization.ModFits(modWithMotif, peptide.BaseSequence, r + 1, peptide.Length, r + 1))
{
possibleModSites.Add(r + 2);
}
}
}
return(possibleModSites);
}
public static bool MotifExist(string baseSeq, string[] motifs)
{
List <Modification> modifications = new List <Modification>();
foreach (var mtf in motifs)
{
if (ModificationMotif.TryGetMotif(mtf, out ModificationMotif aMotif))
{
Modification modWithMotif = new Modification(_target: aMotif, _locationRestriction: "Anywhere.");
modifications.Add(modWithMotif);
}
}
foreach (var modWithMotif in modifications)
{
for (int r = 0; r < baseSeq.Length; r++)
{
//Modification is not considered.
if (ModificationLocalization.ModFits(modWithMotif, baseSeq, r + 1, baseSeq.Length, r + 1))
{
return(true);
}
}
}
return(false);
}
public void Test_FragmentationModNeutralLoss()
{
// Now we'll check the mass of modified peptide with no neutral losses
ModificationMotif.TryGetMotif("T", out ModificationMotif motif);
Modification mod = new Modification(_originalId: "phospho", _modificationType: "testModType", _target: motif, _chemicalFormula: ChemicalFormula.ParseFormula("H1 O3 P1"), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ DissociationType.HCD, new List <double> {
ChemicalFormula.ParseFormula("H3 O4 P1").MonoisotopicMass
} }
}, _locationRestriction: "Anywhere.");
List <Modification> modlist = new List <Modification> {
mod
};
DigestionParams digestionParams = new DigestionParams(
protease: "trypsin",
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var prot = new Protein("PEPTIDE", null, oneBasedModifications: new Dictionary <int, List <Modification> > {
{ 4, modlist }
});
var ye = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).ToList();
var peptideWithNeutralMassMod = ye.Where(v => v.AllModsOneIsNterminus.Count > 0).First();
var myModFragments = peptideWithNeutralMassMod.Fragment(DissociationType.HCD, FragmentationTerminus.Both).ToList();
HashSet <int> neutralMasses = new HashSet <int>(myModFragments.Select(m => (int)m.NeutralMass.ToMz(1)).ToList());
HashSet <int> expectedMasses = new HashSet <int> {
98, 227, 324, 407, 520, 635, 505, 618, 733, //b-ions with and without neutral loss
148, 263, 376, 459, 556, 685, 557, 654, 783, //y-ions with and without neutral loss
782
}; //molecular ion with neutral loss
Assert.That(neutralMasses.SetEquals(expectedMasses));
}
public static void TestPeptideWithSetModifications()
{
var prot = new Protein("M", null);
DigestionParams digestionParams = new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModsForPeptides: 3); // if you pass Custom Protease7 this test gets really flakey.
List <Modification> variableModifications = new List <Modification>();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
variableModifications.Add(new Modification(_originalId: "ProtNmod", _target: motif, _locationRestriction: "N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "pepNmod", _target: motif, _locationRestriction: "Peptide N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "resMod", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "PepCmod", _target: motif, _locationRestriction: "Peptide C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "ProtCmod", _target: motif, _locationRestriction: "C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
var ye = prot.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(3 * 2 * 3, ye.Count);
Assert.AreEqual("[H]M[H][H]", ye.Last().SequenceWithChemicalFormulas);
double m1 = 5 * GetElement("H").PrincipalIsotope.AtomicMass + Residue.ResidueMonoisotopicMass['M'] + GetElement("O").PrincipalIsotope.AtomicMass;
m1 = Math.Round(m1, 9, MidpointRounding.AwayFromZero);
double m2 = ye.Last().MonoisotopicMass;
double m3 = m1 - m2;
Assert.IsTrue(m3 < 1e-9);
}
public void TestInvalidModificationHash()
{
ModificationMotif.TryGetMotif("K", out ModificationMotif motif);
Modification m1 = new Modification(_originalId: "id1", _modificationType: "modificationType", _target: motif, _locationRestriction: "Anywhere.");
Modification m2 = new Modification(_originalId: "id1", _modificationType: "modificationType", _target: motif, _locationRestriction: "Anywhere.");
