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 };
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) };
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 <ModificationWithMass>(), new List <ModificationWithMass>(), new List <ProductType>
{
ProductType.B, ProductType.Y
}, 1, DecoyType.Reverse, new List <DigestionParams> {
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, new OpenSearchMode(), 0, new List <string>());
cse.Run();
Assert.Less(globalPsms[0].Score, 2);
Assert.Greater(globalPsms[0].Score, 1);
}
public static void TestDeltaValues()
{
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, useDeltaScore: true, digestionParams: new DigestionParams(minPeptideLength: 5));
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
};
List <Modification> variableModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.ModificationType, b.IdWithMotif))).ToList();
List <Modification> fixedModifications = GlobalVariables.AllModsKnown.OfType <Modification>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.ModificationType, b.IdWithMotif))).ToList();
// Generate data for files
Protein TargetProtein1 = new Protein("TIDEANTHE", "accession1");
Protein TargetProtein2 = new Protein("TIDELVE", "accession2");
Protein TargetProtein3 = new Protein("TIDENIE", "accession3");
Protein TargetProteinLost = new Protein("PEPTIDEANTHE", "accession4");
Protein DecoyProteinFound = new Protein("PETPLEDQGTHE", "accessiond", isDecoy: true);
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
TargetProtein1.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein2.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein3.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
DecoyProteinFound.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0]
});
var proteinList = new List <Protein> {
TargetProtein1, TargetProtein2, TargetProtein3, TargetProteinLost, DecoyProteinFound
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//check better when using delta
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.None, CommonParameters, 30000, false, new List <FileInfo>(), new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
PeptideSpectralMatch[] allPsmsArrayModern = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArrayModern, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, massDiffAcceptor, 0, new List <string>()).Run();
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
FdrAnalysisResults fdrResultsModernDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassicDelta.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModernDelta.PsmsWithin1PercentFdr == 3);
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
//check worse when using score
FdrAnalysisResults fdrResultsClassic = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
FdrAnalysisResults fdrResultsModern = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassic.PsmsWithin1PercentFdr == 0);
Assert.IsTrue(fdrResultsModern.PsmsWithin1PercentFdr == 0);
//check that when delta is bad, we used the score
// Generate data for files
Protein DecoyProtein1 = new Protein("TLEDAGGTHE", "accession1d", isDecoy: true);
Protein DecoyProtein2 = new Protein("TLEDLVE", "accession2d", isDecoy: true);
Protein DecoyProtein3 = new Protein("TLEDNIE", "accession3d", isDecoy: true);
Protein DecoyProteinShiny = new Protein("GGGGGG", "accessionShinyd", isDecoy: true);
myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
TargetProtein1.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein2.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein3.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
DecoyProteinShiny.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
});
proteinList = new List <Protein>
{
TargetProtein1, DecoyProtein1,
TargetProtein2, DecoyProtein2,
TargetProtein3, DecoyProtein3,
DecoyProteinShiny,
};
listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//check no change when using delta
allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
CommonParameters = new CommonParameters(useDeltaScore: true, digestionParams: new DigestionParams(minPeptideLength: 5));
indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.None, CommonParameters, 30000, false, new List <FileInfo>(), new List <string>());
indexResults = (IndexingResults)indexEngine.Run();
massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
allPsmsArrayModern = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArrayModern, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, massDiffAcceptor, 0, new List <string>()).Run();
fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
fdrResultsModernDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassicDelta.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModernDelta.PsmsWithin1PercentFdr == 3);
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
//check no change when using score
fdrResultsClassic = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
fdrResultsModern = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassic.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModern.PsmsWithin1PercentFdr == 3);
}
public static void TestCompIons_ModernSearch()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("singleN4", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams(protease: protease.Name, minPeptideLength: 1), scoreCutoff: 1);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
