public static void ExampleDigestion()
{
const string fastaFilePath = "Resources/yeast_uniprot_120226.fasta";
IProtease trypsin = Protease.GetProtease("Trypsin");
const int maxMissedCleavages = 3;
const int minPeptideLength = 5;
const int maxPeptideLength = 50;
List <double> masses = new List <double>();
Stopwatch watch = new Stopwatch();
watch.Start();
using (FastaReader reader = new FastaReader(fastaFilePath))
{
foreach (Protein protein in reader.ReadNextProtein())
{
foreach (Peptide peptide in protein.Digest(trypsin, maxMissedCleavages, minPeptideLength, maxPeptideLength))
{
masses.Add(peptide.MonoisotopicMass);
}
}
}
//Console.WriteLine("Average Peptide Mass = {0:F4}", masses.Average());
watch.Stop();
Console.WriteLine("Time elapsed: {0}", watch.Elapsed);
}
public void TestGetNumProteaseTermini()
{
Protease trypsin = new Protease("Trypsin", true, "KR", "P");
Assert.AreEqual(0, trypsin.GetNumProteaseTermini('M', "ABCDE", 'N', '-', 3));
Assert.AreEqual(1, trypsin.GetNumProteaseTermini('M', "ABCDE", 'N', '-', 2));
Assert.AreEqual(2, trypsin.GetNumProteaseTermini('M', "ABCDR", 'N', '-', 2));
}
public void InitiatorMethonineCleaved()
{
List <Peptide> peptides = _proteinA.Digest(Protease.GetProtease("LysC"), 1, initiatorMethonine: true).ToList();
Assert.Contains(new Peptide("MRGFK"), peptides);
Assert.Contains(new Peptide("MMRGFK"), peptides);
}
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>(), null, null,
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 ReadPepXml()
{
WritePepXml();
//string filePath = Path.Combine(Examples.BASE_DIRECTORY, "example.pepXML");
string filePath = @"E:\Desktop\test\27Nov2013_CEM_WellsProtein_CAD_filter.pep.xml";
Console.WriteLine("Reading from " + filePath);
using (PepXmlReader reader = new PepXmlReader(filePath))
{
Protease protease = reader.GetSampleProtease();
Console.WriteLine("Protease: " + protease);
Console.WriteLine();
List <Modification> fixedMods = reader.GetFixedModifications();
Console.WriteLine("==Fixed Modifications==");
foreach (Modification mod in fixedMods)
{
Console.WriteLine("\t" + mod);
}
Console.WriteLine();
List <Modification> varMods = reader.GetVariableModifications();
Console.WriteLine("==Variable Modifications==");
foreach (Modification mod in varMods)
{
Console.WriteLine("\t" + mod);
}
}
}
public static void WritePepXml()
{
string filePath = Path.Combine(Examples.BASE_DIRECTORY, "example.pepXML");
Console.WriteLine("Writting to " + filePath);
using (PepXmlWriter writer = new PepXmlWriter(filePath))
{
writer.WriteSampleProtease(Protease.GetProtease("Trypsin"));
writer.StartSearchSummary("OMSSA", true, true);
writer.WriteProteinDatabase("Resources/yeast_uniprot_120226.fasta");
writer.WriteSearchProtease(Protease.GetProtease("Trypsin"), 3);
writer.WriteModification(ModificationDictionary.GetModification("Acetyl"), ModificationSites.K | ModificationSites.NPep);
writer.WriteModification(ModificationDictionary.GetModification("CAM"), ModificationSites.C);
writer.WriteModification(ModificationDictionary.GetModification("Phospho"), ModificationSites.S | ModificationSites.T | ModificationSites.Y, false);
writer.SetCurrentStage(PepXmlWriter.Stage.Spectra, true);
writer.StartSpectrum(15, 1.234, 523.4324, 3);
PeptideSpectralMatch psm = new PeptideSpectralMatch(PeptideSpectralMatchScoreType.OmssaEvalue);
psm.Score = 1.5e-5;
Protein protein = new Protein("", "Test Protein");
psm.Peptide = new Peptide("DEREK", protein);
psm.Charge = 3;
writer.WritePSM(psm);
writer.EndSpectrum();
}
}
public void TrypsinDigestion()
{
List <Peptide> peptides = _proteinA.Digest(Protease.GetProtease("Trypsin")).ToList();
Peptide pepA = new Peptide("TTGSSSSSSSK");
Assert.Contains(pepA, peptides);
}
private void PopulateChoices()
{
foreach (Protease protease in ProteaseDictionary.Dictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
Protease trypsin = ProteaseDictionary.Dictionary["trypsin"];
proteaseComboBox.SelectedItem = trypsin;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
foreach (string dissassociationType in GlobalVariables.AllSupportedDissociationTypes.Keys)
{
dissociationTypeComboBox.Items.Add(dissassociationType);
}
productMassToleranceComboBox.Items.Add("Da");
productMassToleranceComboBox.Items.Add("ppm");
precursorMassToleranceComboBox.Items.Add("Da");
precursorMassToleranceComboBox.Items.Add("ppm");
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForGrid(hm.Key);
ModSelectionGridItems.Add(theModType);
}
ModSelectionGrid.ItemsSource = ModSelectionGridItems;
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
fixedModsTreeView.DataContext = FixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
variableModsTreeView.DataContext = VariableModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.Where(b => b.ValidModification == true).GroupBy(b => b.ModificationType))
{
LocalizeModTypeForTreeViewObservableCollection.Add(new ModTypeForLoc(hm.Key));
}
}