HashSet <Modification> mods = new HashSet <Modification>(new Modification[] { m1, m2 });
Assert.IsFalse(m1.ValidModification);
Assert.IsFalse(m2.ValidModification);
Assert.True(m1.Equals(m2));
Assert.AreEqual(1, mods.Count);
// test comparing invalid mods with null vs not-null MMs
m1 = new Modification(_originalId: "id1", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
m2 = new Modification(_originalId: "id1", _target: motif, _locationRestriction: "Anywhere.");
mods = new HashSet <Modification>(new Modification[] { m1, m2 });
Assert.IsFalse(m1.ValidModification);
Assert.IsFalse(m2.ValidModification);
Assert.False(m1.Equals(m2));
Assert.AreEqual(2, mods.Count);
// test comparing invalid mods with null vs not-null IDs
m1 = new Modification(_originalId: "id1", _target: motif, _locationRestriction: "Anywhere.");
m2 = new Modification(_target: motif, _locationRestriction: "Anywhere.");
mods = new HashSet <Modification>(new Modification[] { m1, m2 });
Assert.IsFalse(m1.ValidModification);
Assert.IsFalse(m2.ValidModification);
Assert.False(m1.Equals(m2));
Assert.AreEqual(2, mods.Count);
}
public static void TestDigestIndices()
{
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
ModificationMotif.TryGetMotif("R", out ModificationMotif motifR);
Modification modN = new Modification("myMod", null, "myModType", null, motifN, "Anywhere.", null, 10, null, null, null, null, null, null);
Modification modR = new Modification("myMod", null, "myModType", null, motifR, "Anywhere.", null, 10, null, null, null, null, null, null);
IDictionary <int, List <Modification> > modDict = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
modN
} },
{ 8, new List <Modification> {
modR
} }
};
var prot = new Protein("MNNNNKRRRRR", null, null, null, modDict, isDecoy: true);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 5, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var digestedList = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).ToList();
var ok1 = digestedList[1];
var ok2 = digestedList[3];
Assert.AreEqual(1, ok1.NumMods);
Assert.IsTrue(ok1.AllModsOneIsNterminus.ContainsKey(3));
Assert.AreEqual(1, ok2.NumMods);
Assert.IsTrue(ok2.AllModsOneIsNterminus.ContainsKey(3));
}
public static TheoreticalProteoform make_a_theoretical(string a, string d, double mass, ProteinWithGoTerms p, Dictionary <InputFile, Protein[]> dict)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("K", out motif);
string mod_title = "oxidation";
ModificationWithMass m = new ModificationWithMass(mod_title, new Tuple <string, string>("", mod_title), motif, ModificationSites.K, 1, new Dictionary <string, IList <string> >(), new List <double>(), new List <double>(), "");
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("ordered locus", "GENE")
}, new Dictionary <int, List <Modification> > {
{ 1, new List <Modification> {
m
} }
}, new int?[] { 0 }, new int?[] { 0 }, new string[] { "" }, "T2", "T3", true, false, new List <DatabaseReference> {
new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
})
}, new List <GoTerm> {
new GoTerm(new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
}))
});
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm(0, m)
});
return(new TheoreticalProteoform(a, d, new List <ProteinWithGoTerms> {
p
}, mass, 0, set, true, false, dict));
}
/// <summary>
/// Tests that a PeptideWithSetModifications object can be parsed correctly from a string, with mod info
/// </summary>
public static void TestReadPeptideFromString()
{
// set up the test
ModificationMotif.TryGetMotif("T", out ModificationMotif target);
Modification carbamidomethylOnC = new Modification(_originalId: "Carbamidomethyl on C", _modificationType: "Common Fixed", _target: target, _chemicalFormula: ChemicalFormula.ParseFormula("C2H3NO"));
string sequence = "HQVC[Common Fixed:Carbamidomethyl on C]TPGGTTIAGLC[Common Fixed:Carbamidomethyl on C]VMEEK";
// parse the peptide from the string
PeptideWithSetModifications peptide = new PeptideWithSetModifications(sequence, new Dictionary <string, Modification> {
{ carbamidomethylOnC.IdWithMotif, carbamidomethylOnC }
});