CommonParameters withCompIons = new CommonParameters(digestionParams: new DigestionParams(protease: protease.Name, minPeptideLength: 1), scoreCutoff: 1, addCompIons: true);
var fspComp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fspComp.Add(("", CommonParameters));
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, null, null,
1, DecoyType.Reverse, CommonParameters, fsp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
// without complementary ions
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, CommonParameters, fsp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
// with complementary ions
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArray2, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, withCompIons, fspComp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.That(allPsmsArray[0] != null);
Assert.That(allPsmsArray2[0] != null);
Assert.IsTrue(allPsmsArray2[0].Score > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(allPsmsArray2[0].Score <= allPsmsArray[0].Score * 2 && allPsmsArray2[0].Score > allPsmsArray[0].Score + 3);
}
public static void AddCompIonsCommonParams()
{
CommonParameters cp = new CommonParameters(null, DissociationType.HCD, DissociationType.Unknown, DissociationType.Unknown, null, true, true, 3, 12, true, true, 1,
5, 200, 0.01, null, null, false, false, true, false, null, null, null, -1, null, null, null, 1, true, 4, 1);
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Test", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", cp));
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <SilacLabel>(), null, null,
1, DecoyType.Reverse, cp, fsp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(cp.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
// without complementary ions
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
var mse = new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, cp, fsp, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
}
public static void TestIndexEngine()
{
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, 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++;
}
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease p = new Protease("Custom Protease2", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(p.Name, p);
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, digestionParams: new DigestionParams(protease: p.Name, minPeptideLength: 1));
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.None, CommonParameters, 30000, false, new List <FileInfo>(), new List <string>());
var results = (IndexingResults)engine.Run();
Assert.AreEqual(5, results.PeptideIndex.Count);
var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(5, digestedList.Count);
foreach (PeptideWithSetModifications peptide in digestedList)
{
Assert.Contains(peptide, results.PeptideIndex);
var fragments = peptide.Fragment(CommonParameters.DissociationType, FragmentationTerminus.Both).ToList();
int positionInPeptideIndex = results.PeptideIndex.IndexOf(peptide);
foreach (Product fragment in fragments)
{
// mass of the fragment
double fragmentMass = fragment.NeutralMass;
int integerMassRepresentation = (int)Math.Round(fragmentMass * 1000);
// look up the peptides that have fragments with this mass
// the result of the lookup is a list of peptide IDs that have this fragment mass
List <int> fragmentBin = results.FragmentIndex[integerMassRepresentation];
// this list should contain this peptide!
Assert.Contains(positionInPeptideIndex, fragmentBin);
}
}
}
public static void TestIndexEngineLowRes()
{
var proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"indexEngineTestFasta.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var localizeableModifications = new List <Modification>();
Dictionary <Modification, ushort> modsDictionary = new Dictionary <Modification, 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++;
}
CommonParameters CommonParameters = new CommonParameters(dissociationType: DissociationType.LowCID, maxThreadsToUsePerFile: 1, scoreCutoff: 1, digestionParams: new DigestionParams(protease: "trypsin", minPeptideLength: 1));
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.Reverse, CommonParameters, 30000, false, new List <FileInfo>(), new List <string>());
var results = (IndexingResults)engine.Run();
Assert.AreEqual(10, results.PeptideIndex.Count);
var bubba = results.FragmentIndex;
var tooBubba = results.PrecursorIndex;
var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications).ToList();
digestedList.AddRange(proteinList[1].Digest(CommonParameters.DigestionParams, new List <Modification>(), variableModifications));
Assert.AreEqual(10, digestedList.Count);
foreach (PeptideWithSetModifications peptide in digestedList)
{
Assert.Contains(peptide, results.PeptideIndex);
var fragments = peptide.Fragment(CommonParameters.DissociationType, FragmentationTerminus.Both).ToList();
int positionInPeptideIndex = results.PeptideIndex.IndexOf(peptide);
foreach (Product fragment in fragments.Where(f => f.ProductType == ProductType.b || f.ProductType == ProductType.y))
{
// mass of the fragment
double fragmentMass = Math.Round(fragment.NeutralMass / 1.0005079, 0) * 1.0005079;
int integerMassRepresentation = (int)Math.Round(fragmentMass * 1000);
// look up the peptides that have fragments with this mass
// the result of the lookup is a list of peptide IDs that have this fragment mass
List <int> fragmentBin = results.FragmentIndex[integerMassRepresentation];
// this list should contain this peptide!
