private static ThermoMzPeak GetPeak(PSM psm, double oxoniumIon, ThermoRawFile rawFile)
{
DoubleRange rangeOxonium = DoubleRange.FromPPM(oxoniumIon, 20);
List <ThermoMzPeak> peaks;
ThermoSpectrum spec = rawFile.GetSpectrum(psm.scanNumber);
if (spec.TryGetPeaks(rangeOxonium, out peaks))
{
peaks = peaks.OrderBy(x => x.SignalToNoise).ToList();
}
double diff = double.MaxValue;
ThermoMzPeak returnPeak = null;
foreach (ThermoMzPeak peak in peaks)
{
var currDiff = Math.Abs(peak.MZ - oxoniumIon);
if (currDiff < diff)
{
diff = currDiff;
returnPeak = peak;
}
}
return(returnPeak);
}
public static double CheckPeak(ThermoMzPeak peak)
{
double intensity = 0;
if (peak != null)
{
intensity = peak.Intensity;
}
return(intensity);
}
public RTPeak(MZPeak peak, double RT)
{
this._intensity = peak.Intensity;
this._mz = peak.MZ;
this._rt = RT;
this.Peak = peak;
ThermoMzPeak labelPeak = ((ThermoMzPeak)peak);
this.charge = labelPeak.Charge;
this.Sn = labelPeak.GetSignalToNoise();
}
public static ThermoMzPeak GetClosestPeak(List <ThermoMzPeak> peaks, double expMZ)
{
double diff = double.MaxValue;
ThermoMzPeak returnPeak = null;
foreach (var peak in peaks)
{
var currDiff = Math.Abs(peak.MZ - expMZ);
if (currDiff < diff)
{
diff = currDiff;
returnPeak = peak;
}
}
return(returnPeak);
}
static void Main(string[] args)
{
UsefulProteomicsDatabases.Loaders.LoadElements("elements.dat");
var tol = 0.01;
var Compound1 = new Peptide("NNNNN");
var regularMZ = new IsotopicDistribution(Compound1.GetChemicalFormula(), 0.1, 0.001).Masses.Select(b => b.ToMassToChargeRatio(1)).ToList();
Console.WriteLine("NNNNN mz: " + string.Join(", ", regularMZ));
var withAmmoniaLoss = Compound1.GetChemicalFormula();
withAmmoniaLoss.Add(new ChemicalFormula("N-1H-2"));
var withAmmoniaLossMZ = new IsotopicDistribution(withAmmoniaLoss, 0.1, 0.001).Masses.Select(b => b.ToMassToChargeRatio(1)).ToList();
Console.WriteLine("withAmmoniaLoss mz: " + string.Join(", ", withAmmoniaLossMZ));
var deamidated = Compound1.GetChemicalFormula();
deamidated.Add(new ChemicalFormula("H-1N-1O"));
var deamidatedMZ = new IsotopicDistribution(deamidated, 0.1, 0.001).Masses.Select(b => b.ToMassToChargeRatio(1)).ToList();
Console.WriteLine("deamidated mz: " + string.Join(", ", deamidatedMZ));
List <List <double> > allDistributions = new List <List <double> >()
{
regularMZ, withAmmoniaLossMZ, deamidatedMZ
};
foreach (var arg in args)
{
var file = new ThermoRawFile(arg);
file.Open();
string output_filepath = file.FilePath.Remove(file.FilePath.IndexOf(".raw"), ".raw".Length); //removes .raw at end for output
using (System.IO.StreamWriter shiftsFile = new System.IO.StreamWriter(output_filepath + ".tsv"))
{
shiftsFile.WriteLine(file.FilePath);
Console.WriteLine(file.FilePath);
foreach (var scan in file)
{
if (scan.MsnOrder == 1)
{
double bestIntensity = 0;
double monoError = double.NaN;
foreach (var dist in allDistributions)
{
ThermoMzPeak monoisotopicPeak = null;
try { monoisotopicPeak = scan.MassSpectrum.newSpectrumExtract(dist[0] - tol, dist[0] + tol).PeakWithHighestY; }
catch { }
if (monoisotopicPeak != null && bestIntensity < monoisotopicPeak.Intensity)
{
bestIntensity = monoisotopicPeak.Intensity;
monoError = dist[0] - monoisotopicPeak.MZ;
}
}
shiftsFile.WriteLine(scan.ScanNumber + "\t" + monoError);
}
}
}
}
}
