/// <summary>
/// joins the spectra formed by the isotopes of n elements
/// </summary>
/// <param name="ItPeaks">(double[elements,kmax]) spectra of the elements</param>
/// <returns>(double[]) sum spectrum of the n elements</returns>
private static mzI[] joinIsot(double[,] ItPeaks, double thPrecMass)
{
int bound = ItPeaks.GetUpperBound(1);
int bound2 = ItPeaks.GetUpperBound(0);
// massShift was: mass shift from each peak to the next peak
// currently, as most experiments analysed by QuiXoT are 18O,
// it is set to deltaR/2, where deltaR is the difference between
// 16O and 16O
double massShift = 2.00424578 / 2;
mzI[] sum = new mzI[bound + 1];
mzI[] jIsot = new mzI[bound + 1];
//Initialize the matrix sum with the first value of the matrix ItPeaks
for (int i = 0; i <= bound; i++)
{
sum[i].I = ItPeaks[0, i];
sum[i].mz = thPrecMass + i * massShift;
}
//Join the spectra in the matrix sum
if (ItPeaks.GetUpperBound(0) > 1)
{
for (int numSpectra = 1; numSpectra <= bound2; numSpectra++)
{
for (int i = 0; i <= bound; i++)
{
for (int j = 0; j <= bound; j++)
{
if ((i + j) <= bound)
{
jIsot[i + j].I += sum[i].I * ItPeaks[numSpectra, j];
jIsot[i + j].mz = thPrecMass + (i * massShift + j);
}
}
}
jIsot.CopyTo(sum, 0);
if (numSpectra < bound2)
{
jIsot = null;
jIsot = new mzI[bound + 1];
}
}
}
return(jIsot);
}
/// <summary>
/// joins the spectra formed by the isotopes of n elements
/// </summary>
/// <param name="ItPeaks">(double[elements,kmax]) spectra of the elements</param>
/// <returns>(double[]) sum spectrum of the n elements</returns>
private static mzI[] joinIsot(double[,] ItPeaks, double thPrecMass)
{
int bound = ItPeaks.GetUpperBound(1);
int bound2 = ItPeaks.GetUpperBound(0);
double massShift = 1.003;
mzI[] sum = new mzI[bound + 1];
mzI[] jIsot = new mzI[bound + 1];
//Initialize the matrix sum with the first value of the matrix ItPeaks
for (int i = 0; i <= bound; i++)
{
sum[i].I = ItPeaks[0, i];
sum[i].mz = thPrecMass + i * massShift;
}
//Join the spectra in the matrix sum
if (ItPeaks.GetUpperBound(0) > 1)
{
for (int numSpectra = 1; numSpectra <= bound2; numSpectra++)
{
for (int i = 0; i <= bound; i++)
{
for (int j = 0; j <= bound; j++)
{
if ((i + j) <= bound)
{
jIsot[i + j].I += sum[i].I * ItPeaks[numSpectra, j];
jIsot[i + j].mz = thPrecMass + (i * massShift + j);
}
}
}
jIsot.CopyTo(sum, 0);
if (numSpectra < bound2)
{
jIsot = null;
jIsot = new mzI[bound + 1];
}
}
}
return(jIsot);
}
public static ArrayList calIntensitiesAveragine(double MHplus,
int charge,
double calibrationError)
{
ArrayList spectrums = new ArrayList();
mzI[] resultSpectrum = new mzI[5];
//double[] I = new double[5];
double protonMass = 1.007276466812; // source: http://physics.nist.gov/cgi-bin/cuu/Value?mpu
// massShift was: mass shift from each peak to the next peak
// currently, as most experiments analysed by QuiXoT are 18O,
// it is set to deltaR/2, where deltaR is the difference between
// 16O and 16O
double massShift = 2.00424578 / 2;
double M = MHplus - protonMass;
double y0 = -0.01709;
double A0 = 2 * 0.50059;
double t0 = 1767.46064;
double A1_0 = 0.0347;
double A1_1 = 4.78949e-4;
double A1_2 = -2.5366e-7;
double A1_3 = 5.44242e-11;
double A1_4 = -4.67415e-15;
double A2_0 = -0.02581;
double A2_1 = 1.18353e-4;
double A2_2 = 3.05798e-8;
double A2_3 = -1.95685e-11;
double A2_4 = 2.18143e-15;
double A3_0 = 0.01197;
double A3_1 = -3.95885e-5;
double A3_2 = 7.06503e-8;
double A3_3 = -1.77963e-11;
double A3_4 = 1.41202e-15;
double A4_0 = 0.0107;
double A4_1 = -2.85332e-5;
double A4_2 = 2.6899e-8;
double A4_3 = -3.7105e-12;
double A4_4 = 1.98749e-16;
// I0 = y0+A0*exp(-M/t0)
// Ii = A1_0 + A1_1 * M + A1_2 * M^2 + A1_3 * M^3 + A1_4 * M^4
resultSpectrum[0].I = y0 + A0 * Math.Exp(-M / t0);
resultSpectrum[1].I = A1_0 + A1_1 * M + A1_2 * M * M + A1_3 * M * M * M + A1_4 * M * M * M * M;
resultSpectrum[2].I = A2_0 + A2_1 * M + A2_2 * M * M + A2_3 * M * M * M + A2_4 * M * M * M * M;
resultSpectrum[3].I = A3_0 + A3_1 * M + A3_2 * M * M + A3_3 * M * M * M + A3_4 * M * M * M * M;
resultSpectrum[4].I = A4_0 + A4_1 * M + A4_2 * M * M + A4_3 * M * M * M + A4_4 * M * M * M * M;
//Correction by Mass to precursor mass --> monoisotopic mass
int correctionByMass = 0;
double maxI = 0;
for (int i = 0; i < 5; i++)
{
if (resultSpectrum[i].I > maxI)
{
maxI = resultSpectrum[i].I;
correctionByMass = i;
}
}
int secondMostIntense = 0;
double secMaxI = 0;
for (int i = 0; i < 5; i++)
{
if (resultSpectrum[i].I > secMaxI && i != correctionByMass)
{
secMaxI = resultSpectrum[i].I;
secondMostIntense = i;
}
}
resultSpectrum[0].mz = -calibrationError + (M + charge * protonMass - massShift * correctionByMass) / charge;
for (int i = 1; i < 5; i++)
{
resultSpectrum[i].mz = resultSpectrum[0].mz + i * massShift / charge;
}
spectrums.Add(resultSpectrum.Clone());
//uncertainty region for the monoisotopic mass determination
//We solve it by proposing several monoisotopic masses, and testing them by fitting & weighting the results
if (Math.Abs(maxI - secMaxI) <= 0.1)
{
resultSpectrum[0].mz = -calibrationError + (M + charge * protonMass - massShift * secondMostIntense) / charge;
for (int i = 1; i < 5; i++)
{
resultSpectrum[i].mz = resultSpectrum[0].mz + i * massShift / charge;
}
spectrums.Add(resultSpectrum.Clone());
}
return(spectrums);
}
