public static void ParseSearchModeTest()
{
SearchTask searchTask = new SearchTask();
var result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom dot 5 ppm 0,1.0029,2.0052");
Assert.That(result.NumNotches == 3);
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom dot 5 da 0,1.0029,2.0052");
Assert.That(result.NumNotches == 3);
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom interval [0,5];[0,5]");
Assert.That(result.NumNotches == 1);
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom OpenSearch 5");
Assert.That(result.FileNameAddition.Equals("OpenSearch"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom daltonsAroundZero 5");
Assert.That(result.FileNameAddition.Equals("5daltonsAroundZero"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom ppmAroundZero 5");
Assert.That(result.FileNameAddition.Equals("5ppmAroundZero"));
Assert.That(() => SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "TestCustom Test 5"),
Throws.TypeOf <MetaMorpheusException>());
}
public static void MassDiffAceptorTest()
{
SearchTask searchTask = new SearchTask();
var result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, searchTask.SearchParameters.MassDiffAcceptorType, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("1mm"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.TwoMM, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("2mm"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.ThreeMM, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("3mm"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.ModOpen, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("-187andUp"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Open, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("OpenSearch"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Custom, "custom ppmAroundZero 4");
Assert.That(result.FileNameAddition.Equals("4ppmAroundZero"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.Exact, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("5ppmAroundZero"));
result = SearchTask.GetMassDiffAcceptor(searchTask.CommonParameters.PrecursorMassTolerance, MassDiffAcceptorType.PlusOrMinusThreeMM, searchTask.SearchParameters.CustomMdac);
Assert.That(result.FileNameAddition.Equals("PlusOrMinus3Da"));
}
public static void AddCompIonsCommonParams()
{
CommonParameters cp = new CommonParameters(null, DissociationType.HCD, DissociationType.Unknown, 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 indexEngine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <SilacLabel>(),
1, DecoyType.Reverse, cp, SearchParameters.MaxFragmentSize, false, new List <FileInfo>(), 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, massDiffAcceptor, SearchParameters.MaximumMassThatFragmentIonScoreIsDoubled, new List <string>()).Run();
}
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);
}
private void SaveButton_Click(object sender, RoutedEventArgs e)
{
CleavageSpecificity searchModeType = CleavageSpecificity.Full; //classic and modern by default
if (semiSpecificSearchRadioButton.IsChecked.Value) //semi
{
searchModeType = CleavageSpecificity.Semi;
}
else if (nonSpecificSearchRadioButton.IsChecked.Value) //non
{
searchModeType = CleavageSpecificity.None;
}
//else it's the default of full
if (searchModeType != CleavageSpecificity.Full)
{
if (((Protease)proteaseComboBox.SelectedItem).Name.Contains("non-specific"))
{
searchModeType = CleavageSpecificity.None; //prevents an accidental semi attempt of a non-specific protease
if (cTerminalIons.IsChecked.Value)
{
Protease singleC = ProteaseDictionary.Dictionary["singleC"];
proteaseComboBox.SelectedItem = singleC;
}
else //we're not allowing no ion types. It must have N if it doesn't have C.
{
Protease singleN = ProteaseDictionary.Dictionary["singleN"];
proteaseComboBox.SelectedItem = singleN;
}
}
if (!addCompIonCheckBox.IsChecked.Value)
{
MessageBox.Show("Warning: Complementary ions are strongly recommended when using this algorithm.");
}
//only use N or C termini, not both
if (cTerminalIons.IsChecked.Value)
{
nTerminalIons.IsChecked = false;
}
else
{
nTerminalIons.IsChecked = true;
}
}