public static void ParsimonyLocalizeableTreatAsUnique()
{
bool modPeptidesAreUnique = true;
// set up mods
var modDictionary = new Dictionary <int, List <Modification> >();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif1);
var mod = new ModificationWithMass("Oxidation of M", "Common Variable", motif1, TerminusLocalization.Any, 15.99491461957);
TerminusType terminusType = ProductTypeMethod.IdentifyTerminusType(new List <ProductType> {
ProductType.B, ProductType.Y
});
var protease = new Protease("kprotease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
// modified version of protein
var protein1 = new Protein("PEPTIDEM", "accession1");
// unmodified version of protein
var protein2 = new Protein("YYYKPEPTIDEM", "accession2");
var pep1 = protein1.Digest(new DigestionParams {
MinPeptideLength = null, Protease = protease
}, new List <ModificationWithMass> {
mod
}, new List <ModificationWithMass>()).First();
var pep2 = protein2.Digest(new DigestionParams {
MinPeptideLength = null, Protease = protease
}, new List <ModificationWithMass>(), new List <ModificationWithMass>()).ToList()[1];
// check to make sure mod is present
Assert.That(pep1.Sequence != pep2.Sequence);
Assert.That(pep1.NumMods == 1);
Assert.That(pep2.NumMods == 0);
// build the dictionary for input to parsimony
var compactPeptideToProteinPeptideMatching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >();
compactPeptideToProteinPeptideMatching.Add(pep1.CompactPeptide(terminusType), new HashSet <PeptideWithSetModifications> {
pep1
});
compactPeptideToProteinPeptideMatching.Add(pep2.CompactPeptide(terminusType), new HashSet <PeptideWithSetModifications> {
pep2
});
// apply parsimony
ProteinParsimonyEngine pae = new ProteinParsimonyEngine(compactPeptideToProteinPeptideMatching, modPeptidesAreUnique, new List <string>());
pae.Run();
// check to make sure both peptides are NOT associated with both proteins
Assert.That(compactPeptideToProteinPeptideMatching.Count == 2);
foreach (var kvp in compactPeptideToProteinPeptideMatching)
{
Assert.That(kvp.Value.Count == 1);
}
}
public static void TestResolveAmbiguities()
{
Protease protease = new Protease("Custom Protease4", CleavageSpecificity.Full, null, null, new List <DigestionMotif> {
new DigestionMotif("K", null, 1, "")
});
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters_t = new CommonParameters(
dissociationType: MassSpectrometry.DissociationType.HCD,
digestionParams: new DigestionParams(
protease: protease.Name,
minPeptideLength: 1),
scoreCutoff: 1,
reportAllAmbiguity: true);
var fsp_t = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp_t.Add(("", CommonParameters_t));
CommonParameters CommonParameters_f = new CommonParameters(
dissociationType: MassSpectrometry.DissociationType.HCD,
digestionParams: new DigestionParams(
protease: protease.Name,
minPeptideLength: 1),
scoreCutoff: 1,
reportAllAmbiguity: false);
var fsp_f = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp_f.Add(("", CommonParameters_t));
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("MNNKNKNKQQQ", "Prot1"), new Protein("MNNNKQQQ", "Prot2")
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray_withAmbiguity = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
PeptideSpectralMatch[] allPsmsArray_withOutAmbiguity = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = false;
new ClassicSearchEngine(allPsmsArray_withAmbiguity, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters_t, fsp_t, null, new List <string>(), writeSpectralLibrary).Run(); //report all ambiguity TRUE
new ClassicSearchEngine(allPsmsArray_withOutAmbiguity, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, CommonParameters_f, fsp_f, null, new List <string>(), writeSpectralLibrary).Run(); //report all ambiguity FALSE
Assert.AreEqual("QQQ", allPsmsArray_withAmbiguity[0].BaseSequence);
Assert.AreEqual("QQQ", allPsmsArray_withOutAmbiguity[0].BaseSequence);
Assert.IsTrue(allPsmsArray_withAmbiguity[0].ProteinLength == null);
Assert.IsTrue(allPsmsArray_withOutAmbiguity[0].ProteinLength != null);
Assert.IsTrue(allPsmsArray_withAmbiguity[0].OneBasedStartResidueInProtein == null);
Assert.IsTrue(allPsmsArray_withOutAmbiguity[0].OneBasedStartResidueInProtein != null);
}
public static void TestFragments()
{
// creates some test proteins, digest, and fragment
string[] sequences = { "GLSDGEWQQVLNVWGK" }; // just one peptide
var protease = new Protease("tryp", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
var peptides = new HashSet <PeptideWithSetModifications>();
var p = new List <Protein>();
for (int i = 0; i < sequences.Length; i++)
{
p.Add(new Protein(sequences[i], (i + 1).ToString()));
}
DigestionParams digestionParams = new DigestionParams();
foreach (var protein in p)
{
foreach (var peptide in protein.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()))
{
peptides.Add(peptide);
}
}
var CfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var ZdotfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var BfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var YfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
var BYfragmentMasses = new Dictionary <PeptideWithSetModifications, double[]>();
foreach (var peptide in peptides)
{
CfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.C
}));
ZdotfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.Zdot
}));
BfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B
}));
YfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.Y
}));
BYfragmentMasses.Add(peptide, peptide.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> {
ProductType.B, ProductType.Y
}));
}
Assert.That(BfragmentMasses.TryGetValue(peptides.First(), out double[] testB));
Assert.That(YfragmentMasses.TryGetValue(peptides.First(), out double[] testY));
Assert.That(CfragmentMasses.TryGetValue(peptides.First(), out double[] testC));
Assert.That(ZdotfragmentMasses.TryGetValue(peptides.First(), out double[] testZ));
}
public static void TestCombos()
{
List <PeptideSpectralMatch> allIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
ModificationMotif.TryGetMotif("P", out ModificationMotif motifP);
var gptmdModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", "mt", motifN, TerminusLocalization.Any, 21.981943, null),
new ModificationWithMass("16", "mt", motifP, TerminusLocalization.Any, 15.994915, null)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> > {
new Tuple <double, double>(21.981943, 15.994915)
};
Tolerance precursorMassTolerance = new PpmTolerance(10);
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> > dfd = new MzmlScanWithPrecursor(0, new MzmlMzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null, null, "scan=1");
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(dfd, (651.297638557 + 21.981943 + 15.994915).ToMz(1), 1, null);
var parentProtein = new Protein("NNNPPP", "accession");
DigestionParams digestionParams = new DigestionParams();
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var modPep = parentProtein.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).First();
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch match = new PeptideSpectralMatch(peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), 0, 0, 0, scan);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), 0, 0, 0, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
peptidesWithSetModifications.First()
} }
};
List <ProductType> lp = new List <ProductType> {
ProductType.B, ProductType.Y
};
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
match.MatchToProteinLinkedPeptides(matching);
match.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0, 0, false);
allIdentifications = new List <PeptideSpectralMatch> {
match
};
var engine = new GptmdEngine(allIdentifications, gptmdModifications, combos, precursorMassTolerance, new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(1, res.Mods.Count);
Assert.AreEqual(6, res.Mods["accession"].Count);
Assert.AreEqual(3, res.Mods["accession"].Where(b => b.Item2.id.Equals("21")).Count());
Assert.AreEqual(3, res.Mods["accession"].Where(b => b.Item2.id.Equals("16")).Count());
}
public void DuplicatePeptidesReturn()
{
Protein prot = new Protein("DEREKDEREK");
var peptides = prot.Digest(Protease.GetProtease("LysC"), 0).ToList();
Assert.AreEqual(peptides.Count, 2);
}
private void ParseProtease(XmlNode parameters)
{
XmlNode node = xmlHelper.GetFirstChildByNameAndAttribute(parameters, "note", "label", "protein, cleavage site");
Match m = Regex.Match(node.InnerText, @"\[(.+)\]\|\{(.+)\}");
protease = ProteaseManager.FindOrCreateProtease("XTANDEM_PROTEASE", true, m.Groups[1].Value, m.Groups[2].Value);
}
public void SemiTrypiticDigestion()
{
Protein prot = new Protein("MMRGFKQRLIKKTTGSSSSSSSKKKDKEKEKEKSSTTSSTSKKPASASSSSHGTTHSSASSTGSKSTTEKGKQSGSVPSQ");
var peptides = prot.Digest(Protease.GetProtease("Trypsin"), 0, 5, 10, semiDigestion: true).ToList();
Assert.AreEqual(17, peptides.Count);
}
public void DuplicatePeptidesAreEqualivant()
{
Protein prot = new Protein("DEREKDEREK");
var peptides = prot.Digest(Protease.GetProtease("LysC"), 0).ToList();
Assert.AreEqual(peptides[0], peptides[1]);
}
public static void TestCoIsolation()
{
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("CustProtease", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, deconvolutionIntensityRatio: 50, digestionParams: new DigestionParams(protease.Name, minPeptideLength: 1));
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("MNNNKNDNK", null)
};
var searchModes = new SinglePpmAroundZeroSearchMode(5);
Proteomics.AminoAcidPolymer.Peptide pep1 = new Proteomics.AminoAcidPolymer.Peptide("NNNK");
Proteomics.AminoAcidPolymer.Peptide pep2 = new Proteomics.AminoAcidPolymer.Peptide("NDNK");
var dist1 = IsotopicDistribution.GetDistribution(pep1.GetChemicalFormula(), 0.1, 0.01);
var dist2 = IsotopicDistribution.GetDistribution(pep2.GetChemicalFormula(), 0.1, 0.01);
