public static void TestModificationAnalysis()
{
IScan scan = new ThisTestScan();
ModificationMotif.TryGetMotif("N", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "mod1", _modificationType: "myModType", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
ModificationMotif.TryGetMotif("L", out ModificationMotif motif2);
Modification mod2 = new Modification(_originalId: "mod2", _modificationType: "myModType", _target: motif2, _locationRestriction: "Anywhere.", _monoisotopicMass: 10);
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
mod1
} },
{ 5, new List <Modification> {
mod2
} },
{ 7, new List <Modification> {
mod1
} },
};
Protein protein1 = new Protein("MNLDLDNDL", "prot1", oneBasedModifications: oneBasedModifications);
Dictionary <int, Modification> allModsOneIsNterminus1 = new Dictionary <int, Modification>
{
{ 2, mod1 },
};
PeptideWithSetModifications pwsm1 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus1, 0);
Dictionary <int, Modification> allModsOneIsNterminus2 = new Dictionary <int, Modification>
{
{ 2, mod1 },
{ 7, mod1 },
};
PeptideWithSetModifications pwsm2 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus2, 0);
Dictionary <int, Modification> allModsOneIsNterminus3 = new Dictionary <int, Modification>
{
{ 7, mod1 },
};
PeptideWithSetModifications pwsm3 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus3, 0);
Dictionary <int, Modification> allModsOneIsNterminus4 = new Dictionary <int, Modification>
{
{ 8, mod1 },
};
PeptideWithSetModifications pwsm4 = new PeptideWithSetModifications(protein1, new DigestionParams(), 1, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus4, 0);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: int.MaxValue),
scoreCutoff: 1);
var newPsms = new List <PeptideSpectralMatch>
{
new PeptideSpectralMatch(pwsm1, 0, 10, 0, scan, CommonParameters.DigestionParams, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm1, 0, 10, 0, scan, CommonParameters.DigestionParams, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm2, 0, 10, 0, scan, CommonParameters.DigestionParams, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm3, 0, 10, 0, scan, CommonParameters.DigestionParams, new List <MatchedFragmentIon>()),
new PeptideSpectralMatch(pwsm4, 0, 10, 0, scan, CommonParameters.DigestionParams, new List <MatchedFragmentIon>()),
};
foreach (var psm in newPsms)
{
psm.ResolveAllAmbiguities();
}
MassDiffAcceptor searchMode = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = new List <Protein> {
protein1
};
FdrAnalysisEngine fdrAnalysisEngine = new FdrAnalysisEngine(newPsms, searchMode.NumNotches, CommonParameters, new List <string>());
fdrAnalysisEngine.Run();
ModificationAnalysisEngine modificationAnalysisEngine = new ModificationAnalysisEngine(newPsms, new CommonParameters(), new List <string>());
var res = (ModificationAnalysisResults)modificationAnalysisEngine.Run();
Assert.AreEqual(2, res.CountOfEachModSeenOnProteins.Count());
Assert.AreEqual(2, res.CountOfEachModSeenOnProteins[mod1.IdWithMotif]);
Assert.AreEqual(1, res.CountOfEachModSeenOnProteins[mod2.IdWithMotif]);
Assert.AreEqual(1, res.CountOfModsSeenAndLocalized.Count());
Assert.AreEqual(2, res.CountOfModsSeenAndLocalized[mod1.IdWithMotif]);
Assert.AreEqual(0, res.CountOfAmbiguousButLocalizedModsSeen.Count());
Assert.AreEqual(0, res.CountOfUnlocalizedMods.Count());
Assert.AreEqual(0, res.CountOfUnlocalizedFormulas.Count());
}
public static void TestModificationAnalysis()
{
IScan scan = new ThisTestScan();
ModificationMotif.TryGetMotif("N", out ModificationMotif motif1);
ModificationWithMass mod1 = new ModificationWithMass("mod1", null, motif1, TerminusLocalization.Any, 10);
ModificationMotif.TryGetMotif("L", out ModificationMotif motif2);
ModificationWithMass mod2 = new ModificationWithMass("mod2", null, motif2, TerminusLocalization.Any, 10);
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
mod1
} },
{ 5, new List <Modification> {
mod2
} },
{ 7, new List <Modification> {
mod1
} },
};
Protein protein1 = new Protein("MNLDLDNDL", "prot1", oneBasedModifications: oneBasedModifications);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus1 = new Dictionary <int, ModificationWithMass>
{
{ 2, mod1 },
};
PeptideWithSetModifications pwsm1 = new PeptideWithSetModifications(0, protein1, 2, 9, allModsOneIsNterminus1);
CompactPeptideBase pep1 = new CompactPeptide(pwsm1, TerminusType.None);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus2 = new Dictionary <int, ModificationWithMass>
{
{ 2, mod1 },
{ 7, mod1 },
};
PeptideWithSetModifications pwsm2 = new PeptideWithSetModifications(0, protein1, 2, 9, allModsOneIsNterminus2);
CompactPeptideBase pep2 = new CompactPeptide(pwsm2, TerminusType.None);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus3 = new Dictionary <int, ModificationWithMass>
{
{ 7, mod1 },
};