Assert.Contains(positionInPeptideIndex, fragmentBin);
}
}
foreach (var fdfd in digestedList)
{
Assert.Contains(fdfd, results.PeptideIndex);
}
}
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 TestCompIons_ModernSearch()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <ModificationWithMass>();
var fixedModifications = new List <ModificationWithMass>();
var localizeableModifications = new List <ModificationWithMass>();
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
foreach (var mod in fixedModifications)
{
modsDictionary.Add(mod, 0);
}
int ii = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)ii);
ii++;
}
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
SearchTarget = true,
};
CommonParameters CommonParameters = new CommonParameters
{
PrecursorMassTolerance = new PpmTolerance(5),
DigestionParams = new DigestionParams
{
Protease = new Protease("singleN", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null),
MinPeptideLength = null,
},
ConserveMemory = false,
ScoreCutoff = 1,
};
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <ProductType> {
ProductType.B, ProductType.Y
}, 1, DecoyType.Reverse, new List <IDigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, SearchParameters.MaxFragmentSize, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
bool DoPrecursorDeconvolution = true;
bool UseProvidedPrecursorInfo = true;
double DeconvolutionIntensityRatio = 4;
int DeconvolutionMaxAssumedChargeState = 10;
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArray, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, new List <ProductType> {
ProductType.B, ProductType.Y
}, 0, CommonParameters, SearchParameters.AddCompIons, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
SearchParameters.AddCompIons = true;
new ModernSearchEngine(allPsmsArray2, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, new List <ProductType> {
ProductType.B, ProductType.Y
}, 0, CommonParameters, SearchParameters.AddCompIons, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.That(allPsmsArray[0] != null);
Assert.That(allPsmsArray2[0] != null);
Assert.IsTrue(allPsmsArray2[0].Score > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(allPsmsArray2[0].Score <= allPsmsArray[0].Score * 2 && allPsmsArray2[0].Score > allPsmsArray[0].Score + 3);
}
public static void XlTest_BSA_DSSO()
{
//Generate parameters
var commonParameters = new CommonParameters(doPrecursorDeconvolution: false, dissociationType: DissociationType.EThcD,
scoreCutoff: 1, digestionParams: new DigestionParams(minPeptideLength: 5), precursorMassTolerance: new PpmTolerance(10));
var xlSearchParameters = new XlSearchParameters();
//Create databases contain two protein.
var proteinList = new List <Protein> {
new Protein("EKVLTSSAR", "Fake01"), new Protein("LSQKFPK", "Fake02")
};
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
Modification mod1 = new Modification(_originalId: "Oxidation of M", _modificationType: "Common Variable", _target: motif1, _locationRestriction: "Anywhere.", _monoisotopicMass: 15.99491461957);
ModificationMotif.TryGetMotif("C", out ModificationMotif motif2);
Modification mod2 = new Modification(_originalId: "Carbamidomethyl of C", _modificationType: "Common Fixed", _target: motif2, _locationRestriction: "Anywhere.", _monoisotopicMass: 57.02146372068994);
var variableModifications = new List <Modification>()
{
mod1
};
var fixedModifications = new List <Modification>()
{
mod2
};
var localizeableModifications = new List <Modification>();
//Run index engine
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, 1, DecoyType.Reverse, commonParameters, 30000, false, new List <FileInfo>(), new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
var indexedFragments = indexResults.FragmentIndex.Where(p => p != null).SelectMany(v => v).ToList();
Assert.AreEqual(82, indexedFragments.Count);
Assert.AreEqual(3, indexResults.PeptideIndex.Count);
//Get MS2 scans.
var myMsDataFile = new XLTestDataFile();
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
//Generate crosslinker, which is DSSO here.