MsDataScan[] Scans = new MsDataScan[2];
double[] ms1intensities = new double[] { 0.8, 0.8, 0.2, 0.02, 0.2, 0.02 };
double[] ms1mzs = dist1.Masses.Concat(dist2.Masses).OrderBy(b => b).Select(b => b.ToMz(1)).ToArray();
double selectedIonMz = ms1mzs[1];
MzSpectrum MS1 = new MzSpectrum(ms1mzs, ms1intensities, false);
Scans[0] = new MsDataScan(MS1, 1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, null, null, "scan=1");
double[] ms2intensities = new double[] { 1, 1, 1, 1, 1 };
double[] ms2mzs = new double[] { 146.106.ToMz(1), 228.086.ToMz(1), 229.07.ToMz(1), 260.148.ToMz(1), 342.129.ToMz(1) };
MzSpectrum MS2 = new MzSpectrum(ms2mzs, ms2intensities, false);
double isolationMZ = selectedIonMz;
Scans[1] = new MsDataScan(MS2, 2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, null, null, "scan=2", selectedIonMz, null, null, isolationMZ, 2.5, DissociationType.HCD, 1, null);
var myMsDataFile = new MsDataFile(Scans, null);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters(deconvolutionIntensityRatio: 50)).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];;
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
// Two matches for this single scan! Corresponding to two co-isolated masses
Assert.AreEqual(2, allPsmsArray.Length);
Assert.IsTrue(allPsmsArray[0].Score > 1);
Assert.AreEqual(2, allPsmsArray[0].ScanNumber);
Assert.AreEqual("NNNK", allPsmsArray[0].BaseSequence);
Assert.AreEqual("NDNK", allPsmsArray[1].BaseSequence);
}
public static void TestAddCompIonsClassic()
{
var myMsDataFile = new TestDataFile();
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("QXQ", null)
};
var productMassTolerance = new AbsoluteTolerance(0.01);
var searchModes = new OpenSearchMode();
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("Custom Protease3", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: false);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, fsp, new List <string>()).Run();
CommonParameters CommonParameters2 = new CommonParameters(
digestionParams: new DigestionParams(protease: protease.Name, maxMissedCleavages: 0, minPeptideLength: 1),
scoreCutoff: 1,
addCompIons: true);
var fsp2 = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp2.Add(("", CommonParameters2));
PeptideSpectralMatch[] allPsmsArray2 = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray2, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters2, fsp2, new List <string>()).Run();
double scoreT = allPsmsArray2[0].Score;
double scoreF = allPsmsArray[0].Score;
// Single search mode
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
// Single ms2 scan
Assert.AreEqual(allPsmsArray.Length, allPsmsArray2.Length);
Assert.IsTrue(scoreT > 1);
Assert.AreEqual(allPsmsArray[0].ScanNumber, allPsmsArray2[0].ScanNumber);
Assert.IsTrue(scoreT == scoreF * 3 && scoreT > scoreF + 2);
}
public static void TestNonSpecific()
{
Protease p = ProteaseDictionary.Dictionary["non-specific"];
Protein prot = new Protein("MABCDEFGH", null);
DigestionParams digestionParams = new DigestionParams(protease: p.Name, maxMissedCleavages: 8, minPeptideLength: 1, maxPeptideLength: 9, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
Assert.AreEqual(1 + 2 + 3 + 4 + 5 + 6 + 7 + 8, prot.Digest(digestionParams, new List <ModificationWithMass>(), new List <ModificationWithMass>()).Count());
}
public static void TestLocalization()
{
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
Protein parentProteinForMatch = new Protein("MEK", null);
DigestionParams digestionParams = new DigestionParams
{
MinPeptideLength = 1,
};
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", null, motif, TerminusLocalization.Any, 21.981943)
};
List <PeptideWithSetModifications> allPeptidesWithSetModifications = parentProteinForMatch.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(4, allPeptidesWithSetModifications.Count());
PeptideWithSetModifications ps = allPeptidesWithSetModifications.First();
List <ProductType> lp = new List <ProductType> {
ProductType.BnoB1ions, ProductType.Y
};
PeptideWithSetModifications pepWithSetModsForSpectrum = allPeptidesWithSetModifications[1];
IMsDataFile <IMsDataScan <IMzSpectrum <IMzPeak> > > myMsDataFile = new TestDataFile(new List <PeptideWithSetModifications> {
pepWithSetModsForSpectrum
});
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(myMsDataFile.Last() as IMsDataScanWithPrecursor <IMzSpectrum <IMzPeak> >, pepWithSetModsForSpectrum.MonoisotopicMass.ToMz(1), 1, null);
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(ps.CompactPeptide(TerminusType.None), 0, 0, 2, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ ps.CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
ps
} }
};
newPsm.MatchToProteinLinkedPeptides(matching);
LocalizationEngine f = new LocalizationEngine(new List <PeptideSpectralMatch> {
newPsm
}, lp, myMsDataFile, fragmentTolerance, new List <string>(), false);
f.Run();
// Was single peak!!!