// test base sequence and full sequence
Assert.That(peptide.BaseSequence == "HQVCTPGGTTIAGLCVMEEK");
Assert.That(peptide.FullSequence == sequence);
// test peptide mass
Assert.That(Math.Round(peptide.MonoisotopicMass, 5) == 2187.01225);
// test mods (correct id, correct number of mods, correct location of mods)
Assert.That(peptide.AllModsOneIsNterminus.First().Value.IdWithMotif == "Carbamidomethyl on C");
Assert.That(peptide.AllModsOneIsNterminus.Count == 2);
Assert.That(new HashSet <int>(peptide.AllModsOneIsNterminus.Keys).SetEquals(new HashSet <int>()
{
5, 16
}));
// calculate fragments. just check that they exist and it doesn't crash
List <Product> theoreticalFragments = new List <Product>();
peptide.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theoreticalFragments);
Assert.That(theoreticalFragments.Count > 0);
}
public static void XmlTest()
{
ModificationMotif.TryGetMotif("X", out ModificationMotif motif);
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", "mt", motif, TerminusLocalization.Any, null)
};
var ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"xml.xml"), true, DecoyType.Reverse, nice, false, null, out Dictionary <string, Modification> un);
Assert.AreEqual('M', ok[0][0]);
Assert.AreEqual('M', ok[1][0]);
Assert.AreEqual("P62805|H4_HUMAN|Histone H4", ok[0].FullDescription);
Assert.AreEqual("DECOY_P62805|H4_HUMAN|Histone H4", ok[1].FullDescription);
Assert.AreEqual("ENST00000244537", ok[0].DatabaseReferences.First(dbRef => dbRef.Type == "Ensembl").Id);
Assert.AreEqual("protein sequence ID", ok[0].DatabaseReferences.First(dbRef => dbRef.Type == "Ensembl").Properties.First().Item1);
Assert.AreEqual("ENSP00000244537", ok[0].DatabaseReferences.First(dbRef => dbRef.Type == "Ensembl").Properties.First().Item2);
Assert.AreEqual(42, ok[0].GeneNames.Count());
Assert.AreEqual(14, ok[0].GeneNames.Where(t => t.Item1 == "primary").Count());
Assert.AreEqual("HIST1H4A", ok[0].GeneNames.Where(t => t.Item1 == "primary").First().Item2);
Assert.AreEqual(23, ok[0].DatabaseReferences.Count(dbRef => dbRef.Type == "Ensembl"));
Assert.AreEqual(0, ok[0].DisulfideBonds.Count());
Assert.AreEqual(1, ok[0].SequenceVariations.Count());
Assert.AreEqual(1, ok[1].SequenceVariations.Count()); // decoys get the same sequence variations
Assert.AreEqual(64, ok[0].SequenceVariations.First().OneBasedBeginPosition);
Assert.AreEqual(64, ok[0].SequenceVariations.First().OneBasedEndPosition);
Assert.AreEqual(103 - 64 + 2, ok[1].SequenceVariations.First().OneBasedBeginPosition);
Assert.AreEqual(103 - 64 + 2, ok[1].SequenceVariations.First().OneBasedEndPosition);
Assert.AreNotEqual(ok[0].SequenceVariations.First().Description, ok[1].SequenceVariations.First().Description); //decoys and target variations don't have the same desc.
}
public static TheoreticalProteoform make_a_theoretical(string a, string d, double mass, ProteinWithGoTerms p, Dictionary <InputFile, Protein[]> dict)
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("X", out motif);
string mod_title = "oxidation";
Modification m = new Modification(mod_title, _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
ProteinWithGoTerms p1 = new ProteinWithGoTerms("MSSSSSSSSSSS", "T1", new List <Tuple <string, string> > {
new Tuple <string, string>("ordered locus", "GENE")
}, new Dictionary <int, List <Modification> > {
{ 1, new List <Modification> {
m
} }
}, new List <ProteolysisProduct> {
new ProteolysisProduct(1, 12, "")
}, "T2", "T3", true, false, new List <DatabaseReference> {
new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
})
}, new List <GoTerm> {
new GoTerm(new DatabaseReference("GO", ":", new List <Tuple <string, string> > {
new Tuple <string, string>("term", "P:")
}))
});
PtmSet set = new PtmSet(new List <Ptm> {
new Ptm(0, m)
});
return(new TheoreticalProteoform(a, d, p1.BaseSequence, new List <ProteinWithGoTerms> {
p
}, mass, 0, set, true, false, dict));
}
public static void SeqVarXmlTest()
{
ModificationMotif.TryGetMotif("X", out ModificationMotif motif);
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", "mt", motif, TerminusLocalization.Any, null)
};
var ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"seqvartests.xml"), true, DecoyType.Reverse, nice, false, null, out Dictionary <string, Modification> un);
Assert.AreEqual('M', ok[0][0]);
Assert.AreEqual('M', ok[1][0]);
List <SequenceVariation> seqvar0 = ok[0].SequenceVariations.ToList();
List <SequenceVariation> seqvar1 = ok[1].SequenceVariations.ToList();
Assert.AreEqual(seqvar0.Count + 1, seqvar1.Count);
Assert.AreEqual('M', ok[0].SequenceVariations.First().OriginalSequence[0]);
Assert.AreEqual('M', ok[0].SequenceVariations.First().VariantSequence[0]);
Assert.AreEqual('A', ok[1].SequenceVariations.First().OriginalSequence[0]);
Assert.AreEqual('P', ok[1].SequenceVariations.First().VariantSequence[0]);
Assert.AreEqual('M', seqvar0[1].OriginalSequence[0]);
Assert.AreEqual("", seqvar1[1].VariantSequence);
foreach (SequenceVariation s in seqvar0)
{
Assert.AreEqual(s.OriginalSequence, ok[0].BaseSequence.Substring(s.OneBasedBeginPosition - 1, s.OneBasedEndPosition - s.OneBasedBeginPosition + 1));
}
foreach (SequenceVariation s in seqvar1)
{
Assert.AreEqual(s.OriginalSequence, ok[1].BaseSequence.Substring(s.OneBasedBeginPosition - 1, s.OneBasedEndPosition - s.OneBasedBeginPosition + 1));
}
Assert.AreNotEqual(ok[0].SequenceVariations.First().Description, ok[1].SequenceVariations.First().Description); //decoys and target variations don't have the same desc.
}
public void Test_write_with_custom_mods()
{
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", null, null, ModificationSites.A, null, null)
};
ModificationMotif.TryGetMotif("K", out ModificationMotif motif);
ModificationWithMass m = new ModificationWithMass("mod", new Tuple <string, string>("", ""), motif, ModificationSites.Any, 1, new Dictionary <string, IList <string> >(), new List <double> {
-1
}, new List <double>(), "");
Dictionary <string, HashSet <Tuple <int, ModificationWithMass> > > new_mods = new Dictionary <string, HashSet <Tuple <int, ModificationWithMass> > >
{
{ "P53863", new HashSet <Tuple <int, ModificationWithMass> > {
new Tuple <int, ModificationWithMass>(2, m)
} }
};
List <Protein> ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"xml2.xml"), false, nice, false, null, out Dictionary <string, Modification> un);
var newModResEntries = ProteinDbWriter.WriteXmlDatabase(new_mods, ok, Path.Combine(TestContext.CurrentContext.TestDirectory, @"rewrite_xml2.xml"));
Assert.AreEqual(1, newModResEntries.Count);
List <Protein> ok2 = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"rewrite_xml2.xml"), false, nice, false, null, out un);
Assert.AreEqual(ok.Count, ok2.Count);
Assert.True(Enumerable.Range(0, ok.Count).All(i => ok[i].BaseSequence == ok2[i].BaseSequence));
Assert.AreEqual(2, ok[0].OneBasedPossibleLocalizedModifications.Count);
Assert.AreEqual(3, ok2[0].OneBasedPossibleLocalizedModifications.Count);
}
public static void DisulfideXmlTest()
{
ModificationMotif.TryGetMotif("X", out ModificationMotif motif);
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", "mt", motif, TerminusLocalization.Any, null)
};
var ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"disulfidetests.xml"), true, DecoyType.Reverse, nice, false, null, out Dictionary <string, Modification> un);
Assert.AreEqual('M', ok[0][0]);
Assert.AreEqual('M', ok[1][0]);
Assert.AreEqual(3, ok[0].DisulfideBonds.Count());
Assert.AreEqual(31, ok[0].DisulfideBonds.First().OneBasedBeginPosition);
Assert.AreEqual(94, ok[0].DisulfideBonds.First().OneBasedEndPosition);
Assert.AreEqual(93, ok[0].DisulfideBonds.ElementAt(2).OneBasedBeginPosition);
Assert.AreEqual(93, ok[0].DisulfideBonds.ElementAt(2).OneBasedEndPosition);
Assert.AreEqual(3, ok[1].DisulfideBonds.Count());
Assert.AreEqual(79, ok[1].DisulfideBonds.First().OneBasedBeginPosition);
Assert.AreEqual(16, ok[1].DisulfideBonds.First().OneBasedEndPosition);
Assert.AreEqual(17, ok[1].DisulfideBonds.ElementAt(2).OneBasedBeginPosition);
Assert.AreEqual(17, ok[1].DisulfideBonds.ElementAt(2).OneBasedEndPosition);
Assert.AreNotEqual(ok[0].DisulfideBonds.First().Description, ok[1].DisulfideBonds.First().Description); //decoys and target disulfide bonds don't have the same desc.
