A method for improving the calibration of a Fourier transform ion cyclotron resonance mass spectrometer wherein the frequency spectrum of a sample has been measured and the frequency (f) and intensity (I) of at least three species having known mass to charge (m/z) ratios and one specie having an unknown (m/z) ratio have been identified. The method uses the known (m/z) ratios, frequencies, and intensities at least three species to calculate coefficients A, B, and C, wherein the mass to charge ratio of a least one of the three species (m/z)i is equal to A f i + B f i 2 + C · G ⁡ ( I i ) f i Q wherein fi is the detected frequency of the specie, G(Ii) is a predetermined function of the intensity of the species, and Q is a predetermined exponent. Using the calculated values for A, B, and C, the mass to charge ratio of the unknown specie (m/z)ii is calculated as the sum of A f ii + B f ii 2 + C · G ⁡ ( I ii ) f ii Q wherein fii is the measured frequency of the unknown specie, and (Iii) is the measured intensity of the unknown specie.