Assert.AreEqual(0, newPsm.MatchedIonDictOnlyMatches[ProductType.BnoB1ions].Count(b => b > 0));
Assert.AreEqual(1, newPsm.MatchedIonDictOnlyMatches[ProductType.Y].Count(b => b > 0));
// If localizing, three match!!!
Assert.IsTrue(newPsm.LocalizedScores[1] > 3 && newPsm.LocalizedScores[1] < 4);
}
public static void TestGptmdEngine()
{
List <PeptideSpectralMatch> allResultingIdentifications = null;
ModificationMotif.TryGetMotif("N", out ModificationMotif motifN);
var gptmdModifications = new List <ModificationWithMass> {
new ModificationWithMass("21", "mt", motifN, TerminusLocalization.Any, 21.981943)
};
IEnumerable <Tuple <double, double> > combos = new List <Tuple <double, double> >();
Tolerance precursorMassTolerance = new PpmTolerance(10);
allResultingIdentifications = new List <PeptideSpectralMatch>();
var engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, precursorMassTolerance, new List <string>());
var res = (GptmdResults)engine.Run();
Assert.AreEqual(0, res.Mods.Count);
//PsmParent newPsm = new TestParentSpectrumMatch(588.22520189093 + 21.981943);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MzmlScanWithPrecursor(0, new MzmlMzSpectrum(new double[] { 1 }, new double[] { 1 }, false), 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 0, null, null, "scan=1"), (588.22520189093 + 21.981943).ToMz(1), 1, null);
var parentProtein = new Protein("NNNNN", "accession");
var protease = new Protease("Custom Protease", new List <string> {
"K"
}, new List <string>(), TerminusType.C, CleavageSpecificity.Full, null, null, null);
DigestionParams digestionParams = new DigestionParams();
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var modPep = parentProtein.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).First();
var peptidesWithSetModifications = new List <PeptideWithSetModifications> {
modPep
};
PeptideSpectralMatch newPsm = new PeptideSpectralMatch(peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), 0, 0, 0, scan);
Dictionary <ModificationWithMass, ushort> modsDictionary = new Dictionary <ModificationWithMass, ushort>();
Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> > matching = new Dictionary <CompactPeptideBase, HashSet <PeptideWithSetModifications> >
{
{ peptidesWithSetModifications.First().CompactPeptide(TerminusType.None), new HashSet <PeptideWithSetModifications> {
peptidesWithSetModifications.First()
} }
};
List <ProductType> lp = new List <ProductType> {
ProductType.B, ProductType.Y
};
Tolerance fragmentTolerance = new AbsoluteTolerance(0.01);
newPsm.MatchToProteinLinkedPeptides(matching);
newPsm.SetFdrValues(1, 0, 0, 1, 0, 0, 0, 0, 0, false);
allResultingIdentifications.Add(newPsm);
engine = new GptmdEngine(allResultingIdentifications, gptmdModifications, combos, precursorMassTolerance, new List <string>());
res = (GptmdResults)engine.Run();
Assert.AreEqual(1, res.Mods.Count);
Assert.AreEqual(5, res.Mods["accession"].Count);
}
private void PopulateChoices()
{
foreach (var crosslinker in GlobalVariables.Crosslinkers)
{
cbCrosslinkers.Items.Add(crosslinker);
}
Crosslinker DSSO = GlobalVariables.Crosslinkers.First();
cbCrosslinkers.SelectedItem = DSSO;
foreach (string dissassociationType in GlobalVariables.AllSupportedDissociationTypes.Keys)
{
DissociationTypeComboBox.Items.Add(dissassociationType);
ChildScanDissociationTypeComboBox.Items.Add(dissassociationType);
}
cbbXLprecusorMsTl.Items.Add("Da");
cbbXLprecusorMsTl.Items.Add("ppm");
foreach (Protease protease in ProteaseDictionary.Dictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
Protease trypsin = ProteaseDictionary.Dictionary["trypsin"];
proteaseComboBox.SelectedItem = trypsin;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
productMassToleranceComboBox.Items.Add("Da");
productMassToleranceComboBox.Items.Add("ppm");
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
fixedModsTreeView.DataContext = FixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
variableModsTreeView.DataContext = VariableModTypeForTreeViewObservableCollection;
}
public List<string> CreateCleavedPeptides(int argAllowMissCleavage, Protease.Type argProteaseType)
{
_misscleavaged = argAllowMissCleavage;
