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();
}