public void testConstruction() { var testFile = new FileInfo(@"../../../data/mascot_result_protein_newversion.html"); // filter by rank 1 only MascotResult mr = new MascotResultHtmlStandaloneParser(false) .ParseFile(testFile); Assert.AreEqual(2, mr.Count); Assert.AreEqual(3, mr[0][0].Peptides.Count); Assert.AreEqual(3, mr[1][0].Peptides.Count); // filter by rank 1 and score mr = new MascotResultHtmlStandaloneParser(new IdentifiedSpectrumScoreFilter(40), false).ParseFile(testFile); Assert.AreEqual(2, mr.Count); Assert.AreEqual(2, mr[0][0].Peptides.Count); Assert.AreEqual(1, mr[1][0].Peptides.Count); mr = new MascotResultHtmlStandaloneParser(new IdentifiedSpectrumExpectValueFilter( 0.01), false).ParseFile(testFile); Assert.AreEqual(2, mr.Count); Assert.AreEqual(2, mr[0][0].Peptides.Count); Assert.AreEqual(1, mr[1][0].Peptides.Count); mr = new MascotResultHtmlStandaloneParser(new IdentifiedSpectrumExpectValueFilter( 0.0016), false).ParseFile(testFile); Assert.AreEqual(1, mr.Count); Assert.AreEqual(1, mr[0][0].Peptides.Count); mr = new MascotResultHtmlStandaloneParser(new IdentifiedSpectrumExpectValueFilter( 1.0E-5), false).ParseFile(testFile); Assert.AreEqual(0, mr.Count); }
public void testO18Result() { MascotResult mr = new MascotResultHtmlStandaloneParser(true) .ParseFile(new FileInfo(@"../../../data/mascot_result_protein_o18.html")); Assert.AreEqual(1, mr.Count); Assert.AreEqual(6, mr[0].Count); Assert.AreEqual(10, mr[0][0].Peptides.Count); IIdentifiedSpectrum mp = mr[0][0].FindPeptideByQuery(5492).Spectrum; Assert.IsNotNull(mp); Assert.AreEqual("R.ISLPLPNFSSLNLR.E", mp.Sequence); Assert.AreEqual("Label:18O(2) (C-term)", mp.Modifications); }
public void testParseFile1() { MascotResult mr = new MascotResultHtmlStandaloneParser(true) .ParseFile(new FileInfo(@"../../../data/mascot_result_protein_newversion.html")); Assert.AreEqual(33, mr.PValueScore); Assert.AreEqual(0.05, mr.PValue); Assert.AreEqual(IsotopicType.Monoisotopic, mr.PeakIsotopicType); Assert.AreEqual(0.8, mr.PeakTolerance, 0.01); Assert.AreEqual(2, mr.Count); IIdentifiedProtein protein1 = mr[0][0]; Assert.AreEqual("sp|P00489|PHS2_RABIT", protein1.Name); Assert.AreEqual(97610, protein1.MolecularWeight, 1.0); Assert.AreEqual( "Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase) - Oryctolagus cuniculus (Rabbit", protein1.Description); Assert.AreEqual(3, protein1.Peptides.Count); IIdentifiedSpectrum pep11 = protein1.Peptides[0].Spectrum; Assert.AreEqual(1053.5720, pep11.Query.ObservedMz, 0.0001); Assert.AreEqual("Cmpd.6612.6612.1.dta", pep11.Query.FileScan.LongFileName); Assert.AreEqual(2232, pep11.Query.QueryId); Assert.AreEqual(1052.5647, pep11.ExperimentalMass, 0.0001); Assert.AreEqual(1052.5654, pep11.TheoreticalMass, 0.0001); Assert.AreEqual(0.0007, pep11.TheoreticalMinusExperimentalMass, 0.0001); Assert.AreEqual(0, pep11.NumMissedCleavages); Assert.AreEqual(34, pep11.Score); Assert.AreEqual(0.039, pep11.ExpectValue); Assert.AreEqual(1, pep11.Rank); Assert.AreEqual("R.VIFLENYR.V", pep11.Sequence); IIdentifiedSpectrum pep12 = protein1.Peptides[1].Spectrum; Assert.AreEqual(527.7459, pep12.Query.ObservedMz, 0.0001); Assert.AreEqual("Cmpd.5747.5747.2.dta", pep12.Query.FileScan.LongFileName); Assert.AreEqual(2239, pep12.Query.QueryId); Assert.AreEqual(1053.4772, pep12.ExperimentalMass, 0.0001); Assert.AreEqual(1053.4767, pep12.TheoreticalMass, 0.0001); Assert.AreEqual(-0.0005, pep12.TheoreticalMinusExperimentalMass, 0.0001); Assert.AreEqual(0, pep12.NumMissedCleavages); Assert.AreEqual(48, pep12.Score); Assert.AreEqual(5.4E-5, pep12.ExpectValue, 0.001); Assert.AreEqual(1, pep12.Rank); Assert.AreEqual("R.TNFDAFPDK.V", pep12.Sequence); IIdentifiedSpectrum pep13 = protein1.Peptides[2].Spectrum; Assert.AreEqual(527.7464, pep13.Query.ObservedMz, 