if (!GlobalGuiSettings.CheckTaskSettingsValidity(precursorMassToleranceTextBox.Text, productMassToleranceTextBox.Text, missedCleavagesTextBox.Text,
maxModificationIsoformsTextBox.Text, MinPeptideLengthTextBox.Text, MaxPeptideLengthTextBox.Text, maxThreadsTextBox.Text, minScoreAllowed.Text,
peakFindingToleranceTextBox.Text, histogramBinWidthTextBox.Text, DeconvolutionMaxAssumedChargeStateTextBox.Text, NumberOfPeaksToKeepPerWindowTextBox.Text,
MinimumAllowedIntensityRatioToBasePeakTexBox.Text, WindowWidthThomsonsTextBox.Text, NumberOfWindowsTextBox.Text, numberOfDatabaseSearchesTextBox.Text, MaxModNumTextBox.Text, MaxFragmentMassTextBox.Text, QValueTextBox.Text))
{
return;
}
Protease protease = (Protease)proteaseComboBox.SelectedItem;
DissociationType dissociationType = GlobalVariables.AllSupportedDissociationTypes[dissociationTypeComboBox.SelectedItem.ToString()];
CustomFragmentationWindow.Close();
FragmentationTerminus fragmentationTerminus = FragmentationTerminus.Both;
if (nTerminalIons.IsChecked.Value && !cTerminalIons.IsChecked.Value)
{
fragmentationTerminus = FragmentationTerminus.N;
}
else if (!nTerminalIons.IsChecked.Value && cTerminalIons.IsChecked.Value)
{
fragmentationTerminus = FragmentationTerminus.C;
}
else if (!nTerminalIons.IsChecked.Value && !cTerminalIons.IsChecked.Value) //why would you want this
{
fragmentationTerminus = FragmentationTerminus.None;
MessageBox.Show("Warning: No ion types were selected. MetaMorpheus will be unable to search MS/MS spectra.");
}
//else both
int maxMissedCleavages = string.IsNullOrEmpty(missedCleavagesTextBox.Text) ? int.MaxValue : (int.Parse(missedCleavagesTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int minPeptideLengthValue = (int.Parse(MinPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int maxPeptideLengthValue = string.IsNullOrEmpty(MaxPeptideLengthTextBox.Text) ? int.MaxValue : (int.Parse(MaxPeptideLengthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture));
int MinVariantDepth = int.Parse(MinVariantDepthTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int MaxHeterozygousVariants = int.Parse(MaxHeterozygousVariantsTextBox.Text, NumberStyles.Any, CultureInfo.InvariantCulture);
int maxModificationIsoformsValue = (int.Parse(maxModificationIsoformsTextBox.Text, CultureInfo.InvariantCulture));
int maxModsForPeptideValue = (int.Parse(MaxModNumTextBox.Text, CultureInfo.InvariantCulture));
InitiatorMethionineBehavior initiatorMethionineBehavior = ((InitiatorMethionineBehavior)initiatorMethionineBehaviorComboBox.SelectedIndex);
DigestionParams digestionParamsToSave = new DigestionParams(
protease: protease.Name,
maxMissedCleavages: maxMissedCleavages,
minPeptideLength: minPeptideLengthValue,
maxPeptideLength: maxPeptideLengthValue,
maxModificationIsoforms: maxModificationIsoformsValue,
initiatorMethionineBehavior: initiatorMethionineBehavior,
maxModsForPeptides: maxModsForPeptideValue,
searchModeType: searchModeType,
fragmentationTerminus: fragmentationTerminus,
generateUnlabeledProteinsForSilac: CheckBoxQuantifyUnlabeledForSilac.IsChecked.Value);
Tolerance ProductMassTolerance;
if (productMassToleranceComboBox.SelectedIndex == 0)
{
ProductMassTolerance = new AbsoluteTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
ProductMassTolerance = new PpmTolerance(double.Parse(productMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
Tolerance PrecursorMassTolerance;
if (precursorMassToleranceComboBox.SelectedIndex == 0)
{
PrecursorMassTolerance = new AbsoluteTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
else
{
PrecursorMassTolerance = new PpmTolerance(double.Parse(precursorMassToleranceTextBox.Text, CultureInfo.InvariantCulture));
}
TheTask.SearchParameters.MaxFragmentSize = Double.Parse(MaxFragmentMassTextBox.Text, CultureInfo.InvariantCulture);
var listOfModsVariable = new List <(string, string)>();
foreach (var heh in VariableModTypeForTreeViewObservableCollection)
{
listOfModsVariable.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
var listOfModsFixed = new List <(string, string)>();
foreach (var heh in FixedModTypeForTreeViewObservableCollection)
{
