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);
}
private (List <PeptideSpectralMatch>, DataPointAquisitionResults) GetDataAcquisitionResults(IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile, string currentDataFile, List <ModificationWithMass> variableModifications, List <ModificationWithMass> fixedModifications, List <Protein> proteinList, string taskId, ICommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol)
{
var fileNameWithoutExtension = Path.GetFileNameWithoutExtension(currentDataFile);
MassDiffAcceptor searchMode;
if (initPrecTol is PpmTolerance)
{
searchMode = new SinglePpmAroundZeroSearchMode(initPrecTol.Value);
}
else
{
searchMode = new SingleAbsoluteAroundZeroSearchMode(initPrecTol.Value);
}
FragmentTypes fragmentTypesForCalibration = FragmentTypes.None;
if (combinedParameters.BIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.b;
}
if (combinedParameters.YIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.y;
}
if (combinedParameters.CIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.c;
}
if (combinedParameters.ZdotIons)
{
fragmentTypesForCalibration = fragmentTypesForCalibration | FragmentTypes.zdot;
}
var listOfSortedms2Scans = GetMs2Scans(myMsDataFile, currentDataFile, combinedParameters.DoPrecursorDeconvolution, combinedParameters.UseProvidedPrecursorInfo, combinedParameters.DeconvolutionIntensityRatio, combinedParameters.DeconvolutionMaxAssumedChargeState, combinedParameters.DeconvolutionMassTolerance).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
List <ProductType> lp = new List <ProductType>();
if (combinedParameters.BIons)
{
lp.Add(ProductType.B);
}
if (combinedParameters.YIons)
{
lp.Add(ProductType.Y);
}
if (combinedParameters.CIons)
{
lp.Add(ProductType.C);
}
if (combinedParameters.ZdotIons)
{
lp.Add(ProductType.Zdot);
}
Log("Searching with searchMode: " + searchMode, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
Log("Searching with productMassTolerance: " + initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, proteinList, lp, searchMode, false, combinedParameters, initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> allPsms = allPsmsArray.ToList();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > compactPeptideToProteinPeptideMatching = ((SequencesToActualProteinPeptidesEngineResults) new SequencesToActualProteinPeptidesEngine(allPsms, proteinList, fixedModifications, variableModifications, lp, new List <IDigestionParams> {
combinedParameters.DigestionParams
}, combinedParameters.ReportAllAmbiguity, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run()).CompactPeptideToProteinPeptideMatching;
foreach (var huh in allPsms)
{
if (huh != null)
{
huh.MatchToProteinLinkedPeptides(compactPeptideToProteinPeptideMatching);
}
}
allPsms = allPsms.Where(b => b != null).OrderByDescending(b => b.Score).ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue).GroupBy(b => (b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
new FdrAnalysisEngine(allPsms, searchMode.NumNotches, false, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.01 && !b.IsDecoy && b.FullSequence != null).ToList();
if (!goodIdentifications.Any())
{
Warn("No PSMs below 1% FDR observed!");
return(new List <PeptideSpectralMatch>(), null);
}
var dissociationTypes = MetaMorpheusEngine.DetermineDissociationType(lp);
foreach (var psm in allPsms)
{
var theScan = myMsDataFile.GetOneBasedScan(psm.ScanNumber);
double thePrecursorMass = psm.ScanPrecursorMass;
foreach (var huh in lp)
{
var ionMasses = psm.CompactPeptides.First().Key.ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
huh
});
Array.Sort(ionMasses);
List <double> matchedIonMassesList = new List <double>();
List <double> productMassErrorDaList = new List <double>();
