/// <summary>
/// Basic overview of how peptides can be used and modified
/// </summary>
private static void PeptideExamples()
{
Console.WriteLine("**Peptide Examples**");
// Simple Peptide creation
Peptide peptide1 = new Peptide("ACDEFGHIKLMNPQRSTVWY");
WritePeptideToConsole(peptide1);
// Fragmenting a peptide is simple, you can include as many fragment types as you want
Console.WriteLine("{0,-4} {1,-20} {2,-10} {3,-10} {4,-5}", "Type", "Formula", "Mass", "m/z +1", "Sequence");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y))
{
WriteFragmentToConsole(fragment);
}
// Modifications can be applied to any residue or termini
Console.WriteLine("Lets add some Iron to our peptide...");
peptide1.SetModification(new ChemicalFormula("Fe"), Terminus.C | Terminus.N);
WritePeptideToConsole(peptide1);
// A chemicalmodification is a simple wrapper for a chemical formula. You can name your mods if you want
Console.WriteLine("Add a modification of Oxygen with the name \"Oxidation\" to all Methionines");
ChemicalFormulaModification oxMod = new ChemicalFormulaModification("O", "Oxidation");
peptide1.SetModification(oxMod, 'M');
WritePeptideToConsole(peptide1);
// If you fragment a modified peptide, the modifications stay part of the fragments
Console.WriteLine("{0,-4} {1,-20} {2,-20} {3,-5}", "Type", "Formula", "Mass", "m/z +1");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y, 2))
{
WriteFragmentToConsole(fragment);
}
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
ChemicalFormulaModification carbamidomethylationOfCMod = new ChemicalFormulaModification("H3C2NO", "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
DefaultMzSpectrum MS1 = createSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
DefaultMzSpectrum MS2 = createMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
MsDataScan <IMzSpectrum <MzPeak> >[] Scans = new MsDataScan <IMzSpectrum <MzPeak> > [2];
Scans[0] = new MsDataScan <IMzSpectrum <MzPeak> >(1, MS1.newSpectrumApplyFunctionToX(b => b + 0.000001 * b + 0.000001), "spectrum 1", 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "FTMS first spectrum", MZAnalyzerType.Unknown, 1, MS1.SumOfAllY);
Scans[1] = new MsDataScan <IMzSpectrum <MzPeak> >(2, MS2.newSpectrumApplyFunctionToX(b => b + 0.00001 * b + 0.00001), "spectrum 2", 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "FTMS second spectrum", MZAnalyzerType.Unknown, 1, MS2.SumOfAllY, "spectrum 1", 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 0.141146966879759, 1134.26091302033);
var myMsDataFile = new FakeMsDataFile(@"myFakeFile.mzML", Scans);
MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(myMsDataFile, Path.Combine(Path.GetDirectoryName(myMsDataFile.FilePath), Path.GetFileNameWithoutExtension(myMsDataFile.FilePath)) + ".mzML");
Mzml okay = new Mzml(@"myFakeFile.mzML");
okay.Open();
okay.GetScan(2);
Assert.AreEqual(1, okay.GetSpectrumNumber(1));
Assert.AreEqual(2, okay.GetSpectrumNumber(2));
}
public void SetCTerminusModStringRepresentationofChemicalModification()
{
IChemicalFormula formula = new ChemicalFormulaModification("Fe", "Test");
_mockPeptideEveryAminoAcid.SetModification(formula, Terminus.C);
Assert.AreEqual("ACDEFGHIKLMNPQRSTVWY-[Test]", _mockPeptideEveryAminoAcid.ToString());
}