Crosslinker crosslinker = GlobalVariables.Crosslinkers.Where(p => p.CrosslinkerName == "DSSO").First();
CrosslinkSpectralMatch[] possiblePsms = new CrosslinkSpectralMatch[listOfSortedms2Scans.Length];
new CrosslinkSearchEngine(possiblePsms, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, 0, commonParameters, crosslinker, xlSearchParameters.RestrictToTopNHits, xlSearchParameters.CrosslinkSearchTopNum, xlSearchParameters.XlQuench_H2O, xlSearchParameters.XlQuench_NH2, xlSearchParameters.XlQuench_Tris, new List <string> {
}).Run();
var newPsms = possiblePsms.Where(p => p != null).ToList();
foreach (var item in newPsms)
{
item.SetFdrValues(0, 0, 0, 0, 0, 0, 0, 0, 0, false);
}
//Test newPsms
Assert.AreEqual(3, newPsms.Count);
//Test Output
var task = new XLSearchTask();
task.WritePepXML_xl(newPsms, proteinList, null, variableModifications, fixedModifications, null, TestContext.CurrentContext.TestDirectory, "pep.XML", new List <string> {
});
//Test PsmCross.XlCalculateTotalProductMasses
//var psmCrossAlpha = new CrosslinkSpectralMatch(digestedList[1], 0, 0, 0, listOfSortedms2Scans[0], commonParameters.DigestionParams, new List<MatchedFragmentIon>());
//var psmCrossBeta = new CrosslinkSpectralMatch(digestedList[2], 0, 0, 0, listOfSortedms2Scans[0], commonParameters.DigestionParams, new List<MatchedFragmentIon>());
//var linkPos = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), digestedList[1]);
//var productMassesAlphaList = CrosslinkedPeptide.XlGetTheoreticalFragments(DissociationType.EThcD, false, crosslinker, linkPos, digestedList[2].MonoisotopicMass, digestedList[1]);
//Assert.AreEqual(productMassesAlphaList.First().Value.Count, 50); //TO DO: The number here should be manually verified.
File.Delete(@"singlePsms.tsv");
File.Delete(@"pep.XML.pep.xml");
File.Delete(@"allPsms.tsv");
}
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);
}
public static void TestDeltaValues()
{
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, useDeltaScore: true, digestionParams: new DigestionParams(minPeptideLength: 5));
SearchParameters SearchParameters = new SearchParameters
{
MassDiffAcceptorType = MassDiffAcceptorType.Exact,
};
List <ModificationWithMass> variableModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsVariable.Contains((b.modificationType, b.id))).ToList();
List <ModificationWithMass> fixedModifications = GlobalVariables.AllModsKnown.OfType <ModificationWithMass>().Where(b => CommonParameters.ListOfModsFixed.Contains((b.modificationType, b.id))).ToList();
// Generate data for files
Protein TargetProtein1 = new Protein("TIDEANTHE", "accession1");
Protein TargetProtein2 = new Protein("TIDELVE", "accession2");
Protein TargetProtein3 = new Protein("TIDENIE", "accession3");
Protein TargetProteinLost = new Protein("PEPTIDEANTHE", "accession4");
Protein DecoyProteinFound = new Protein("PETPLEDQGTHE", "accessiond", isDecoy: true);
MsDataFile myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
TargetProtein1.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein2.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein3.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
DecoyProteinFound.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0]
});
var proteinList = new List <Protein> {
TargetProtein1, TargetProtein2, TargetProtein3, TargetProteinLost, DecoyProteinFound
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
bool DoPrecursorDeconvolution = true;
bool UseProvidedPrecursorInfo = true;
double DeconvolutionIntensityRatio = 4;
int DeconvolutionMaxAssumedChargeState = 10;
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//check better when using delta
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, new List <ProductType> {
ProductType.B, ProductType.Y
}, searchModes, CommonParameters, new List <string>()).Run();
var indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <ProductType>
{
ProductType.B, ProductType.Y
