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 CommonParameters(
string taskDescriptor = null,
bool bIons = true,
bool yIons = true,
bool zDotIons = false,
bool cIons = false,
bool doPrecursorDeconvolution = true,
bool useProvidedPrecursorInfo = true,
double deconvolutionIntensityRatio = 3,
int deconvolutionMaxAssumedChargeState = 12,
bool reportAllAmbiguity = true,
bool addCompIons = false,
int totalPartitions = 1,
double scoreCutoff = 5,
int topNpeaks = 200,
double minRatio = 0.01,
bool trimMs1Peaks = false,
bool trimMsMsPeaks = true,
bool useDeltaScore = false,
bool calculateEValue = false,
Tolerance productMassTolerance = null,
Tolerance precursorMassTolerance = null,
Tolerance deconvolutionMassTolerance = null,
int maxThreadsToUsePerFile = -1,
DigestionParams digestionParams = null,
IEnumerable <(string, string)> listOfModsVariable = null,
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));
}
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))));
}
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);
}
/// <summary>
/// Gets peptides for digestion of a protein
/// </summary>
public IEnumerable <PeptideWithSetModifications> Digest(DigestionParams digestionParams, IEnumerable <Modification> allKnownFixedModifications,
List <Modification> variableModifications)
{
ProteinDigestion digestion = new ProteinDigestion(digestionParams, allKnownFixedModifications, variableModifications);
return(digestionParams.SemiProteaseDigestion ? digestion.SemiSpecificDigestion(this) : digestion.Digestion(this));
}
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 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);
}
public static void TestAllNaN()
{
IDictionary <int, List <Modification> > mods = new Dictionary <int, List <Modification> >();
var prot = new Protein("XMMM", 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, 3, 4 };
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, 0, 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));
ClassicSearchEngine cse = new ClassicSearchEngine(globalPsms, arrayOfSortedMS2Scans, new List <Modification>(), new List <Modification>(), null, null, null, new List <Protein> {
prot
}, new OpenSearchMode(), CommonParameters, null, new List <string>());
cse.Run();
Assert.IsNull(globalPsms[0]);
}
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 void testingTMTonBigScan()
{
Dictionary <string, MsDataFile> MyMsDataFiles = new Dictionary <string, MsDataFile>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\tmt18test.mzML");
FilteringParams filter = new FilteringParams();
MyMsDataFiles[origDataFile] = Mzml.LoadAllStaticData(origDataFile, filter, 1);
var scans2 = MyMsDataFiles[origDataFile].GetAllScansList();
var trimmedScans = scans2.Where(m => m.MsnOrder == 3).ToList();
Protein p = new Protein("LAALNPESNTAGLDIFAK", "accession");
List <Modification> fixedModifications = new List <Modification>();
fixedModifications.AddRange(GlobalVariables.AllModsKnown);
List <Modification> tmt18Mods = fixedModifications.Where(m => m.ModificationType == "Multiplex Label" && m.IdWithMotif.Contains("TMT18")).ToList();
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
var aPeptideWithSetModifications = p.Digest(digestionParams, tmt18Mods, new List <Modification>()).First();
var theseTheoreticalFragments = new List <Product>();
aPeptideWithSetModifications.Fragment(DissociationType.HCD, FragmentationTerminus.Both, theseTheoreticalFragments);
theseTheoreticalFragments = theseTheoreticalFragments.Where(n => n.ProductType == ProductType.D).ToList();
double ppmTolerance = 20;
int roundTo = 5;
List <double> diagnosticIons = new List <double>();
for (int k = 0; k < theseTheoreticalFragments.Count(); k++)
{
diagnosticIons.Add(Math.Round(theseTheoreticalFragments[k].NeutralMass, roundTo));
}
int i = 460;
do
{
if (i == trimmedScans.Count())
{
break;
}
var massList = trimmedScans[i].MassSpectrum.XArray.ToList();
for (int j = 0; j < massList.Count(); j++)
{
massList[j] = Math.Round(massList[j], roundTo);
}
for (int l = 0; l < massList.Count(); l++)
{
for (int m = 0; m < diagnosticIons.Count(); m++)
{
double toleranceValue = ppmTolerance / Math.Pow(10, 6) * massList[l];
if ((massList[l] < diagnosticIons[m] + toleranceValue) & (massList[l] > diagnosticIons[m] - toleranceValue))
{
diagnosticIons.Remove(diagnosticIons[m]);
}
}
}
i++;
} while (diagnosticIons.Count() > 0);
Assert.AreEqual(0, diagnosticIons.Count());
}
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 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 void TestFragments()
{
// creates some test proteins, digest, and fragment
string[] sequences = { "GLSDGEWQQVLNVWGK" }; // just one peptide
var protease = new Protease("tryp", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
var peptides = new HashSet <PeptideWithSetModifications>();
var p = new List <Protein>();
for (int i = 0; i < sequences.Length; i++)
{