listOfModsFixed.AddRange(heh.Children.Where(b => b.Use).Select(b => (b.Parent.DisplayName, b.ModName)));
}
if (!GlobalGuiSettings.VariableModCheck(listOfModsVariable))
{
return;
}
bool TrimMs1Peaks = trimMs1.IsChecked.Value;
bool TrimMsMsPeaks = trimMsMs.IsChecked.Value;
int?numPeaksToKeep = null;
if (int.TryParse(NumberOfPeaksToKeepPerWindowTextBox.Text, out int numberOfPeaksToKeeep))
{
numPeaksToKeep = numberOfPeaksToKeeep;
}
double?minimumAllowedIntensityRatioToBasePeak = null;
if (double.TryParse(MinimumAllowedIntensityRatioToBasePeakTexBox.Text, out double minimumAllowedIntensityRatio))
{
minimumAllowedIntensityRatioToBasePeak = minimumAllowedIntensityRatio;
}
double?windowWidthThompsons = null;
if (double.TryParse(WindowWidthThomsonsTextBox.Text, out double windowWidth))
{
windowWidthThompsons = windowWidth;
}
int?numberOfWindows = null;
if (int.TryParse(NumberOfWindowsTextBox.Text, out int numWindows))
{
numberOfWindows = numWindows;
}
bool normalizePeaksAccrossAllWindows = normalizePeaksInWindowCheckBox.IsChecked.Value;
bool parseMaxThreadsPerFile = !maxThreadsTextBox.Text.Equals("") && (int.Parse(maxThreadsTextBox.Text) <= Environment.ProcessorCount && int.Parse(maxThreadsTextBox.Text) > 0);
CommonParameters commonParamsToSave = new CommonParameters(
taskDescriptor: OutputFileNameTextBox.Text != "" ? OutputFileNameTextBox.Text : "SearchTask",
maxThreadsToUsePerFile: parseMaxThreadsPerFile ? int.Parse(maxThreadsTextBox.Text, CultureInfo.InvariantCulture) : new CommonParameters().MaxThreadsToUsePerFile,
useDeltaScore: deltaScoreCheckBox.IsChecked.Value,
reportAllAmbiguity: allAmbiguity.IsChecked.Value,
deconvolutionMaxAssumedChargeState: int.Parse(DeconvolutionMaxAssumedChargeStateTextBox.Text, CultureInfo.InvariantCulture),
totalPartitions: int.Parse(numberOfDatabaseSearchesTextBox.Text, CultureInfo.InvariantCulture),
doPrecursorDeconvolution: deconvolutePrecursors.IsChecked.Value,
useProvidedPrecursorInfo: useProvidedPrecursor.IsChecked.Value,
scoreCutoff: double.Parse(minScoreAllowed.Text, CultureInfo.InvariantCulture),
listOfModsFixed: listOfModsFixed,
listOfModsVariable: listOfModsVariable,
dissociationType: dissociationType,
precursorMassTolerance: PrecursorMassTolerance,
productMassTolerance: ProductMassTolerance,
digestionParams: digestionParamsToSave,
trimMs1Peaks: TrimMs1Peaks,
trimMsMsPeaks: TrimMsMsPeaks,
numberOfPeaksToKeepPerWindow: numPeaksToKeep,
minimumAllowedIntensityRatioToBasePeak: minimumAllowedIntensityRatioToBasePeak,
windowWidthThomsons: windowWidthThompsons,
numberOfWindows: numberOfWindows, //maybe change this some day
normalizePeaksAccrossAllWindows: normalizePeaksAccrossAllWindows, //maybe change this some day
addCompIons: addCompIonCheckBox.IsChecked.Value,
qValueOutputFilter: QValueCheckBox.IsChecked.Value ? double.Parse(QValueTextBox.Text, CultureInfo.InvariantCulture) : 1.0,
assumeOrphanPeaksAreZ1Fragments: protease.Name != "top-down",
minVariantDepth: MinVariantDepth,
maxHeterozygousVariants: MaxHeterozygousVariants);
if (classicSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Classic;
}
else if (modernSearchRadioButton.IsChecked.Value)
{
TheTask.SearchParameters.SearchType = SearchType.Modern;
}
else //both semi and nonspecific are termed "nonspecific", because they both contain at least one nonspecific cleavage and they share the same algorithm
{
TheTask.SearchParameters.SearchType = SearchType.NonSpecific;
}
TheTask.SearchParameters.DoParsimony = checkBoxParsimony.IsChecked.Value;
TheTask.SearchParameters.NoOneHitWonders = checkBoxNoOneHitWonders.IsChecked.Value;
TheTask.SearchParameters.DoQuantification = !checkBoxNoQuant.IsChecked.Value;
//SilacLabel deconvolution
{
if (StaticSilacLabelsObservableCollection.Count == 0)
{
TheTask.SearchParameters.SilacLabels = null;
}
else
{
List <Proteomics.SilacLabel> labelsToSave = new List <Proteomics.SilacLabel>();
foreach (SilacInfoForDataGrid info in StaticSilacLabelsObservableCollection)
{
Proteomics.SilacLabel labelToAdd = info.SilacLabel[0];
//This is needed to prevent double adding of additional labels.
//A quick test is to create a silac condition with two labels, save, reopen the task, save, and reopen again.