List <double> productMassErrorPpmList = new List <double>();
LocalizationEngine.MatchIons(theScan, initProdTol, ionMasses, matchedIonMassesList, productMassErrorDaList, productMassErrorPpmList, thePrecursorMass, dissociationTypes, false);
double[] matchedIonMassesOnlyMatches = matchedIonMassesList.ToArray();
psm.MatchedIonDictOnlyMatches.Add(huh, matchedIonMassesOnlyMatches);
psm.ProductMassErrorDa.Add(huh, productMassErrorDaList.ToArray());
psm.ProductMassErrorPpm.Add(huh, productMassErrorPpmList.ToArray());
}
}
DataPointAquisitionResults currentResult = (DataPointAquisitionResults) new DataPointAcquisitionEngine(
goodIdentifications,
myMsDataFile,
initPrecTol,
initProdTol,
CalibrationParameters.NumFragmentsNeededForEveryIdentification,
CalibrationParameters.MinMS1IsotopicPeaksNeededForConfirmedIdentification,
CalibrationParameters.MinMS2IsotopicPeaksNeededForConfirmedIdentification,
fragmentTypesForCalibration,
new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
return(goodIdentifications, currentResult);
}
private DataPointAquisitionResults GetDataAcquisitionResults(MsDataFile myMsDataFile, string currentDataFile, List <Modification> variableModifications, List <Modification> fixedModifications, List <Protein> proteinList, string taskId, CommonParameters combinedParameters, Tolerance initPrecTol, Tolerance initProdTol)
{
var fileNameWithoutExtension = Path.GetFileNameWithoutExtension(currentDataFile);
MassDiffAcceptor searchMode = initPrecTol is PpmTolerance ?
(MassDiffAcceptor) new SinglePpmAroundZeroSearchMode(initPrecTol.Value) :
new SingleAbsoluteAroundZeroSearchMode(initPrecTol.Value);
var listOfSortedms2Scans = GetMs2Scans(myMsDataFile, currentDataFile, combinedParameters).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
Log("Searching with searchMode: " + searchMode, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
Log("Searching with productMassTolerance: " + initProdTol, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
});
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchMode, combinedParameters, FileSpecificParameters, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> allPsms = allPsmsArray.Where(b => b != null).ToList();
allPsms = allPsms.OrderByDescending(b => b.Score)
.ThenBy(b => b.PeptideMonisotopicMass.HasValue ? Math.Abs(b.ScanPrecursorMass - b.PeptideMonisotopicMass.Value) : double.MaxValue)
.GroupBy(b => (b.FullFilePath, b.ScanNumber, b.PeptideMonisotopicMass)).Select(b => b.First()).ToList();
new FdrAnalysisEngine(allPsms, searchMode.NumNotches, CommonParameters, FileSpecificParameters, new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
List <PeptideSpectralMatch> goodIdentifications = allPsms.Where(b => b.FdrInfo.QValueNotch < 0.001 && !b.IsDecoy && b.FullSequence != null).ToList();
if (!goodIdentifications.Any())
{
return(new DataPointAquisitionResults(null, new List <PeptideSpectralMatch>(), new List <LabeledDataPoint>(), new List <LabeledDataPoint>(), 0, 0, 0, 0));
}
//get the deconvoluted ms2scans for the good identifications
List <Ms2ScanWithSpecificMass> goodScans = new List <Ms2ScanWithSpecificMass>();
List <PeptideSpectralMatch> unfilteredPsms = allPsmsArray.ToList();
foreach (PeptideSpectralMatch psm in goodIdentifications)
{
goodScans.Add(listOfSortedms2Scans[unfilteredPsms.IndexOf(psm)]);
}
DataPointAquisitionResults currentResult = (DataPointAquisitionResults) new DataPointAcquisitionEngine(
goodIdentifications,
goodScans,
myMsDataFile,
initPrecTol,
initProdTol,
CalibrationParameters.MinMS1IsotopicPeaksNeededForConfirmedIdentification,
CommonParameters,
FileSpecificParameters,
new List <string> {
taskId, "Individual Spectra Files", fileNameWithoutExtension
}).Run();
return(currentResult);
}
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);
}