p.Add(new Protein(sequences[i], (i + 1).ToString()));
}
DigestionParams digestionParams = new DigestionParams();
foreach (var protein in p)
{
foreach (var peptide in protein.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()))
{
peptides.Add(peptide);
}
}
var CfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var ZdotfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var BfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var YfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var BYfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
foreach (var peptide in peptides)
{
CfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.C
}));
ZdotfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.Zdot
}));
BfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B
}));
YfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.Y
}));
BYfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}));
}
Assert.That(BfragmentMasses.TryGetValue(peptides.First(), out double[] testB));
Assert.That(YfragmentMasses.TryGetValue(peptides.First(), out double[] testY));
Assert.That(CfragmentMasses.TryGetValue(peptides.First(), out double[] testC));
Assert.That(ZdotfragmentMasses.TryGetValue(peptides.First(), out double[] testZ));
}
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 TestNonSpecific()
{
Protease p = ProteaseDictionary.Dictionary["non-specific"];
Protein prot = new Protein("MABCDEFGH", null);
DigestionParams digestionParams = new DigestionParams(protease: p.Name, maxMissedCleavages: 8, minPeptideLength: 1, maxPeptideLength: 9, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
Assert.AreEqual(1 + 2 + 3 + 4 + 5 + 6 + 7 + 8, prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).Count());
}
private readonly string ProteinAccession; // used to get protein object after deserialization
public InSilicoPeptide(Protein protein, DigestionParams digestionParams, int oneBasedStartResidueInProtein, int oneBasedEndResidueInProtein, CleavageSpecificity cleavageSpecificity,
string peptideDescription, int missedCleavages, Dictionary <int, Modification> allModsOneIsNterminus, int numFixedMods, string baseSeqeunce, bool isPeptideUnique) : base(protein, digestionParams, oneBasedStartResidueInProtein, oneBasedEndResidueInProtein,
cleavageSpecificity, peptideDescription, missedCleavages, allModsOneIsNterminus, numFixedMods, baseSeqeunce)
{
_allModsOneIsNterminus = allModsOneIsNterminus;
_digestionParams = digestionParams;
ProteinAccession = protein.Accession;
UniquePeptide = isPeptideUnique;
}
public void Test_FragmentationTwoModNeutralLossTwoFragTypes()
{
// Now we'll check the mass of modified peptide with no neutral losses
ModificationMotif.TryGetMotif("T", out ModificationMotif motif);
Dictionary <DissociationType, List <double> > myNeutralLosses = new Dictionary <DissociationType, List <double> >()
{
{ DissociationType.HCD, new List <double> {
ChemicalFormula.ParseFormula("H3 O4 P1").MonoisotopicMass
} },
{ DissociationType.ETD, new List <double>()
{
ChemicalFormula.ParseFormula("H3 N1").MonoisotopicMass
} } // this makes no sense in real life, it's just for a unit test
};
Modification mod = new Modification(_originalId: "phospho", _modificationType: "testModType", _target: motif, _chemicalFormula: ChemicalFormula.ParseFormula("H1 O3 P1"), _neutralLosses: myNeutralLosses, _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 == 1).First();
var myModFragmentsHCD = peptideWithNeutralMassMod.Fragment(DissociationType.HCD, FragmentationTerminus.Both);
var neutralMassesHCD = myModFragmentsHCD.Select(m => (int)m.NeutralMass.ToMz(1));
var expectedMassesHCD = 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(expectedMassesHCD.SetEquals(neutralMassesHCD));
//Now try the other half
var myModFragmentsETD = peptideWithNeutralMassMod.Fragment(DissociationType.ETD, FragmentationTerminus.Both);
var neutralMassesETD = myModFragmentsETD.Select(m => (int)m.NeutralMass.ToMz(1));
var expectedMassesETD = new HashSet <int> {
115, 244, 341, 505, 618, 733, 522, 635, 750, // c-ions and c-17 ions
148, 263, 376, 540, 637, 766, 557, 654, 783, // y and y-17 ions
133, 248, 361, 525, 622, 751, 542, 639, 768, // z+1 and z+1-17 ions
863
}; //Molecular ions minus ammonia
Assert.That(expectedMassesHCD.SetEquals(neutralMassesHCD));
}
public static void TestLocalization()
{
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.Last() as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >, pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, fragmentTolerance, new List <string>(), false);
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonDictOnlyMatches[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonDictOnlyMatches[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public static void TestPsmHeader()
{
DigestionParams digestionParams = new DigestionParams();
PeptideWithSetModifications pepWithSetMods = new Protein(
"MQQQQQQQ",
"accession1",
"org",