PeptideWithSetModifications pwsm3 = new PeptideWithSetModifications(0, protein1, 2, 9, allModsOneIsNterminus3);
CompactPeptideBase pep3 = new CompactPeptide(pwsm3, TerminusType.None);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus4 = new Dictionary <int, ModificationWithMass>
{
{ 8, mod1 },
};
PeptideWithSetModifications pwsm4 = new PeptideWithSetModifications(0, protein1, 1, 9, allModsOneIsNterminus4);
CompactPeptideBase pep4 = new CompactPeptide(pwsm4, TerminusType.None);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(
maxMissedCleavages: 0,
minPeptideLength: 1,
maxModificationIsoforms: int.MaxValue),
scoreCutoff: 1);
var newPsms = new List <PeptideSpectralMatch>
{
new PeptideSpectralMatch(pep1, 0, 10, 0, scan, CommonParameters.DigestionParams),
new PeptideSpectralMatch(pep1, 0, 10, 0, scan, CommonParameters.DigestionParams),
new PeptideSpectralMatch(pep2, 0, 10, 0, scan, CommonParameters.DigestionParams),
new PeptideSpectralMatch(pep3, 0, 10, 0, scan, CommonParameters.DigestionParams),
new PeptideSpectralMatch(pep4, 0, 10, 0, scan, CommonParameters.DigestionParams),
};
MassDiffAcceptor searchMode = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = new List <Protein> {
protein1
};
SequencesToActualProteinPeptidesEngine sequencesToActualProteinPeptidesEngine = new SequencesToActualProteinPeptidesEngine
(newPsms, proteinList, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <ProductType>
{
ProductType.B, ProductType.Y
}, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, CommonParameters, new List <string>());
var nice = (SequencesToActualProteinPeptidesEngineResults)sequencesToActualProteinPeptidesEngine.Run();
foreach (var psm in newPsms)
{
psm.MatchToProteinLinkedPeptides(nice.CompactPeptideToProteinPeptideMatching);
}
FdrAnalysisEngine fdrAnalysisEngine = new FdrAnalysisEngine(newPsms, searchMode.NumNotches, CommonParameters, new List <string>());
fdrAnalysisEngine.Run();
ModificationAnalysisEngine modificationAnalysisEngine = new ModificationAnalysisEngine(newPsms, new CommonParameters(), new List <string>());
var res = (ModificationAnalysisResults)modificationAnalysisEngine.Run();
Assert.AreEqual(2, res.AllModsOnProteins.Count());
Assert.AreEqual(2, res.AllModsOnProteins[mod1.id]);
Assert.AreEqual(1, res.AllModsOnProteins[mod2.id]);
Assert.AreEqual(1, res.ModsSeenAndLocalized.Count());
Assert.AreEqual(2, res.ModsSeenAndLocalized[mod1.id]);
Assert.AreEqual(0, res.AmbiguousButLocalizedModsSeen.Count());
Assert.AreEqual(0, res.UnlocalizedMods.Count());
Assert.AreEqual(0, res.UnlocalizedFormulas.Count());
}
public static void TestModificationAnalysisWithNonLocalizedPtms()
{
IScan scan = new ThisTestScan();
ModificationMotif.TryGetMotif("N", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "mod1", _modificationType: "mt", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 10, _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ MassSpectrometry.DissociationType.AnyActivationType, new List <double> {
10
} }
});
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
mod1
} },
{ 7, new List <Modification> {
mod1
} },
};
Protein protein1 = new Protein("MNLDLDNDL", "prot1", oneBasedModifications: oneBasedModifications);
Dictionary <int, Modification> allModsOneIsNterminus1 = new Dictionary <int, Modification>
{
{ 2, mod1 },
};
PeptideWithSetModifications pwsm1 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus1, 0);
Dictionary <int, Modification> allModsOneIsNterminus3 = new Dictionary <int, Modification>
{
{ 7, mod1 },
};
PeptideWithSetModifications pwsm2 = new PeptideWithSetModifications(protein1, new DigestionParams(), 2, 9, CleavageSpecificity.Unknown, null, 0, allModsOneIsNterminus3, 0);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1), scoreCutoff: 1);
PeptideSpectralMatch myPsm = new PeptideSpectralMatch(pwsm1, 0, 10, 0, scan, new DigestionParams(), new List <MatchedFragmentIon>());
myPsm.AddOrReplace(pwsm2, 10, 0, true, new List <MatchedFragmentIon>(), 0);
myPsm.ResolveAllAmbiguities();
MassDiffAcceptor searchMode = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = new List <Protein> {
protein1
};
FdrAnalysisEngine fdrAnalysisEngine = new FdrAnalysisEngine(new List <PeptideSpectralMatch> {
myPsm
}, searchMode.NumNotches, CommonParameters, new List <string>());
fdrAnalysisEngine.Run();
ModificationAnalysisEngine modificationAnalysisEngine = new ModificationAnalysisEngine(new List <PeptideSpectralMatch> {
myPsm
}, new CommonParameters(), new List <string>());
var res = (ModificationAnalysisResults)modificationAnalysisEngine.Run();
Assert.AreEqual(1, res.CountOfEachModSeenOnProteins.Count());
Assert.AreEqual(2, res.CountOfEachModSeenOnProteins[mod1.IdWithMotif]);
Assert.AreEqual(0, res.CountOfModsSeenAndLocalized.Count());
Assert.AreEqual(0, res.CountOfAmbiguousButLocalizedModsSeen.Count);
Assert.AreEqual(1, res.CountOfUnlocalizedMods[mod1.IdWithMotif]); // Saw it, but not sure where!
