public void TestOutput()
{
double isolationMz = 1000.0;
double precursorMz = 999.5;
int charge = 2;
double isolationWindow = 1.0;
var peaks = new List <Centroid> {
new Centroid {
Mz = 800.0, Intensity = 100
},
new Centroid {
Mz = 999.5, Intensity = 100
},
new Centroid {
Mz = 999.9, Intensity = 100
},
new Centroid {
Mz = 1000.0, Intensity = 100
},
new Centroid {
Mz = 1000.1, Intensity = 100
},
new Centroid {
Mz = 1200.0, Intensity = 100
}
};
double output = IsolationSpecificityCalculator.calculate(peaks, isolationMz, precursorMz, charge, isolationWindow);
Assert.Equal(0.5, output, 3);
}
/// <summary>
/// Run a single Monocle scan.
/// </summary>
/// <param name="Ms1ScansCentroids"></param>
/// <param name="ParentScan"></param>
/// <param name="precursor"></param>
public static void Run(List <Scan> Ms1ScansCentroids, Scan ParentScan, Precursor precursor, MonocleOptions Options)
{
double precursorMz = precursor.IsolationMz;
if (precursorMz < 1)
{
precursorMz = precursor.Mz;
}
int precursorCharge = precursor.Charge;
if (Options.UseMostIntense && precursor.IsolationWidth > 0)
{
// Re-assign the precursor m/z to that of the most intense peak in the isolation window.
int peakIndex = PeakMatcher.MostIntenseIndex(ParentScan, precursor.IsolationMz, precursor.IsolationWidth / 2, PeakMatcher.DALTON);
if (peakIndex >= 0)
{
precursorMz = ParentScan.Centroids[peakIndex].Mz;
}
}
// Search for ion in parent scan, use parent ion mz for future peaks
int index = PeakMatcher.Match(ParentScan, precursorMz, 50, PeakMatcher.PPM);
if (index >= 0)
{
precursorMz = ParentScan.Centroids[index].Mz;
}
// For charge detection
int bestCharge = 0;
double bestScore = -1;
int bestIndex = 0;
List <double> bestPeaks = new List <double>();
List <double> bestPeakIntensities = new List <double>();
//Create new class to maintain ref class options
ChargeRange chargeRange = new ChargeRange(precursorCharge, precursorCharge);
if (Options.Charge_Detection || precursorCharge == 0)
{
chargeRange.Low = Options.Charge_Range.Low;
chargeRange.High = Options.Charge_Range.High;
}
for (int charge = chargeRange.Low; charge <= chargeRange.High; charge++)
{
// Restrict number of isotopes to consider based on precursor mass.
double mass = precursor.Mz * charge;
var isotopeRange = new IsotopeRange(mass);
// Generate expected relative intensities.
List <double> expected = PeptideEnvelopeCalculator.GetTheoreticalEnvelope(precursorMz, charge, isotopeRange.CompareSize);
Vector.Scale(expected);
PeptideEnvelope envelope = PeptideEnvelopeExtractor.Extract(Ms1ScansCentroids, precursorMz, charge, isotopeRange.Left, isotopeRange.Isotopes);
// Get best match using dot product.
// Limit the number of isotopeRange peaks to test
for (int i = 0; i < (isotopeRange.Isotopes - (isotopeRange.CompareSize - 1)); ++i)
{
List <double> observed = envelope.averageIntensity.GetRange(i, expected.Count);
Vector.Scale(observed);
PeptideEnvelopeExtractor.ScaleByPeakCount(observed, envelope, i);
double score = Vector.Dot(observed, expected);
// add 5% to give bias toward left peaks.
if (score > bestScore * 1.05)
{
bestScore = score;
if (score > 0.1)
{
// A peak to the left is included, so add
// offset to get monoisotopic index.
bestIndex = i + 1;
bestCharge = charge;
bestPeaks = envelope.mzs[bestIndex];
bestPeakIntensities = envelope.intensities[bestIndex];
}
}
}
} // end charge for loop
if (bestCharge > 0)
{
precursor.Charge = bestCharge;
}
// Calculate m/z
if (bestPeaks.Count > 0)
{
precursor.Mz = Vector.WeightedAverage(bestPeaks, bestPeakIntensities);
}
else
{
precursor.Mz = precursorMz;
}
precursor.IsolationSpecificity = IsolationSpecificityCalculator.calculate(
ParentScan.Centroids,
precursor.IsolationMz,
precursor.Mz,
precursor.Charge,
precursor.IsolationWidth
);
}