List<string> peptides = new List<string>();
foreach (ProteinInfo prot in _proteinInfo)
{
peptides.AddRange(prot.CreateCleavage(_misscleavaged, argProteaseType));
}
return peptides;
}
public static void XlTestXlPosCal()
{
var prot = new Protein("MNNNKQQQQ", null);
Protease protease = new Protease("New Custom Protease", new List <Tuple <string, TerminusType> > {
new Tuple <string, TerminusType>("K", TerminusType.C)
}, new List <Tuple <string, TerminusType> >(), CleavageSpecificity.Full, null, null, null);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(protease: protease.Name, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <ModificationWithMass> variableModifications = new List <ModificationWithMass>();
var ye = prot.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
var pep = ye[0];
Assert.AreEqual(pep.BaseSequence, "MNNNK");
CrosslinkerTypeClass crosslinker = new CrosslinkerTypeClass();
crosslinker.SelectCrosslinker(CrosslinkerType.DSS);
Assert.AreEqual(crosslinker.CrosslinkerModSites, "K");
Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSites).MonoisotopicMass, 128.09496301518999, 1e-9);
var n = pep.CompactPeptide(TerminusType.None).NTerminalMasses;
var c = pep.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n.Count(), 4);
Assert.AreEqual(c.Count(), 4);
Assert.AreEqual(c[0], 128.09496301518999, 1e-6);
var x = PsmCross.XlPosCal(pep.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray();
Assert.AreEqual(x[0], 4);
var pep2 = ye[2];
Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence);
var n2 = pep2.CompactPeptide(TerminusType.None).NTerminalMasses;
var c2 = pep2.CompactPeptide(TerminusType.None).CTerminalMasses;
Assert.AreEqual(n2.Count(), 8);
Assert.AreEqual(c2.Count(), 8);
Assert.AreEqual(n2[4] - n2[3], 128.09496301518999, 1e-6);
var x2 = PsmCross.XlPosCal(pep2.CompactPeptide(TerminusType.None), crosslinker.CrosslinkerModSites).ToArray();
Assert.AreEqual(x2[0], 4);
//Test crosslinker with multiple types of mod
var protSTC = new Protein("GASTACK", null);
var peps = protSTC.Digest(digestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
var pepSTC = peps[0];
Assert.AreEqual(pepSTC.BaseSequence, "GASTACK");
CrosslinkerTypeClass crosslinker2 = new CrosslinkerTypeClass("ST", "C", "crosslinkerSTC", false, -18.01056, 0, 0, 0, 0, 0, 0);
string crosslinkerModSitesAll = new string((crosslinker2.CrosslinkerModSites + crosslinker2.CrosslinkerModSites2).ToCharArray().Distinct().ToArray());
Assert.AreEqual(crosslinkerModSitesAll, "STC");
}
public void TestIsCleavageSite()
{
Protease trypsin = new Protease("Trypsin", true, "KR", "P");
Assert.AreEqual(true, trypsin.IsCleavageSite('K', 'A', '-'));
Assert.AreEqual(true, trypsin.IsCleavageSite('R', 'A', '-'));
Assert.AreEqual(true, trypsin.IsCleavageSite('K', '-', '-'));
Assert.AreEqual(true, trypsin.IsCleavageSite('R', '-', '-'));
Assert.AreEqual(false, trypsin.IsCleavageSite('K', 'P', '-'));
Assert.AreEqual(false, trypsin.IsCleavageSite('R', 'P', '-'));
Assert.AreEqual(false, trypsin.IsCleavageSite('N', 'A', '-'));
}
public static void XlTestXlPosCal()
{
var prot = new Protein("MNNNKQQQQ", null);
List <DigestionMotif> motifs = new List <DigestionMotif> {
new DigestionMotif("K", null, 1, null)
};
Protease protease = new Protease("New Custom Protease", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
DigestionParams digestionParams = new DigestionParams(protease: protease.Name, minPeptideLength: 1, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List <Modification> variableModifications = new List <Modification>();
var ye = prot.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
var pep = ye[0];
Assert.AreEqual(pep.BaseSequence, "MNNNK");
Crosslinker crosslinker = GlobalVariables.Crosslinkers.Where(p => p.CrosslinkerName == "DSS").First();
Assert.AreEqual(crosslinker.CrosslinkerModSites, "K");
Assert.AreEqual(Residue.GetResidue(crosslinker.CrosslinkerModSites).MonoisotopicMass, 128.09496301518999, 1e-9);
var n = pep.Fragment(DissociationType.HCD, FragmentationTerminus.N);
var c = pep.Fragment(DissociationType.HCD, FragmentationTerminus.C);
Assert.AreEqual(n.Count(), 4);
Assert.AreEqual(c.Count(), 4);
Assert.AreEqual(c.First().NeutralMass, 146.10552769899999, 1e-6);