Assert.AreEqual(0, res.CountOfUnlocalizedFormulas.Count());
}
public static void TestModificationAnalysisWithNonLocalizedPtms()
{
IScan scan = new ThisTestScan();
ModificationMotif.TryGetMotif("N", out ModificationMotif motif1);
ModificationWithMass mod1 = new ModificationWithMass("mod1", "mt", motif1, TerminusLocalization.Any, 10, neutralLosses: new List <double> {
10
});
IDictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >
{
{ 2, new List <Modification> {
mod1
} },
{ 7, new List <Modification> {
mod1
} },
};
Protein protein1 = new Protein("MNLDLDNDL", "prot1", oneBasedModifications: oneBasedModifications);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus1 = new Dictionary <int, ModificationWithMass>
{
{ 2, mod1 },
};
PeptideWithSetModifications pwsm1 = new PeptideWithSetModifications(0, protein1, 2, 9, allModsOneIsNterminus1);
CompactPeptideBase pep1 = new CompactPeptide(pwsm1, TerminusType.None);
Dictionary <int, ModificationWithMass> allModsOneIsNterminus3 = new Dictionary <int, ModificationWithMass>
{
{ 7, mod1 },
};
PeptideWithSetModifications pwsm3 = new PeptideWithSetModifications(0, protein1, 2, 9, allModsOneIsNterminus3);
CompactPeptideBase pep3 = new CompactPeptide(pwsm3, TerminusType.None);
var newPsms = new List <PeptideSpectralMatch>
{
new PeptideSpectralMatch(pep1, 0, 10, 0, scan),
new PeptideSpectralMatch(pep3, 0, 10, 0, scan),
};
MassDiffAcceptor searchMode = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = new List <Protein> {
protein1
};
CommonParameters CommonParameters = new CommonParameters
{
DigestionParams = new DigestionParams
{
MinPeptideLength = null,
MaxMissedCleavages = 0,
MaxModificationIsoforms = int.MaxValue
},
ConserveMemory = false,
ScoreCutoff = 1,
};
SequencesToActualProteinPeptidesEngine sequencesToActualProteinPeptidesEngine = new SequencesToActualProteinPeptidesEngine(newPsms, proteinList, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <ProductType> {
ProductType.B, ProductType.Y
}, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, new List <string>());
var nice = (SequencesToActualProteinPeptidesEngineResults)sequencesToActualProteinPeptidesEngine.Run();
foreach (var psm in newPsms)
{
psm.MatchToProteinLinkedPeptides(nice.CompactPeptideToProteinPeptideMatching);
}
Assert.AreEqual(2, nice.CompactPeptideToProteinPeptideMatching[pep1].Count);
FdrAnalysisEngine fdrAnalysisEngine = new FdrAnalysisEngine(newPsms, searchMode.NumNotches, false, new List <string>());
fdrAnalysisEngine.Run();
ModificationAnalysisEngine modificationAnalysisEngine = new ModificationAnalysisEngine(newPsms, new List <string>());
var res = (ModificationAnalysisResults)modificationAnalysisEngine.Run();
Assert.AreEqual(1, res.AllModsOnProteins.Count());
Assert.AreEqual(2, res.AllModsOnProteins[mod1.id]);
Assert.AreEqual(0, res.ModsSeenAndLocalized.Count());
Assert.AreEqual(0, res.AmbiguousButLocalizedModsSeen.Count);
Assert.AreEqual(1, res.UnlocalizedMods[mod1.id]); // Saw it, but not sure where!
Assert.AreEqual(0, res.UnlocalizedFormulas.Count());
}
