/// <summary> /// Returns the index of the most intense peak in the window. /// Returns -1 if none is found. /// </summary> /// <param name="scan">The scan that will be searched</param> /// <param name="targetMz">The center of the window where peaks will be considered</param> /// <param name="tolerance">window will be +/- this value</param> /// <param name="tolUnits">Units can be DALTON or PPM</param> /// <returns></returns> public static int MostIntenseIndex(Scan scan, double targetMz, double tolerance, int tolUnits) { double lowMz = targetMz - tolerance; double highMz = targetMz + tolerance; if (tolUnits == PPM) { double delta = tolerance * targetMz / 1000000; lowMz = targetMz - delta; highMz = targetMz + delta; } var peaks = scan.Centroids; int i = PeakMatcher.NearestIndex(peaks, lowMz); if (peaks[i].Mz < lowMz) { ++i; } double maxIntensity = 0; int bestIndex = -1; for ( ; i < peaks.Count && peaks[i].Mz < highMz; ++i) { if (peaks[i].Intensity > maxIntensity) { maxIntensity = peaks[i].Intensity; bestIndex = i; } } return(bestIndex); }
public static double calculate(List <Centroid> peaks, double isolationMz, double precursorMz, int charge, double isolationWindow) { if (peaks.Count == 0) { return(0); } double precursorIntensity = 0; double totalIntensity = 0; double lowMz = isolationMz - (isolationWindow / 2.0); double highMz = isolationMz + (isolationWindow / 2.0); int i = PeakMatcher.NearestIndex(peaks, lowMz); if (peaks[i].Mz < lowMz) { ++i; } for ( ; i < peaks.Count && peaks[i].Mz < highMz; ++i) { var peak = peaks[i]; // if the peak is within 20 ppm of any isotope bool isPrecursor = false; for (int j = -6; j < 7; ++j) { double theoreticalMass = precursorMz + (j * (Mass.AVERAGINE_DIFF / charge)); if (System.Math.Abs(PeakMatcher.getPpm(theoreticalMass, peak.Mz)) < 20) { isPrecursor = true; break; } } if (isPrecursor) { precursorIntensity += peak.Intensity; } totalIntensity += peak.Intensity; } if (totalIntensity < 1) { return(0); } return(precursorIntensity / totalIntensity); }