public void TestIsotopePeakAlignment(string rawFilePath, string idFilePath)
{
var idFileReader = IdFileReaderFactory.CreateReader(idFilePath);
var lcms = PbfLcMsRun.GetLcMsRun(rawFilePath);
var ids = idFileReader.Read();
var idList = ids.ToList();
var rawFileName = Path.GetFileNameWithoutExtension(rawFilePath);
foreach (var id in idList)
{
id.LcMs = lcms;
id.RawFileName = rawFileName;
}
var prsms = idList.Where(prsm => prsm.Sequence.Count > 0);
const double relIntThres = 0.1;
var tolerance = new Tolerance(10, ToleranceUnit.Ppm);
var toleranceValue = tolerance.GetValue();
const int maxCharge = 15;
var ionTypeFactory = new IonTypeFactory(maxCharge);
var ionTypes = ionTypeFactory.GetAllKnownIonTypes().ToArray();
var psmsValidated = 0;
var ionsValidated = 0;
var validationErrors = new List <string>();
foreach (var prsm in prsms)
{
foreach (var ionType in ionTypes)
{
var composition = prsm.Sequence.Aggregate(Composition.Zero, (current, aa) => current + aa.Composition);
var ion = ionType.GetIon(composition);
var observedPeaks = prsm.Ms2Spectrum.GetAllIsotopePeaks(ion, tolerance, relIntThres);
if (observedPeaks == null)
{
continue;
}
var errors = IonUtils.GetIsotopePpmError(observedPeaks, ion, relIntThres);
foreach (var error in errors)
{
if (error == null)
{
continue;
}
if (error > toleranceValue)
{
validationErrors.Add(string.Format("In scan {0}, PSM {1} has error {2:F1} for ion at {3} m/z",
prsm.Scan, prsm.SequenceText, error, ion.GetIsotopeMz(0)));
}
ionsValidated++;
}
}
psmsValidated++;
}
Console.WriteLine("Validated {0:N0} ions for {1:N0} PSMs", ionsValidated, psmsValidated);
if (validationErrors.Count <= 0)
{
return;
}
var validationMsg = string.Format("{0} ions had errors greater than {1} ppm", validationErrors.Count, tolerance);
Console.WriteLine(validationMsg);
foreach (var item in validationErrors.Take(10))
{
Console.WriteLine(item);
}
Assert.Fail(validationMsg);
}
/// <summary>
/// Get the peaks for the ion.
/// </summary>
/// <param name="spectrum">The spectrum to get the peaks from</param>
/// <param name="o">Object required for cache</param>
/// <returns>The peaks for the ion.</returns>
private IList <PeakDataPoint> GetPeakDataPoints(Tuple <Spectrum, bool> spectrum, object o)
{
var tolerance = this.IsFragmentIon
? IcParameters.Instance.ProductIonTolerancePpm
: IcParameters.Instance.PrecursorTolerancePpm;
var noPeaks = new List <PeakDataPoint>
{
new PeakDataPoint(double.NaN, double.NaN, double.NaN, double.NaN, this.Label)
{
TheoMonoisotopicMass = this.Ion.Composition.Mass,
IonType = this.IonType,
Index = this.Index
}
};
var peakDataPoints = new List <PeakDataPoint>();
IonType ionType = null;
if (this.IsFragmentIon)
{
ionType = this.IonType;
}
var deconvoluted = spectrum.Item2;
Ion ion;
if (deconvoluted)
{
if (this.IonType.Charge > 1)
{
return(peakDataPoints); // Deconvoluted spectrum means decharged (only charge 1 ions shown)
}
if (!this.IsFragmentIon)
{
ion = new Ion(this.Composition, 1);
}
else
{
var ionTypeFactory = IcParameters.Instance.DeconvolutedIonTypeFactory;
var ionTypeName = this.IonType.Name.Insert(1, @"'");
ion = ionTypeFactory.GetIonType(ionTypeName).GetIon(this.Composition);
}
}
else
{
ion = this.Ion;
}
var labeledIonPeaks = IonUtils.GetIonPeaks(ion, spectrum.Item1, tolerance, deconvoluted);
if (labeledIonPeaks.Item1 == null)
{
return(noPeaks);
}
var peaks = labeledIonPeaks.Item1;
var correlation = labeledIonPeaks.Item2;
if (correlation < IcParameters.Instance.IonCorrelationThreshold)
{
return(noPeaks);
}
var errors = IonUtils.GetIsotopePpmError(peaks, ion, 0.1, deconvoluted);
peakDataPoints = new List <PeakDataPoint> {
Capacity = errors.Length
};
for (int i = 0; i < errors.Length; i++)
{
if (errors[i] != null)
{
peakDataPoints.Add(new PeakDataPoint(peaks[i].Mz, peaks[i].Intensity, errors[i].Value, correlation, this.Label)
{
MonoisotopicMass = (peaks[i].Mz * this.Ion.Charge) - InformedProteomics.Backend.Data.Biology.Constants.Proton * this.Ion.Charge,
TheoMonoisotopicMass = this.Ion.Composition.Mass,
Index = this.Index,
IonType = ionType,
});
}
}
peakDataPoints = peakDataPoints.OrderByDescending(x => x.Y).ToList();
return(peakDataPoints);
}
