public static void TestMs2ScanWithSpecificMass()
{
Ms2ScanWithSpecificMass scanB = new Ms2ScanWithSpecificMass(
new MsDataScan(
new MzSpectrum(new double[] { }, new double[] { }, false),
2, 1, true, Polarity.Positive, double.NaN, null, null, MZAnalyzerType.Orbitrap, double.NaN, null, null, "scan=1", double.NaN, null, null, double.NaN, null, DissociationType.AnyActivationType, 1, null),
100, 1, null, new CommonParameters(), null);
var closestExperimentalMassB = scanB.GetClosestExperimentalIsotopicEnvelope(10);
Assert.IsNull(closestExperimentalMassB);
}
//Based on our implementation of Graph localization. We need to calculate cost between two nearby nodes (glycosites)
public static double CalculateCost(Ms2ScanWithSpecificMass theScan, Tolerance productTolerance, List <double> fragments)
{
double score = 0;
foreach (var f in fragments)
{
var closestExperimentalMass = theScan.GetClosestExperimentalIsotopicEnvelope(f);
// is the mass error acceptable?
if (productTolerance.Within(closestExperimentalMass.MonoisotopicMass, f) && closestExperimentalMass.Charge <= theScan.PrecursorCharge)
{
score += 1 + closestExperimentalMass.Peaks.Sum(p => p.intensity) / theScan.TotalIonCurrent;
}
}
return(score);
}
public static double[] ScanOxoniumIonFilter(Ms2ScanWithSpecificMass theScan, MassDiffAcceptor massDiffAcceptor, DissociationType dissociationType)
{
double[] oxoniumIonsintensities = new double[Glycan.AllOxoniumIons.Length];
if (dissociationType != DissociationType.HCD && dissociationType != DissociationType.CID && dissociationType != DissociationType.EThcD)
{
return(oxoniumIonsintensities);
}
for (int i = 0; i < Glycan.AllOxoniumIons.Length; i++)
{
var oxoMass = ((double)Glycan.AllOxoniumIons[i] / 1E5).ToMass(1);
var envelope = theScan.GetClosestExperimentalIsotopicEnvelope(oxoMass);
if (massDiffAcceptor.Accepts(envelope.MonoisotopicMass, oxoMass) >= 0)
{
oxoniumIonsintensities[i] = envelope.TotalIntensity;
}
}
return(oxoniumIonsintensities);
}