new List <Tuple <string, string> > {
new Tuple <string, string>("geneNameType", "geneName")
},
new Dictionary <int, List <Modification> > {
{ 2, new List <Modification> {
new Modification("mod", "mod")
} }
},
name: "name",
full_name: "fullName",
sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(2, "P", "Q", "changed this sequence")
})
.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).First();
MsDataFile myMsDataFile = new TestDataFile(pepWithSetMods, "quadratic");
MsDataScan scann = myMsDataFile.GetOneBasedScan(2);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(scann, 4, 1, null);
PeptideSpectralMatch psm = new PeptideSpectralMatch(pepWithSetMods.CompactPeptide(TerminusType.None), 1, 2, 3, scan, digestionParams);
var t = psm.ToString();
var tabsepheader = PeptideSpectralMatch.GetTabSeparatedHeader();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ pepWithSetMods.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
pepWithSetMods
} }
};
psm.MatchToProteinLinkedPeptides(matching);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
Tolerance fragmentTolerance = new PpmTolerance(10);
List <ProductType> lp = new List <ProductType> {
ProductType.B
};
new LocalizationEngine(new List <PeptideSpectralMatch> {
psm
}, lp, myMsDataFile, new CommonParameters(productMassTolerance: fragmentTolerance), new List <string>()).Run();
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
psm.SetFdrValues(6, 6, 6, 6, 6, 6, 0, 0, 0, true);
Assert.AreEqual(psm.ToString().Count(f => f == '\t'), PeptideSpectralMatch.GetTabSeparatedHeader().Count(f => f == '\t'));
}
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 XlTestXlPosCal()
{
var prot = new Protein("MNNNKQQQQ", null);
Protease protease = new Protease("New Custom Protease", new List <Tuple <string, TerminusType> > {
new Tuple <string, TerminusType>("K", TerminusType.C)
}, new List <Tuple <string, TerminusType> >(), CleavageSpecificity.Full, null, null, null);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(protease: protease.Name, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
var pep = ye[0];
Assert.AreEqual(pep.BaseSequence, "MNNNK");
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(CrosslinkerType.DSS);
Assert.AreEqual(crosslinker.CrosslinkerModSites, "K");
Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSites).MonoisotopicMass, 128.09496301518999, 1e-9);
var n = pep.CompactPeptide(TerminusType.None).NTerminalMasses;
var c = pep.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n.Count(), 4);
Assert.AreEqual(c.Count(), 4);
Assert.AreEqual(c[0], 128.09496301518999, 1e-6);
var x = PsmCross.XlPosCal(pep.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray();
Assert.AreEqual(x[0], 4);
var pep2 = ye[2];
Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence);
var n2 = pep2.CompactPeptide(TerminusType.None).NTerminalMasses;
var c2 = pep2.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n2.Count(), 8);
Assert.AreEqual(c2.Count(), 8);
Assert.AreEqual(n2[4] - n2[3], 128.09496301518999, 1e-6);
var x2 = PsmCross.XlPosCal(pep2.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray();
Assert.AreEqual(x2[0], 4);
//Test crosslinker with multiple types of mod
var protSTC = new Protein("GASTACK", null);
var peps = protSTC.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
var pepSTC = peps[0];
Assert.AreEqual(pepSTC.BaseSequence, "GASTACK");
CrosslinkerTypeClass crosslinker2 = new CrosslinkerTypeClass("ST", "C", "crosslinkerSTC", false, -18.01056, 0, 0, 0, 0, 0, 0);
string crosslinkerModSitesAll = new string((crosslinker2.CrosslinkerModSites + crosslinker2.CrosslinkerModSites2).ToCharArray().Distinct().ToArray());
Assert.AreEqual(crosslinkerModSitesAll, "STC");
}
public static void XlTestXlPosCal()
{
var prot = new Protein("MNNNKQQQQ", null);
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("New Custom Protease", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(protease: protease.Name, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications = new List <Modification>();
var ye = prot.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
var pep = ye[0];
Assert.AreEqual(pep.BaseSequence, "MNNNK");
Crosslinker crosslinker = GlobalVariables.Crosslinkers.Where(p => p.CrosslinkerName == "DSS").First();
Assert.AreEqual(crosslinker.CrosslinkerModSites, "K");
Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSites).MonoisotopicMass, 128.09496301518999, 1e-9);
var n = pep.Fragment(DissociationType.HCD, FragmentationTerminus.N);
var c = pep.Fragment(DissociationType.HCD, FragmentationTerminus.C);
Assert.AreEqual(n.Count(), 4);
Assert.AreEqual(c.Count(), 4);
Assert.AreEqual(c.First().NeutralMass, 146.10552769899999, 1e-6);
var x = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), pep).ToArray();
Assert.AreEqual(x[0], 5);
var pep2 = ye[2];
Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence);