var x = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), pep).ToArray();
Assert.AreEqual(x[0], 5);
var pep2 = ye[2];
Assert.AreEqual("MNNNKQQQQ", pep2.BaseSequence);
var n2 = pep2.Fragment(DissociationType.HCD, FragmentationTerminus.N);
var c2 = pep2.Fragment(DissociationType.HCD, FragmentationTerminus.C);
Assert.AreEqual(n2.Count(), 8);
Assert.AreEqual(c2.Count(), 8);
var x2 = CrosslinkSpectralMatch.GetPossibleCrosslinkerModSites(crosslinker.CrosslinkerModSites.ToCharArray(), pep2).ToArray();
Assert.AreEqual(x2[0], 5);
//Test crosslinker with multiple types of mod
var protSTC = new Protein("GASTACK", null);
var peps = protSTC.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
var pepSTC = peps[0];
Assert.AreEqual(pepSTC.BaseSequence, "GASTACK");
Crosslinker crosslinker2 = new Crosslinker("ST", "C", "crosslinkerSTC", false, -18.01056, 0, 0, 0, 0, 0, 0);
string crosslinkerModSitesAll = new string((crosslinker2.CrosslinkerModSites + crosslinker2.CrosslinkerModSites2).ToCharArray().Distinct().ToArray());
Assert.AreEqual(crosslinkerModSitesAll, "STC");
}
public void MultipleProteaseDigestion()
{
List <IProtease> proteases = new List <IProtease> {
Protease.GetProtease("Trypsin"), Protease.GetProtease("GluC")
};
List <Peptide> peptides = _proteinA.Digest(proteases, maxMissedCleavages: 1, maxLength: 5).ToList();
Assert.Contains(new Peptide("NWSK"), peptides);
Assert.Contains(new Peptide("ENWSK"), peptides);
}
public void TestParseProtease()
{
using (var sr = new StreamReader(@TestContext.CurrentContext.TestDirectory + "/../../../data//F001264.dat"))
{
Protease p = ParseEnzyme(sr);
Assert.AreEqual("semiTrypsin", p.Name);
Assert.AreEqual("KR", p.CleaveageResidues);
Assert.AreEqual("P", p.NotCleaveResidues);
Assert.AreEqual(true, p.IsEndoProtease);
}
}
public static void TestIndexEngine()
{
var proteinList = new List <Protein> {
new Protein("MNNNKQQQ", null)
};
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 i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
Protease p = new Protease("Custom Protease2", new List <Tuple <string, TerminusType> > {
new Tuple <string, TerminusType>("K", TerminusType.C)
}, new List <Tuple <string, TerminusType> >(), CleavageSpecificity.Full, null, null, null);
ProteaseDictionary.Dictionary.Add(p.Name, p);
CommonParameters CommonParameters = new CommonParameters(scoreCutoff: 1, digestionParams: new DigestionParams(protease: p.Name, minPeptideLength: 1));
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <ProductType>
{
ProductType.B, ProductType.Y
}, 1, DecoyType.Reverse, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var results = (IndexingResults)engine.Run();
Assert.AreEqual(5, results.PeptideIndex.Count);
var digestedList = proteinList[0].Digest(CommonParameters.DigestionParams, new List <ModificationWithMass>(), variableModifications).ToList();
Assert.AreEqual(5, digestedList.Count);
foreach (var fdfd in digestedList)
{
Assert.Contains(fdfd.CompactPeptide(TerminusType.None), results.PeptideIndex);
}
}
public static void TestIndexEngineWithWeirdSeq()
{
var proteinList = new List <Protein> {
new Protein("MQXQ", null)
};
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 i = 1;
foreach (var mod in variableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
foreach (var mod in localizeableModifications)
{
modsDictionary.Add(mod, (ushort)i);
i++;
}
Protease protease = new Protease("Custom Protease", new List <Tuple <string, TerminusType> > {
new Tuple <string, TerminusType>("K", TerminusType.C)
}, new List <Tuple <string, TerminusType> >(), CleavageSpecificity.Full, null, null, null);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(
protease: protease.Name,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain),
scoreCutoff: 1);
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, new List <ProductType> {
ProductType.B, ProductType.Y
}, 1, DecoyType.Reverse, new List <DigestionParams> {
CommonParameters.DigestionParams
}, CommonParameters, 30000, new List <string>());
var results = (IndexingResults)engine.Run();
Assert.AreEqual(1, results.PeptideIndex.Count);
Assert.IsNaN(results.PeptideIndex[0].MonoisotopicMassIncludingFixedMods);