0.0001); Assert.AreEqual("Cmpd.5743.5743.2.dta", pep13.Query.FileScan.LongFileName); Assert.AreEqual(2240, pep13.Query.QueryId); Assert.AreEqual(1053.4782, pep13.ExperimentalMass, 0.0001); Assert.AreEqual(1053.4767, pep13.TheoreticalMass, 0.0001); Assert.AreEqual(-0.0015, pep13.TheoreticalMinusExperimentalMass, 0.0001); Assert.AreEqual(0, pep13.NumMissedCleavages); Assert.AreEqual(47, pep13.Score); Assert.AreEqual(0.0018, pep13.ExpectValue, 0.001); Assert.AreEqual(1, pep13.Rank); Assert.AreEqual("R.TNFDAFPDK.V", pep13.Sequence); IIdentifiedProtein protein2 = mr[1][0]; Assert.AreEqual("REVERSED_0008631", protein2.Name); Assert.AreEqual("", protein2.Description); Assert.AreEqual(2, protein2.Peptides.Count); IIdentifiedSpectrum pep21 = protein2.Peptides[0].Spectrum; Assert.AreEqual(699.4770, pep21.Query.ObservedMz, 0.0001); Assert.AreEqual("Standard_Protein_FIT_060222.6065.6065.1.dta", pep21. Query.FileScan.LongFileName); Assert.AreEqual(932, pep21.Query.QueryId); Assert.AreEqual(698.4697, pep21.ExperimentalMass, 0.0001); Assert.AreEqual(698.4115, pep21.TheoreticalMass, 0.0001); Assert.AreEqual(-0.0582, pep21.TheoreticalMinusExperimentalMass, 0.0001); Assert.AreEqual(0, pep21.NumMissedCleavages); Assert.AreEqual(33, pep21.Score); Assert.AreEqual(0.049, pep21.ExpectValue); Assert.AreEqual(1, pep21.Rank); Assert.AreEqual("R.WPAVVK.L", pep21.Sequence); Assert.AreSame(protein1.Peptides[2], protein2.Peptides[1]); }
public void testParseFileWithSameMatchProteins() { MascotResult mr = new MascotResultHtmlStandaloneParser(false) .ParseFile(new FileInfo(@"../../../data/mascot_result_Caseins00001.htm")); Assert.AreEqual(44, mr.PValueScore); Assert.AreEqual(0.05, mr.PValue); Assert.AreEqual(IsotopicType.Monoisotopic, mr.PeakIsotopicType); Assert.AreEqual(0.8, mr.PeakTolerance, 0.01); Assert.AreEqual(8, mr.Count); Assert.AreEqual("TAU_HUMAN", mr[6][0].Name); Assert.AreEqual(2, mr[6].Count); Assert.AreEqual("TAU_PANTR", mr[6][1].Name); }
public void testParseFile2() { MascotResult mr = new MascotResultHtmlStandaloneParser(true) .ParseFile(new FileInfo(@"../../../data/mascot_result_Caseins00001.htm")); Assert.AreEqual(44, mr.PValueScore); Assert.AreEqual(0.05, mr.PValue); Assert.AreEqual(IsotopicType.Monoisotopic, mr.PeakIsotopicType); Assert.AreEqual(0.8, mr.PeakTolerance, 0.01); Assert.AreEqual(1, mr.Count); IIdentifiedProtein protein1 = mr[0][0]; Assert.AreEqual("ALBU_HUMAN", protein1.Name); Assert.AreEqual("Serum albumin precursor - H**o sapiens (Human)", protein1 .Description); Assert.AreEqual(2, protein1.Peptides.Count); IIdentifiedSpectrum pep11 = protein1.Peptides[0].Spectrum; Assert.AreEqual(547.22, pep11.Query.ObservedMz, 0.01); Assert.AreEqual("Cmpd.51.51.3.dta", pep11.Query.FileScan.LongFileName); Assert.AreEqual(118, pep11.Query.QueryId); Assert.AreEqual(1638.6382, pep11.ExperimentalMass, 0.0001); Assert.AreEqual(1638.9304, pep11.TheoreticalMass, 0.0001); Assert.AreEqual(0.2922, pep11.TheoreticalMinusExperimentalMass, 0.0001); Assert.AreEqual(1, pep11.NumMissedCleavages); Assert.AreEqual(50, pep11.Score); Assert.AreEqual(0.0091, pep11.ExpectValue, 0.0001); Assert.AreEqual(1, pep11.Rank); Assert.AreEqual("K.KVPQVSTPTLVEVSR.N", pep11.Sequence); IIdentifiedSpectrum pep12 = protein1.Peptides[1].Spectrum; Assert.AreEqual(547.23, pep12.Query.ObservedMz, 0.01); Assert.AreEqual("Cmpd.47.47.3.dta", pep12.Query.FileScan.LongFileName); Assert.AreEqual(119, pep12.Query.QueryId); Assert.AreEqual(1638.6682, pep12.ExperimentalMass, 0.0001); Assert.AreEqual(1638.9304, pep12.TheoreticalMass, 0.0001); Assert.AreEqual(0.2622, pep12.TheoreticalMinusExperimentalMass, 0.0001); Assert.AreEqual(1, pep12.NumMissedCleavages); Assert.AreEqual(52, pep12.Score); Assert.AreEqual(0.0062, pep12.ExpectValue, 0.0001); Assert.AreEqual(1, pep12.Rank); Assert.AreEqual("K.KVPQVSTPTLVEVSR.N", pep12.Sequence); }