var n2 = pep2.Fragment(DissociationType.HCD, FragmentationTerminus.N);
var c2 = pep2.Fragment(DissociationType.HCD, FragmentationTerminus.C);
Assert.AreEqual(n2.Count(), 8);
Assert.AreEqual(c2.Count(), 8);
var x2 = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), pep2).ToArray();
Assert.AreEqual(x2[0], 5);
//Test crosslinker with multiple types of mod
var protSTC = new Protein("GASTACK", null);
var peps = protSTC.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
var pepSTC = peps[0];
Assert.AreEqual(pepSTC.BaseSequence, "GASTACK");
Crosslinker crosslinker2 = new Crosslinker("ST", "C", "crosslinkerSTC", false, -18.01056, 0, 0, 0, 0, 0, 0);
string crosslinkerModSitesAll = new string((crosslinker2.CrosslinkerModSites + crosslinker2.CrosslinkerModSites2).ToCharArray().Distinct().ToArray());
Assert.AreEqual(crosslinkerModSitesAll, "STC");
}
public static void TestNoCleavage()
{
List <Modification> fixedModifications = new List <Modification>();
var prot = new Protein("MNNNKQQQQ", null, null, null, new Dictionary <int, List <Modification> >(), new List <ProteolysisProduct> {
new ProteolysisProduct(5, 6, "lala")
});
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 5);
var ye = prot.Digest(digestionParams, fixedModifications, new List <Modification>()).ToList();
Assert.AreEqual(3, ye.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 <ModificationWithMass>(), new List <ModificationWithMass>()).First();
var massArray = thePep.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
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 };
MzmlMzSpectrum massSpectrum = new MzmlMzSpectrum(mz, intensities, false);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > scan = new MzmlScanWithPrecursor(1, massSpectrum, 1, true, Polarity.Positive, 1, new MzRange(300, 2000), "", MZAnalyzerType.Unknown, massSpectrum.SumOfAllY, 0, null, null, 0, null, DissociationType.Unknown, 1, null, null, "scan=1");
PeptideSpectralMatch[] globalPsms = new PeptideSpectralMatch[1];
Ms2ScanWithSpecificMass[] arrayOfSortedMS2Scans = { new Ms2ScanWithSpecificMass(scan, 600, 1, null) };
CommonParameters CommonParameters = new CommonParameters
{
ProductMassTolerance = new PpmTolerance(5),
DigestionParams = new DigestionParams
{
MaxMissedCleavages = 0,
MinPeptideLength = null,
MaxModificationIsoforms = int.MaxValue,
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
},
ConserveMemory = false,
ScoreCutoff = 1
};
var indexEngine = new IndexingEngine(new List <Protein> {
prot
}, new List <ModificationWithMass>(), new List <ModificationWithMass>(), new List <ProductType> {
ProductType.B, ProductType.Y
}, 1, DecoyType.Reverse, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var cse = new ModernSearchEngine(globalPsms, arrayOfSortedMS2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, new List <ProductType> {
ProductType.B, ProductType.Y
}, 0, CommonParameters, false, new OpenSearchMode(), 0, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public static void TestLocalization()
{
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 1);
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.GetAllScansList().Last(), pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan, digestionParams);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
CommonParameters commonParameters = new CommonParameters(productMassTolerance: fragmentTolerance);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, commonParameters, new List <string>());
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonMassToChargeRatioDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonMassToChargeRatioDict[ProductType.Y].Count(b => b > 0));
Assert.AreEqual(0, newPsm.MatchedIonIntensitiesDict[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonIntensitiesDict[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
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);
}
public static void TestNoCleavage()
{
List <ModificationWithMass> fixedModifications = new List <ModificationWithMass>();
var prot = new Protein("MNNNKQQQQ", null, null, null, new Dictionary <int, List <Modification> >(), new List <ProteolysisProduct> {
new ProteolysisProduct(5, 6, "lala")
});
var protease = new Protease("Custom Protease", null, null, TerminusType.None, CleavageSpecificity.None, null, null, null);
DigestionParams digestionParams = new DigestionParams();
var ye = prot.Digest(digestionParams, fixedModifications, new List <ModificationWithMass>()).ToList();
Assert.AreEqual(3, ye.Count);
}
public static void TestNonSpecificProtease()
{
var empty = new List <Modification>();
DigestionParams myDigestionParams = new DigestionParams("non-specific", minPeptideLength: 1, maxMissedCleavages: 0);
// create a protein
Protein myProtein = new Protein("PRO", "myAccession");
// digest it into peptides
var myPeptides = myProtein.Digest(myDigestionParams, empty, empty).ToList();
Assert.AreEqual(myPeptides.Count(), 3);
}