//Without this line, the second label will be doubled (K+8)&(R+10)&(R+10)
if (labelToAdd.AdditionalLabels != null)
{
labelToAdd.AdditionalLabels.Clear();
}
for (int infoIndex = 1; infoIndex < info.SilacLabel.Count; infoIndex++)
{
labelToAdd.AddAdditionalSilacLabel(info.SilacLabel[infoIndex]);
}
labelsToSave.Add(labelToAdd);
}
TheTask.SearchParameters.SilacLabels = labelsToSave;
}
}
TheTask.SearchParameters.Normalize = checkBoxNormalize.IsChecked.Value;
TheTask.SearchParameters.MatchBetweenRuns = checkBoxMatchBetweenRuns.IsChecked.Value;
TheTask.SearchParameters.ModPeptidesAreDifferent = modPepsAreUnique.IsChecked.Value;
TheTask.SearchParameters.QuantifyPpmTol = double.Parse(peakFindingToleranceTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.SearchTarget = checkBoxTarget.IsChecked.Value;
TheTask.SearchParameters.WriteMzId = ckbMzId.IsChecked.Value;
TheTask.SearchParameters.WriteDecoys = writeDecoyCheckBox.IsChecked.Value;
TheTask.SearchParameters.WriteContaminants = writeContaminantCheckBox.IsChecked.Value;
//TheTask.SearchParameters.OutPepXML = ckbPepXML.IsChecked.Value;
if (checkBoxDecoy.IsChecked.Value)
{
if (radioButtonReverseDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Reverse;
}
else //if (radioButtonSlideDecoy.IsChecked.Value)
{
TheTask.SearchParameters.DecoyType = DecoyType.Slide;
}
}
else
{
TheTask.SearchParameters.DecoyType = DecoyType.None;
}
if (massDiffAcceptExact.IsChecked.HasValue && massDiffAcceptExact.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Exact;
}
if (massDiffAccept1mm.IsChecked.HasValue && massDiffAccept1mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.OneMM;
}
if (massDiffAccept2mm.IsChecked.HasValue && massDiffAccept2mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.TwoMM;
}
if (massDiffAccept3mm.IsChecked.HasValue && massDiffAccept3mm.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ThreeMM;
}
if (massDiffAccept187.IsChecked.HasValue && massDiffAccept187.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.ModOpen;
}
if (massDiffAcceptOpen.IsChecked.HasValue && massDiffAcceptOpen.IsChecked.Value)
{
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Open;
}
if (massDiffAcceptCustom.IsChecked.HasValue && massDiffAcceptCustom.IsChecked.Value)
{
try
{
MassDiffAcceptor customMassDiffAcceptor = SearchTask.GetMassDiffAcceptor(null, MassDiffAcceptorType.Custom, customkMdacTextBox.Text);
}
catch (Exception ex)
{
MessageBox.Show("Could not parse custom mass difference acceptor: " + ex.Message, "Error", MessageBoxButton.OK, MessageBoxImage.Error);
return;
}
TheTask.SearchParameters.MassDiffAcceptorType = MassDiffAcceptorType.Custom;
TheTask.SearchParameters.CustomMdac = customkMdacTextBox.Text;
}
//determine if semi or nonspecific with a specific protease.
if (searchModeType == CleavageSpecificity.Semi || protease.CleavageSpecificity == CleavageSpecificity.Semi)
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific, FdrCategory.SemiSpecific
};
}
else if (searchModeType == CleavageSpecificity.None && protease.CleavageSpecificity != CleavageSpecificity.None)
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific, FdrCategory.SemiSpecific, FdrCategory.NonSpecific
};
}
else
{
TheTask.SearchParameters.LocalFdrCategories = new List <FdrCategory> {
FdrCategory.FullySpecific
};
}
// displays warning if classic search is enabled with an open search mode
if (TheTask.SearchParameters.SearchType == SearchType.Classic &&
(TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.ModOpen || TheTask.SearchParameters.MassDiffAcceptorType == MassDiffAcceptorType.Open))
{
MessageBoxResult result = MessageBox.Show("Modern Search mode is recommended when conducting open precursor mass searches to reduce search time.\n\n" +
"Continue anyway?", "Modern search recommended", MessageBoxButton.OKCancel);
if (result == MessageBoxResult.Cancel)
{
return;
}
}
TheTask.SearchParameters.DoHistogramAnalysis = checkBoxHistogramAnalysis.IsChecked.Value;
TheTask.SearchParameters.HistogramBinTolInDaltons = double.Parse(histogramBinWidthTextBox.Text, CultureInfo.InvariantCulture);
TheTask.SearchParameters.WritePrunedDatabase = writePrunedDBCheckBox.IsChecked.Value;
SetModSelectionForPrunedDB();
TheTask.CommonParameters = commonParamsToSave;
DialogResult = true;
}
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 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);
}