Assert.AreEqual(30000000 + 1, results.FragmentIndex.Length);
}
public static void TestIndexEngineWithWeirdSeq()
{
var proteinList = new List <Protein> {
new Protein("MQXQ", 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 protease = new Protease("Custom Protease", CleavageSpecificity.Full, null, null, motifs);
ProteaseDictionary.Dictionary.Add(protease.Name, protease);
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(
protease: protease.Name,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain),
scoreCutoff: 1);
var fsp = new List <(string fileName, CommonParameters fileSpecificParameters)>();
fsp.Add(("", CommonParameters));
var engine = new IndexingEngine(proteinList, variableModifications, fixedModifications, null, null, null, 1, DecoyType.Reverse, CommonParameters,
fsp, 30000, false, new List <FileInfo>(), TargetContaminantAmbiguity.RemoveContaminant, new List <string>());
var results = (IndexingResults)engine.Run();
Assert.AreEqual(1, results.PeptideIndex.Count);
Assert.IsNaN(results.PeptideIndex[0].MonoisotopicMass);
Assert.AreEqual(30000000 + 1, results.FragmentIndex.Length);
}
private void PopulateChoices()
{
ChildScanDissociationTypeComboBox.Items.Add("Null");
foreach (var dissassociationType in GlobalVariables.AllSupportedDissociationTypes.Where(p => p.Value != DissociationType.Autodetect))
{
DissociationTypeComboBox.Items.Add(dissassociationType.Key);
ChildScanDissociationTypeComboBox.Items.Add(dissassociationType.Key);
}
cbbPrecusorMsTl.Items.Add("Da");
cbbPrecusorMsTl.Items.Add("ppm");
CmbOGlycanDatabase.ItemsSource = GlobalVariables.OGlycanLocations.Select(p => Path.GetFileName(p));
CmbNGlycanDatabase.ItemsSource = GlobalVariables.NGlycanLocations.Select(p => Path.GetFileName(p));
foreach (Protease protease in ProteaseDictionary.Dictionary.Values)
{
proteaseComboBox.Items.Add(protease);
}
Protease trypsin = ProteaseDictionary.Dictionary["trypsin"];
proteaseComboBox.SelectedItem = trypsin;
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
initiatorMethionineBehaviorComboBox.Items.Add(initiatior_methionine_behavior);
}
productMassToleranceComboBox.Items.Add("Da");
productMassToleranceComboBox.Items.Add("ppm");
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
FixedModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
fixedModsTreeView.DataContext = FixedModTypeForTreeViewObservableCollection;
foreach (var hm in GlobalVariables.AllModsKnown.GroupBy(b => b.ModificationType))
{
var theModType = new ModTypeForTreeView(hm.Key, false);
VariableModTypeForTreeViewObservableCollection.Add(theModType);
foreach (var uah in hm)
{
theModType.Children.Add(new ModForTreeView(uah.ToString(), false, uah.IdWithMotif, false, theModType));
}
}
variableModsTreeView.DataContext = VariableModTypeForTreeViewObservableCollection;
}
public void WriteSearchProtease(Protease protease, int maxMissedClevages, bool semiDigested = false)
{
if (CurrentStage != Stage.SearchSummary)
{
throw new ArgumentException("You must be in the Search Summary stage to write modifications");
}
_writer.WriteStartElement("enzymatic_search_constraint");
_writer.WriteAttributeString("enzyme", protease.Name);
_writer.WriteAttributeString("max_num_internal_clevages", maxMissedClevages.ToString());
_writer.WriteAttributeString("min_number_termini", (semiDigested) ? "1" : "2");
_writer.WriteEndElement();
}
public void TestGetMissCleavageSiteCount()
{
Protease trypsin = new Protease("Trypsin", true, "KR", "P");
Assert.AreEqual(0, trypsin.GetMissCleavageSiteCount("EGEABDR"));
Assert.AreEqual(0, trypsin.GetMissCleavageSiteCount("EGEKPABDR"));
Assert.AreEqual(0, trypsin.GetMissCleavageSiteCount("EGERPABDR"));
Assert.AreEqual(1, trypsin.GetMissCleavageSiteCount("EGEKABDR"));
Assert.AreEqual(1, trypsin.GetMissCleavageSiteCount("EGERABDR"));
Assert.AreEqual(2, trypsin.GetMissCleavageSiteCount("EGEKARBDR"));
Protease noenzyme = new Protease("Noenzyme", true, "", "");
Assert.AreEqual(0, noenzyme.GetMissCleavageSiteCount("EGEABDR"));
}
public List<string> CreateCleavage(int argAllowMissCleavage, Protease.Type argProteaseType)
{
return CreateCleavage(_sequence,argAllowMissCleavage, new List<Protease.Type>() { argProteaseType });
}
