public static void TestCombos()
{
List <PeptideSpectralMatch> allIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
ModificationMotif.TryGetMotif("P", out ModificationMotif motifP);
var gptmdModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", "mt", motifN, TerminusLocalization.Any, 21.981943, null),
new ModificationWithMass("16", "mt", motifP, TerminusLocalization.Any, 15.994915, null)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> > {
new Tuple <double, double>(21.981943, 15.994915)
};
Tolerance precursorMassTolerance = new PpmTolerance(10);
MsDataScan dfd = new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 0, 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=1", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(dfd, (651.297638557 + 21.981943 + 15.994915).ToMz(1), 1, "filepath");
var parentProtein = new Protein("NNNPPP", "accession");
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 5);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var modPep = parentProtein.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).First();
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch match = new PeptideSpectralMatch(peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), 0, 0, 0, scan, digestionParams);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), 0, 0, 0, scan, digestionParams);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
peptidesWithSetModifications.First()
} }
};
List <ProductType> lp = new List <ProductType> {
ProductType.B, ProductType.Y
};
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
match.MatchToProteinLinkedPeptides(matching);
match.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0, 0, false);
allIdentifications = new List <PeptideSpectralMatch> {
match
};
var engine = new GptmdEngine(allIdentifications, gptmdModifications, combos, new Dictionary <string, Tolerance> {
{ "filepath", precursorMassTolerance }
}, new CommonParameters(), new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(1, res.Mods.Count);
Assert.AreEqual(6, res.Mods["accession"].Count);
Assert.AreEqual(3, res.Mods["accession"].Where(b => b.Item2.id.Equals("21")).Count());
Assert.AreEqual(3, res.Mods["accession"].Where(b => b.Item2.id.Equals("16")).Count());
}
public static void TestGptmdEngine()
{
List <PeptideSpectralMatch> allResultingIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
var gptmdModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", "mt", motifN, TerminusLocalization.Any, 21.981943)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> >();
Tolerance precursorMassTolerance = new PpmTolerance(10);
allResultingIdentifications = new List <PeptideSpectralMatch>();
var engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, precursorMassTolerance, new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(0, res.Mods.Count);
//PsmParent newPsm = new TestParentSpectrumMatch(588.22520189093 + 21.981943);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MzmlScanWithPrecursor(0, new MzmlMzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null, null, "scan=1"), (588.22520189093 + 21.981943).ToMz(1), 1, null);
var parentProtein = new Protein("NNNNN", "accession");
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
DigestionParams digestionParams = new DigestionParams();
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var modPep = parentProtein.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).First();
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), 0, 0, 0, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
peptidesWithSetModifications.First()
} }
};
List <ProductType> lp = new List <ProductType> {
ProductType.B, ProductType.Y
};
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
newPsm.MatchToProteinLinkedPeptides(matching);
newPsm.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0, 0, false);
allResultingIdentifications.Add(newPsm);
engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, precursorMassTolerance, new List <string>());
res = (GptmdResults)engine.Run();
Assert.AreEqual(1, res.Mods.Count);
Assert.AreEqual(5, res.Mods["accession"].Count);
}
public static void TestGptmdEngine(string proteinSequence, string accession, string sequenceVariantDescription, int numModifiedResidues)
{
List <PeptideSpectralMatch> allResultingIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
var gptmdModifications = new List <Modification> {
new Modification(_originalId: "21", _modificationType: "mt", _target: motifN, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> >();
Tolerance precursorMassTolerance = new PpmTolerance(10);
allResultingIdentifications = new List <PeptideSpectralMatch>();
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", new CommonParameters()));
var engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, new Dictionary <string, Tolerance> {
{ "filepath", precursorMassTolerance }
}, new CommonParameters(), fsp, new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(0, res.Mods.Count);
var parentProtein = new Protein(proteinSequence, accession, sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(1, "N", "A", sequenceVariantDescription)
});
var variantProteins = parentProtein.GetVariantProteins();
CommonParameters commonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
List <Modification> variableModifications = new List <Modification>();
var modPep = variantProteins.SelectMany(p => p.Digest(commonParameters.DigestionParams, new List <Modification>(), variableModifications)).First();
//PsmParent newPsm = new TestParentSpectrumMatch(588.22520189093 + 21.981943);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 0, 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=1", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null), (new Proteomics.AminoAcidPolymer.Peptide(modPep.BaseSequence).MonoisotopicMass + 21.981943).ToMz(1), 1, "filepath", new CommonParameters());
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First(), 0, 0, 0, scan, commonParameters, new List <MatchedFragmentIon>());
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
newPsm.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0);
allResultingIdentifications.Add(newPsm);
engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, new Dictionary <string, Tolerance> {
{ "filepath", precursorMassTolerance }
}, new CommonParameters(), null, new List <string>());
res = (GptmdResults)engine.Run();
Assert.AreEqual(1, res.Mods.Count);
Assert.AreEqual(numModifiedResidues, res.Mods["accession"].Count);
}
public static void TestCombos(string proteinSequence, string accession, string variantAA, string sequenceVariantDescription, int numModHashes, int numModifiedResidues, int numModifiedResiduesN, int numModifiedResiduesP, int numModifiedResiduesNP)
{
List <PeptideSpectralMatch> allIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
ModificationMotif.TryGetMotif("P", out ModificationMotif motifP);
var gptmdModifications = new List <Modification> {
new Modification(_originalId: "21", _modificationType: "mt", _target: motifN, _locationRestriction: "Anywhere.", _monoisotopicMass: 21.981943),
new Modification(_originalId: "16", _modificationType: "mt", _target: motifP, _locationRestriction: "Anywhere.", _monoisotopicMass: 15.994915)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> > {
new Tuple <double, double>(21.981943, 15.994915)
};
Tolerance precursorMassTolerance = new PpmTolerance(10);
var parentProtein = new Protein(proteinSequence, accession, sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(1, "N", variantAA, sequenceVariantDescription)
});
var variantProteins = parentProtein.GetVariantProteins();
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 5);
List <Modification> variableModifications = new List <Modification>();
var modPep = variantProteins.SelectMany(p => p.Digest(digestionParams, new List <Modification>(), variableModifications)).First();
MsDataScan dfd = new MsDataScan(new MzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 0, 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=1", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(dfd, (new Proteomics.AminoAcidPolymer.Peptide(modPep.BaseSequence).MonoisotopicMass + 21.981943 + 15.994915).ToMz(1), 1, "filepath", new CommonParameters());
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch match = new PeptideSpectralMatch(peptidesWithSetModifications.First(), 0, 0, 0, scan, digestionParams, new List <MatchedFragmentIon>());
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First(), 0, 0, 0, scan, digestionParams, new List <MatchedFragmentIon>());
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
match.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0);
allIdentifications = new List <PeptideSpectralMatch> {
match
};
var engine = new GptmdEngine(allIdentifications, gptmdModifications, combos, new Dictionary <string, Tolerance> {
{ "filepath", precursorMassTolerance }
}, new CommonParameters(), new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(numModHashes, res.Mods.Count);
Assert.AreEqual(numModifiedResidues, res.Mods["accession"].Count);
Assert.AreEqual(numModifiedResiduesN, res.Mods["accession"].Where(b => b.Item2.OriginalId.Equals("21")).Count());
Assert.AreEqual(numModifiedResiduesP, res.Mods["accession"].Where(b => b.Item2.OriginalId.Equals("16")).Count());
res.Mods.TryGetValue("accession_N1P", out var hash);
Assert.AreEqual(numModifiedResiduesNP, (hash ?? new HashSet <Tuple <int, Modification> >()).Count);
}