}
public void Test_modification4_hash_set()
{
ModificationMotif.TryGetMotif("K", out ModificationMotif motif);
ModificationWithMassAndCf m1 = new ModificationWithMassAndCf(null, new Tuple <string, string>("item1", "item2"), motif, ModificationSites.K, new ChemicalFormula(), 1.11111d, new Dictionary <string, IList <string> >(), new List <double> {
2.222222
}, new List <double> {
5.55555
}, "modificationType");
ModificationWithMassAndCf m2 = new ModificationWithMassAndCf(null, new Tuple <string, string>("item1", "item2"), motif, ModificationSites.K, new ChemicalFormula(), 1.11111d, new Dictionary <string, IList <string> >(), new List <double> {
2.222222
}, new List <double> {
5.55555
}, "modificationType");
m1.linksToOtherDbs.Add("key", new List <string> {
"value"
});
m2.linksToOtherDbs.Add("key", new List <string> {
"value"
});
HashSet <Modification> mods = new HashSet <Modification>(new Modification[] { m1, m2 });
Assert.AreEqual(1, mods.Count);
Assert.True(m1.Equals(m2));
}
public static void XmlTest_2entry()
{
ModificationMotif.TryGetMotif("X", out ModificationMotif motif);
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", "mt", motif, TerminusLocalization.Any, null)
};
var ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, @"xml2.xml"), true, DecoyType.Reverse, nice, false, null, out Dictionary <string, Modification> un);
Assert.True(ok.All(p => p.ProteolysisProducts.All(d => d.OneBasedBeginPosition == null || d.OneBasedBeginPosition > 0)));
Assert.True(ok.All(p => p.ProteolysisProducts.All(d => d.OneBasedEndPosition == null || d.OneBasedEndPosition <= p.Length)));
Assert.False(ok.All(p => p.BaseSequence.Contains(" ")));
Assert.False(ok.All(p => p.BaseSequence.Contains("\t")));
Assert.False(ok.All(p => p.BaseSequence.Contains("\n")));
//GoTerm checks
List <Protein> targets = ok.Where(p => !p.IsDecoy).ToList();
Assert.AreEqual(2, targets.Count);
Assert.AreEqual(1, targets[0].DatabaseReferences.Count(dbRef => dbRef.Type == "EnsemblFungi"));
Assert.AreEqual(1, targets[1].DatabaseReferences.Count(dbRef => dbRef.Type == "EnsemblFungi"));
}
public static Modification OGlycanToModification(Glycan glycan)
{
//TO THINK: what the neutralLoss for O-Glyco?
Dictionary <DissociationType, List <double> > neutralLosses = new Dictionary <DissociationType, List <double> >();
if (glycan.Ions != null)
{
List <double> lossMasses = glycan.Ions.Select(p => (double)p.LossIonMass / 1E5).OrderBy(p => p).ToList();
neutralLosses.Add(DissociationType.HCD, lossMasses);
neutralLosses.Add(DissociationType.CID, lossMasses);
neutralLosses.Add(DissociationType.EThcD, lossMasses);
}
Dictionary <DissociationType, List <double> > diagnosticIons = new Dictionary <DissociationType, List <double> >();
diagnosticIons.Add(DissociationType.HCD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.CID, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
diagnosticIons.Add(DissociationType.EThcD, glycan.DiagnosticIons.Select(p => (double)p / 1E5).ToList());
ModificationMotif.TryGetMotif("X", out ModificationMotif finalMotif); //TO DO: only one motif can be write here.
