public void testConstruction()
{
var testFile = new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../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 testParseFile2()
{
MascotResult mr = new MascotResultHtmlStandaloneParser(true)
.ParseFile(new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../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);
}
public void testO18Result()
{
MascotResult mr = new MascotResultHtmlStandaloneParser(true)
.ParseFile(new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../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 testParseFileWithSameMatchProteins()
{
MascotResult mr = new MascotResultHtmlStandaloneParser(false)
.ParseFile(new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../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 IEnumerable <string> Process(string htmlFilename)
{
MascotResult mr = new MascotResultHtmlStandaloneParser(true).
ParseFile(new FileInfo(htmlFilename));
mr.Sort();
mr.BuildGroupIndex();
foreach (IdentifiedProteinGroup mpg in mr)
{
if (mpg.Count > 0)
{
mpg[0].SortPeptides();
}
}
String resultFile = FileUtils.ChangeExtension(htmlFilename, ".txt");
new MascotResultTextFormat().WriteToFile(resultFile, mr);
return(new[] { resultFile });
}
public void testParseFile1()
{
MascotResult mr = new MascotResultHtmlStandaloneParser(true)
.ParseFile(new FileInfo(@TestContext.CurrentContext.TestDirectory + "/../../../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]);
}