}, 1, DecoyType.None, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var indexResults = (IndexingResults)indexEngine.Run();
MassDiffAcceptor massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
PeptideSpectralMatch[] allPsmsArrayModern = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArrayModern, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, new List <ProductType> {
ProductType.B, ProductType.Y
}, 0, CommonParameters, massDiffAcceptor, 0, new List <string>()).Run();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > compactPeptideToProteinPeptideMatching =
new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >();
if (proteinList.Any())
{
SequencesToActualProteinPeptidesEngine sequencesToActualProteinPeptidesEngine = new SequencesToActualProteinPeptidesEngine(allPsmsArray.ToList(), proteinList, fixedModifications, variableModifications, new List <ProductType>
{
ProductType.B, ProductType.Y
}, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, CommonParameters, new List <string>());
var res = (SequencesToActualProteinPeptidesEngineResults)sequencesToActualProteinPeptidesEngine.Run();
compactPeptideToProteinPeptideMatching = res.CompactPeptideToProteinPeptideMatching;
}
foreach (var psm in allPsmsArray)
{
psm.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
foreach (var psm in allPsmsArrayModern)
{
psm.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
FdrAnalysisResults fdrResultsModernDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassicDelta.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModernDelta.PsmsWithin1PercentFdr == 3);
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
//check worse when using score
FdrAnalysisResults fdrResultsClassic = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
FdrAnalysisResults fdrResultsModern = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassic.PsmsWithin1PercentFdr == 0);
Assert.IsTrue(fdrResultsModern.PsmsWithin1PercentFdr == 0);
//check that when delta is bad, we used the score
// Generate data for files
Protein DecoyProtein1 = new Protein("TLEDAGGTHE", "accession1d", isDecoy: true);
Protein DecoyProtein2 = new Protein("TLEDLVE", "accession2d", isDecoy: true);
Protein DecoyProtein3 = new Protein("TLEDNIE", "accession3d", isDecoy: true);
Protein DecoyProteinShiny = new Protein("GGGGGG", "accessionShinyd", isDecoy: true);
myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications>
{
TargetProtein1.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein2.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
TargetProtein3.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
DecoyProteinShiny.Digest(CommonParameters.DigestionParams, fixedModifications, variableModifications).ToList()[0],
});
proteinList = new List <Protein>
{
TargetProtein1, DecoyProtein1,
TargetProtein2, DecoyProtein2,
TargetProtein3, DecoyProtein3,
DecoyProteinShiny,
};
listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, DoPrecursorDeconvolution, UseProvidedPrecursorInfo, DeconvolutionIntensityRatio, DeconvolutionMaxAssumedChargeState, DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
//check no change when using delta
allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, new List <ProductType> {
ProductType.B, ProductType.Y
}, searchModes, CommonParameters, new List <string>()).Run();
CommonParameters = new CommonParameters(useDeltaScore: true, digestionParams: new DigestionParams(minPeptideLength: 5));
indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <ProductType>
{
ProductType.B, ProductType.Y
}, 1, DecoyType.None, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
indexResults = (IndexingResults)indexEngine.Run();
massDiffAcceptor = SearchTask.GetMassDiffAcceptor(CommonParameters.PrecursorMassTolerance, SearchParameters.MassDiffAcceptorType, SearchParameters.CustomMdac);
allPsmsArrayModern = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ModernSearchEngine(allPsmsArrayModern, listOfSortedms2Scans, indexResults.PeptideIndex, indexResults.FragmentIndex, new List <ProductType> {