var id = Glycan.GetKindString(glycan.Kind);
Modification modification = new Modification(
_originalId: id,
_modificationType: "O-Glycosylation",
_monoisotopicMass: (double)glycan.Mass / 1E5,
_locationRestriction: "Anywhere.",
_target: finalMotif,
_neutralLosses: neutralLosses,
_diagnosticIons: diagnosticIons
);
return(modification);
}
public static void TestLastPeaks()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
var prot = new Protein("MMMM", null, null, null, mods);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
PeptideWithSetModifications thePep = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).First();
var massArray = thePep.Fragment(DissociationType.HCD, FragmentationTerminus.Both).Select(p => p.NeutralMass).ToArray();
Array.Sort(massArray);
double[] intensities = new double[] { 1, 1, 1 };
double[] mz = new double[] { 1, 2, massArray[4].ToMz(1) };
MzSpectrum massSpectrum = new MzSpectrum(mz, intensities, false);
MsDataScan scan = new MsDataScan(massSpectrum, 1, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, null, null, "scan=1", 0, null, null, 0, null, DissociationType.Unknown, 1, null);
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 0, 1, null, new CommonParameters()) };
CommonParameters CommonParameters = new CommonParameters(
scoreCutoff: 1,
productMassTolerance: new PpmTolerance(5),
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: int.MaxValue,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain));
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <Modification>(), new List <Modification>(), null, new List <Protein> {
prot
}, new OpenSearchMode(), CommonParameters, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public static void GlyTest_ModificationSites()
{
PeptideWithSetModifications pep = new PeptideWithSetModifications("ELNPTPNVEVNVECR", null);
string[] motifs = new string[] { "Nxs", "Nxt" };
var sites = GlycoSpectralMatch.GetPossibleModSites(pep, motifs);
Assert.That(sites.Count() == 1 && sites[0] == 4);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "Carbamidomethyl of C", _modificationType: "Common Fixed", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 57.02146372068994);
ModificationMotif.TryGetMotif("N", out ModificationMotif motif2);
Modification mod2 = new Modification(_originalId: "Test of N", _modificationType: "Common Fixed", _target: motif2, _locationRestriction: "Anywhere.");
var testN = new PeptideWithSetModifications("C[Common Fixed:Carbamidomethyl of C]N[Common Fixed:Test of N]SSDQPKL[Common Fixed:Carbamidomethyl of C]NLSGIETP", new Dictionary <string, Modification> {
{ "Carbamidomethyl of C", mod1 }, { "Test of N", mod2 }
});
var testSites = GlycoSpectralMatch.GetPossibleModSites(testN, motifs);
Assert.That(testSites.Count() == 1 && testSites[0] == 11);
var testC = new PeptideWithSetModifications("TELAAYLSC[Common Fixed:Carbamidomethyl of C]NATK", new Dictionary <string, Modification> {
{ "Carbamidomethyl of C", mod1 }
});
var testCSites = GlycoSpectralMatch.GetPossibleModSites(testC, motifs);
Assert.That(testCSites.Count() == 1 && testSites[0] == 11);
}
public static void TestPeptideWithFixedModifications()
{
var prot = new Protein("M", null);
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
List <ModificationWithMass> fixedMods = new List <ModificationWithMass>();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
fixedMods.Add(new ModificationWithMassAndCf("ProtNmod", null, motif, TerminusLocalization.NProt, Chemistry.ChemicalFormula.ParseFormula("H"), GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new ModificationWithMassAndCf("PepNmod", null, motif, TerminusLocalization.NPep, Chemistry.ChemicalFormula.ParseFormula("H"), GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new ModificationWithMassAndCf("resMod", null, motif, TerminusLocalization.Any, Chemistry.ChemicalFormula.ParseFormula("H"), GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new ModificationWithMassAndCf("PepCmod", null, motif, TerminusLocalization.PepC, Chemistry.ChemicalFormula.ParseFormula("H"), GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new ModificationWithMassAndCf("ProtCmod", null, motif, TerminusLocalization.ProtC, Chemistry.ChemicalFormula.ParseFormula("H"), GetElement(1).PrincipalIsotope.AtomicMass));
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
var ok = prot.Digest(digestionParams, fixedMods, new List <ModificationWithMass>()).ToList();
Assert.AreEqual(1, ok.Count);
Assert.AreEqual("[:PepNmod]M[:resMod][:ProtCmod]", ok.Last().Sequence);
Assert.AreEqual("[H]M[H][H]", ok.Last().SequenceWithChemicalFormulas);
Assert.AreEqual(5 * GetElement("H").PrincipalIsotope.AtomicMass + Residue.ResidueMonoisotopicMass['M'] + GetElement("O").PrincipalIsotope.AtomicMass, ok.Last().MonoisotopicMass, 1e-9);
}
