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);
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
DigestionParams digestionParams = new DigestionParams
{
InitiatorMethionineBehavior = InitiatorMethionineBehavior.Retain,
MaxMissedCleavages = 2,
Protease = protease,
MinPeptideLength = 1
};
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.CrosslinkerModSite, 'K');
Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSite).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).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).ToArray();
Assert.AreEqual(x2[0], 4);
}
public static void XlTest_BSA_DSSO()
{
//Generate parameters
var commonParameters = new CommonParameters(doPrecursorDeconvolution: false, cIons: true, zDotIons: true, scoreCutoff: 2, digestionParams: new DigestionParams(minPeptideLength: 5));
var xlSearchParameters = new XlSearchParameters {
XlCharge_2_3_PrimeFragment = true
};
//Create databases contain two protein.
var proteinList = new List <Protein> {
new Protein("EKVLTSSAR", "Fake01"), new Protein("LSQKFPK", "Fake02")
};
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
ModificationWithMass mod1 = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif2);
ModificationWithMass mod2 = new ModificationWithMass("Carbamidomethyl of C", "Common Fixed", motif2, TerminusLocalization.Any, 57.02146372068994);
var variableModifications = new List <ModificationWithMass>()
{
mod1
};
var fixedModifications = new List <ModificationWithMass>()
{
mod2
};
var localizeableModifications = new List <ModificationWithMass>();
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y, ProductType.C, ProductType.Zdot
};
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
//Generate digested peptide lists.
List <PeptideWithSetModifications> digestedList = new List <PeptideWithSetModifications>();
foreach (var item in proteinList)
{
var digested = item.Digest(commonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
digestedList.AddRange(digested);
}
foreach (var fdfd in digestedList)
{
fdfd.CompactPeptide(TerminusType.None);
}
//Run index engine
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, lp, 1, DecoyType.Reverse, new List <DigestionParams>
{
commonParameters.DigestionParams
}, commonParameters, 30000, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var fragmentIndexCount = indexResults.FragmentIndex.Count(p => p != null);
var fragmentIndexAll = indexResults.FragmentIndex.Select((s, j) => new { j, s }).Where(p => p.s != null).Select(t => t.j).ToList();
Assert.IsTrue(fragmentIndexAll.Count() > 0);
//Get MS2 scans.
var myMsDataFile = new XLTestDataFile();
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, commonParameters.DoPrecursorDeconvolution, commonParameters.UseProvidedPrecursorInfo, commonParameters.DeconvolutionIntensityRatio, commonParameters.DeconvolutionMaxAssumedChargeState, commonParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//Generate crosslinker, which is DSSO here.
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(xlSearchParameters.CrosslinkerType);
//TwoPassCrosslinkSearchEngine.Run().
List <PsmCross> newPsms = new List <PsmCross>();
new TwoPassCrosslinkSearchEngine(newPsms, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, lp, 0, commonParameters, false, xlSearchParameters.XlPrecusorMsTl, crosslinker, xlSearchParameters.CrosslinkSearchTop, xlSearchParameters.CrosslinkSearchTopNum, xlSearchParameters.XlQuench_H2O, xlSearchParameters.XlQuench_NH2, xlSearchParameters.XlQuench_Tris, xlSearchParameters.XlCharge_2_3, xlSearchParameters.XlCharge_2_3_PrimeFragment, new List <string> {
}).Run();
var compactPeptideToProteinPeptideMatch = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >();
new CrosslinkAnalysisEngine(newPsms, compactPeptideToProteinPeptideMatch, proteinList, variableModifications, fixedModifications, lp, null, crosslinker, TerminusType.None, commonParameters, new List <string> {
}).Run();
foreach (var item in newPsms)
{
item.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
}
//Test newPsms
Assert.AreEqual(newPsms.Count(), 3);
//Test Output
var task = new XLSearchTask();
task.WriteAllToTsv(newPsms, TestContext.CurrentContext.TestDirectory, "allPsms", new List <string> {
});
task.WritePepXML_xl(newPsms, proteinList, null, variableModifications, fixedModifications, null, TestContext.CurrentContext.TestDirectory, "pep.XML", new List <string> {
});
task.WriteSingleToTsv(newPsms.Where(p => p.CrossType == PsmCrossType.Singe).ToList(), TestContext.CurrentContext.TestDirectory, "singlePsms", new List <string> {
});
//Test PsmCross.XlCalculateTotalProductMasses.
var psmCrossAlpha = new PsmCross(digestedList[1].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams);
var psmCrossBeta = new PsmCross(digestedList[2].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0], commonParameters.DigestionParams);
var linkPos = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker.CrosslinkerModSites);
var productMassesAlphaList = PsmCross.XlCalculateTotalProductMasses(psmCrossAlpha, psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass, crosslinker, lp, true, false, linkPos);
Assert.AreEqual(productMassesAlphaList[0].ProductMz.Length, 99);
}
public static void XlTestLocalization()
{
var CommonParameters = new CommonParameters();
var proteinList = new List <Protein> {
new Protein("CASIQKFGERLCVLHEKTPVSEK", null)
};
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
ModificationWithMass mod1 = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif2);
ModificationWithMass mod2 = new ModificationWithMass("Carbamidomethyl of C", "Common Fixed", motif2, TerminusLocalization.Any, 57.02146372068994);
var variableModifications = new List <ModificationWithMass>()
{
mod1
};
var fixedModifications = new List <ModificationWithMass>()
{
mod2
};
var localizeableModifications = new List <ModificationWithMass>();
var lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, lp, 1, DecoyType.Reverse, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var results = (IndexingResults)engine.Run();
var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList();
foreach (var fdfd in digestedList)
{
fdfd.CompactPeptide(TerminusType.None);
//Assert.Contains(fdfd.CompactPeptide(TerminusType.None), results.PeptideIndex);
}
var productMasses = digestedList[3].CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
});
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(CrosslinkerType.DSS);
var x = PsmCross.XlPosCal(digestedList[3].CompactPeptide(TerminusType.None), crosslinker).ToArray();
Assert.AreEqual(x[0], 5);
var myMsDataFile = new XLTestDataFile();
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, CommonParameters.DoPrecursorDeconvolution, CommonParameters.UseProvidedPrecursorInfo, CommonParameters.DeconvolutionIntensityRatio, CommonParameters.DeconvolutionMaxAssumedChargeState, CommonParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
var psmCrossAlpha = new PsmCross(digestedList[3].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0]);
var psmCrossBeta = new PsmCross(digestedList[5].CompactPeptide(TerminusType.None), 0, 0, i, listOfSortedms2Scans[0]);
var modMassAlpha1 = psmCrossBeta.compactPeptide.MonoisotopicMassIncludingFixedMods + crosslinker.TotalMass;
//Another method to calculate modification mass of cross-linked peptides
//var modMassAlpha2 = listOfSortedms2Scans[0].PrecursorMass - psmCrossAlpha.compactPeptide.MonoisotopicMassIncludingFixedMods;
var linkPos = PsmCross.XlPosCal(psmCrossAlpha.compactPeptide, crosslinker);
var productMassesAlphaList = PsmCross.XlCalculateTotalProductMasses(psmCrossAlpha, modMassAlpha1, crosslinker, lp, true, false, linkPos);
Assert.AreEqual(productMassesAlphaList[0].ProductMz.Length, 35);
Assert.AreEqual(productMassesAlphaList[0].ProductMz[26], 2312.21985342336);
}