/// <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 override PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
double[] eMasses = massSpectrum.MassSpectrum.GetMasses();
double[] eIntenisties = massSpectrum.MassSpectrum.GetIntensities();
double tic = massSpectrum.MassSpectrum.GetTotalIonCurrent();
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType) {Peptide = peptide};
double[] tMasses = peptide.Fragment(fragmentTypes).Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1)).OrderBy(val => val).ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
return psm;
}
public void TestMultipleModificationsAtSingleResidue()
{
Peptide a = new Peptide("ACDEFGHIKLMNPQRSTVWY");
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.D));
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H"), ModificationSites.D));
var products = a.Fragment(FragmentTypes.b | FragmentTypes.y, true);
foreach (Fragment fragment in products)
{
}
foreach (IHasChemicalFormula fragment in products)
{
}
}
private void GenerateMzFeatures()
{
// add precursor to mzFeatures in case Anji is interested in tracking it
this.mzFeatures.Add(new MzFeature(this.peptide, this.precursorCharge));
// fragment peptide in-silico to determine all theoretical peptide fragments;
var peptideFragments = peptide.Fragment(FragmentTypes.b | FragmentTypes.y).ToList();
foreach (var fragment in peptideFragments)
{
for (var charge = maxFragmentCharge; charge > 0; charge--)
{
this.mzFeatures.Add(new MzFeature(fragment, charge));
}
}
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
OldSchoolChemicalFormulaModification carbamidomethylationOfCMod = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H3C2NO"), "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
MzmlMzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
MzmlMzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
IMzmlScan[] Scans = new IMzmlScan[2];
Scans[0] = new MzmlScan(1, MS1, 1, true, Polarity.Positive, 1.0, new MzRange(300, 2000), " first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, "scan=1");
Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, true, Polarity.Positive, 2.0, new MzRange(100, 1500), " second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 1134.26091302033, 1, "scan=2");
var myMsDataFile = new FakeMsDataFile(Scans);
var oldFirstValue = myMsDataFile.GetOneBasedScan(1).MassSpectrum.FirstX;
var secondScan = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan.IsolationRange.Maximum - secondScan.IsolationRange.Minimum);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, "argh.mzML", false);
Mzml okay = Mzml.LoadAllStaticData(@"argh.mzML");
okay.GetOneBasedScan(2);
Assert.AreEqual(1, okay.GetClosestOneBasedSpectrumNumber(1));
Assert.AreEqual(2, okay.GetClosestOneBasedSpectrumNumber(2));
var newFirstValue = okay.GetOneBasedScan(1).MassSpectrum.FirstX;
Assert.AreEqual(oldFirstValue.Value, newFirstValue.Value, 1e-9);
var secondScan2 = okay.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan2.IsolationRange.Maximum - secondScan2.IsolationRange.Minimum);
secondScan2.MassSpectrum.ReplaceXbyApplyingFunction((a) => 44);
Assert.AreEqual(44, secondScan2.MassSpectrum.LastX);
}
public override PeptideSpectralMatch Search(IMassSpectrum massSpectrum, Peptide peptide, FragmentTypes fragmentTypes, Tolerance productMassTolerance)
{
double[] eMasses = massSpectrum.MassSpectrum.GetMasses();
double[] eIntenisties = massSpectrum.MassSpectrum.GetIntensities();
double tic = massSpectrum.MassSpectrum.GetTotalIonCurrent();
PeptideSpectralMatch psm = new PeptideSpectralMatch(DefaultPsmScoreType)
{
Peptide = peptide
};
double[] tMasses = peptide.Fragment(fragmentTypes).Select(frag => Mass.MzFromMass(frag.MonoisotopicMass, 1)).OrderBy(val => val).ToArray();
double score = Search(eMasses, eIntenisties, tMasses, productMassTolerance, tic);
psm.Score = score;
return(psm);
}
public void TestClearModifications()
{
Peptide a = new Peptide("ACDEFGHIKLMNPQRSTVWY");
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.D));
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H"), ModificationSites.E));
Assert.AreEqual(2, a.ModificationCount());
a.ClearModifications();
Assert.AreEqual(0, a.ModificationCount());
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.NTerminus));
a.AddModification(new OldSchoolModification(1), ModificationSites.TerminusC);
Assert.AreEqual(2, a.ModificationCount());
a.Fragment(FragmentTypes.y);
Peptide peptide = new Peptide("[C2H3NO]-LLL-[C2H3NO]");
ModificationSites ff = ModificationSites.NPep | ModificationSites.PepC;
peptide.ClearModifications(ff);
Assert.AreEqual("LLL", peptide.GetSequenceWithModifications());
}
public void TestFormulaTerminusMods()
{
var pep1 = new Peptide("ACDEFG");
pep1.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H"), ModificationSites.NTerminus));
Assert.IsTrue(pep1.Fragment(FragmentTypes.b, true).First() is IHasChemicalFormula);
var pep2 = new Peptide("ACDEFG");
pep2.AddModification(new OldSchoolModification(2, "haha", ModificationSites.NTerminus));
Assert.IsFalse(pep2.Fragment(FragmentTypes.b, true).First() is IHasChemicalFormula);
var pep3 = new Peptide("ACDEFG");
pep3.AddModification(new OldSchoolModification(3, "haha", ModificationSites.D));
var list = pep3.Fragment(FragmentTypes.b, true).ToList();
Assert.IsTrue(list[0] is IHasChemicalFormula);
Assert.IsFalse(list[2] is IHasChemicalFormula);
}
public void Setup()
{
Environment.CurrentDirectory = TestContext.CurrentContext.TestDirectory;
UsefulProteomicsDatabases.Loaders.LoadElements();
double[] mz = { 328.73795, 329.23935, 447.73849, 448.23987, 482.23792, 482.57089, 482.90393, 500.95358, 501.28732, 501.62131, 611.99377, 612.32806, 612.66187, 722.85217, 723.35345 };
double[] intensities = { 81007096.0, 28604418.0, 78353512.0, 39291696.0, 122781408.0, 94147520.0, 44238040.0, 71198680.0, 54184096.0, 21975364.0, 44514172.0, 43061628.0, 23599424.0, 56022696.0, 41019144.0 };
_mzSpectrumA = new MzSpectrum(mz, intensities, false);
var peptide = new Peptide("KQEEQMETEQQNKDEGK");
MzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
MzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
MsDataScan[] Scans = new MsDataScan[2];
Scans[0] = new MsDataScan(MS1, 1, 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, null, "scan=1");
Scans[1] = new MsDataScan(MS2, 2, 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1, null, "scan=2", 693.9892, 3, .3872, 693.99, 1, DissociationType.Unknown, 1, 693.6550);
myMsDataFile = new FakeMsDataFile(Scans);
}
public void FragmentNumberToLow()
{
Assert.Throws <IndexOutOfRangeException>(() => _mockPeptideEveryAminoAcid.Fragment(FragmentTypes.b, 0).ToList());
}
/// <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);
}
}