A method and system for deconvolution of a frequency spectrum obtained in an ICR mass spectrometer based on a detection of ion oscillation overtones of the M-th order (where the integer M>1). A plurality of frequency peaks is collected within the frequency spectrum corresponding respectively to oscillations of different groups of ions, and associates at least one of the frequency peaks having a frequency f and a measured amplitude A with a particular group of the ions. The method and system identify whether the frequency peak is related to one of an overtone frequency, a subharmonic frequency, a higher harmonic frequency, or a side-shifted frequency of the oscillations of the different group of ions. The method and system derive calculated amplitudes of the overtone frequency peaks associated with the groups of ions by incorporating measured amplitudes of the frequency peaks related to the subharmonic frequency, the higher harmonic frequency, or the side-shifted frequency associated with the groups of ions into the calculated amplitudes of the overtone frequency peaks. The method and system generate a deconvoluted frequency spectrum including the overtone frequency peaks associated with the different groups of ions.