ProductType.B, ProductType.Y
}, 0, CommonParameters, massDiffAcceptor, 0, new List <string>()).Run();
var compactPeptideToProteinPeptideMatching2 = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >();
if (proteinList.Any())
{
SequencesToActualProteinPeptidesEngine sequencesToActualProteinPeptidesEngine2 = new SequencesToActualProteinPeptidesEngine(allPsmsArray.ToList(), proteinList, fixedModifications, variableModifications, new List <ProductType> {
ProductType.B, ProductType.Y
}, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters.ReportAllAmbiguity, CommonParameters, new List <string>());
var res = (SequencesToActualProteinPeptidesEngineResults)sequencesToActualProteinPeptidesEngine2.Run();
compactPeptideToProteinPeptideMatching2 = res.CompactPeptideToProteinPeptideMatching;
}
foreach (var psm in allPsmsArray)
{
psm.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching2);
}
foreach (var psm in allPsmsArrayModern)
{
psm.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching2);
}
fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
fdrResultsModernDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassicDelta.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModernDelta.PsmsWithin1PercentFdr == 3);
CommonParameters = new CommonParameters(digestionParams: new DigestionParams(minPeptideLength: 5));
//check no change when using score
fdrResultsClassic = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.ToList(), 1, CommonParameters, new List <string>()).Run());
fdrResultsModern = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArrayModern.ToList(), 1, CommonParameters, new List <string>()).Run());
Assert.IsTrue(fdrResultsClassic.PsmsWithin1PercentFdr == 3);
Assert.IsTrue(fdrResultsModern.PsmsWithin1PercentFdr == 3);
}
private void GenerateIndexes(IndexingEngine indexEngine, List <DbForTask> dbFilenameList, ref List <CompactPeptide> peptideIndex, ref List <int>[] fragmentIndex, string taskId)
{
string pathToFolderWithIndices = GetExistingFolderWithIndices(indexEngine, dbFilenameList);
if (pathToFolderWithIndices == null)
{
var output_folderForIndices = GenerateOutputFolderForIndices(dbFilenameList);
Status("Writing params...", new List <string> {
taskId
});
var paramsFile = Path.Combine(output_folderForIndices, "indexEngine.params");
WriteIndexEngineParams(indexEngine, paramsFile);
FinishedWritingFile(paramsFile, new List <string> {
taskId
});
Status("Running Index Engine...", new List <string> {
taskId
});
var indexResults = (IndexingResults)indexEngine.Run();
peptideIndex = indexResults.PeptideIndex;
fragmentIndex = indexResults.FragmentIndex;
Status("Writing peptide index...", new List <string> {
taskId
});
var peptideIndexFile = Path.Combine(output_folderForIndices, "peptideIndex.ind");
WritePeptideIndex(peptideIndex, peptideIndexFile);
FinishedWritingFile(peptideIndexFile, new List <string> {
taskId
});
Status("Writing fragment index...", new List <string> {
taskId
});
var fragmentIndexFile = Path.Combine(output_folderForIndices, "fragmentIndex.ind");
WriteFragmentIndexNetSerializer(fragmentIndex, fragmentIndexFile);
FinishedWritingFile(fragmentIndexFile, new List <string> {
taskId
});
}
else
{
Status("Reading peptide index...", new List <string> {
taskId
});
var messageTypes = GetSubclassesAndItself(typeof(List <CompactPeptide>));
var ser = new NetSerializer.Serializer(messageTypes);
using (var file = File.OpenRead(Path.Combine(pathToFolderWithIndices, "peptideIndex.ind")))
{
peptideIndex = (List <CompactPeptide>)ser.Deserialize(file);
}
Status("Reading fragment index...", new List <string> {
taskId
});
messageTypes = GetSubclassesAndItself(typeof(List <int>[]));
ser = new NetSerializer.Serializer(messageTypes);
using (var file = File.OpenRead(Path.Combine(pathToFolderWithIndices, "fragmentIndex.ind")))
{
fragmentIndex = (List <int>[])ser.Deserialize(file);
}
}
}