public TestDataFile(PeptideWithSetModifications pepWithSetMods, int charge, double intensity, double rt) : base(2, new SourceFile(null, null, null, null, null)) { var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(charge), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(charge), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(charge) }; var intensities1 = new double[] { intensity, intensity * 10, intensity / 10 }; var MassSpectrum1 = new MzSpectrum(mz1, intensities1, false); var ScansHere = new List <MsDataScan> { new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, rt, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1") }; List <double> mz2 = new List <double>(); List <double> intensities2 = new List <double>(); foreach (var aok in pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both)) { mz2.Add(aok.NeutralMass.ToMz(1)); mz2.Add((aok.NeutralMass + 1.003).ToMz(1)); intensities2.Add(intensity); intensities2.Add(intensity); } var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false); var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, rt + 0.01, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2)); scan2.ComputeSelectedPeakIntensity(MassSpectrum1); scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1); ScansHere.Add(scan2); Scans = ScansHere.ToArray(); }
public TestDataFile(PeptideWithSetModifications pepWithSetMods) : base(2, new SourceFile(@"no nativeID format", "mzML format", null, "SHA-1", @"C:\fake.mzML", null)) { var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + Constants.C13MinusC12).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2 * Constants.C13MinusC12).ToMz(2) }; var intensities1 = new double[] { 1, 1, 1 }; var MassSpectrum1 = new MzSpectrum(mz1, intensities1, false); var ScansHere = new List <MsDataScan> { new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1") }; List <double> mz2 = new List <double>(); List <double> intensities2 = new List <double>(); foreach (var aok in pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both)) { mz2.Add(aok.NeutralMass.ToMz(1)); mz2.Add((aok.NeutralMass + Constants.C13MinusC12).ToMz(1)); intensities2.Add(1); intensities2.Add(1); } var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false); var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2)); scan2.ComputeSelectedPeakIntensity(MassSpectrum1); scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1); ScansHere.Add(scan2); Scans = ScansHere.ToArray(); }
public TestDataFile(PeptideWithSetModifications pepWithSetMods, string v) : base(2, new SourceFile(null, null, null, null, null)) { if (v.Equals("quadratic")) { // Add three ms1 peaks with charge 2, exact var MassSpectrum1 = new MzSpectrum(new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + Constants.C13MinusC12).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2 * Constants.C13MinusC12).ToMz(2) }, new double[] { 1, 1, 1 }, false); List <double> mz2 = new List <double>(); List <double> intensities2 = new List <double>(); foreach (var aok in pepWithSetMods.Fragment(DissociationType.HCD, FragmentationTerminus.Both)) { var t1 = aok.NeutralMass.ToMz(1); var c = 0.0000001; mz2.Add(t1 + c * Math.Pow(t1, 2)); var t2 = (aok.NeutralMass + Constants.C13MinusC12).ToMz(1); mz2.Add(t2 + c * Math.Pow(t2, 2)); intensities2.Add(1); intensities2.Add(1); } var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false); var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2)); scan2.ComputeSelectedPeakIntensity(MassSpectrum1); scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1); var ScansHere = new List <MsDataScan> { new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1"), scan2 }; Scans = ScansHere.ToArray(); } }
public TestDataFile(PeptideWithSetModifications pepWithSetMods) : base(2, new SourceFile(@"no nativeID format", "mzML format", null, "SHA-1", @"C:\fake.mzML", null)) { var mz1 = new double[] { pepWithSetMods.MonoisotopicMass.ToMz(2), (pepWithSetMods.MonoisotopicMass + 1.003).ToMz(2), (pepWithSetMods.MonoisotopicMass + 2.005).ToMz(2) }; var intensities1 = new double[] { 1, 1, 1 }; var MassSpectrum1 = new MzSpectrum(mz1, intensities1, false); var ScansHere = new List <MsDataScan> { new MsDataScan(MassSpectrum1, 1, 1, true, Polarity.Positive, 1, new MzLibUtil.MzRange(0, 10000), "ff", MZAnalyzerType.Unknown, 1000, 1, null, "scan=1") }; List <double> mz2 = new List <double>(); List <double> intensities2 = new List <double>(); foreach (var aok in pepWithSetMods.CompactPeptide(TerminusType.None).ProductMassesMightHaveDuplicatesAndNaNs(new List <ProductType> { ProductType.B, ProductType.Y })) { mz2.Add(aok.ToMz(1)); mz2.Add((aok + 1.003).ToMz(1)); intensities2.Add(1); intensities2.Add(1); } var MassSpectrum2 = new MzSpectrum(mz2.OrderBy(b => b).ToArray(), intensities2.ToArray(), false); var scan2 = new MsDataScan(MassSpectrum2, 2, 2, true, Polarity.Positive, 2, new MzLibUtil.MzRange(0, 10000), "df", MZAnalyzerType.Orbitrap, 234734, 1, null, "scan=2", pepWithSetMods.MonoisotopicMass.ToMz(2), 2, 1, pepWithSetMods.MonoisotopicMass.ToMz(2), 2, DissociationType.HCD, 1, pepWithSetMods.MonoisotopicMass.ToMz(2)); scan2.ComputeSelectedPeakIntensity(MassSpectrum1); scan2.ComputeMonoisotopicPeakIntensity(MassSpectrum1); ScansHere.Add(scan2); Scans = ScansHere.ToArray(); }