A method is disclosed for operating a mass spectrometer having a Fourier Transform (FT) analyzer, such as an orbital electrostatic trap mass analyzer, to avoid peak coalescence and/or other phenomena arising from frequency-shifting caused by ion-ion interactions. Ions of a first group are mass analyzed, for example in a quadrupole ion trap analyzer, to generate a mass spectrum. The estimated frequency shift of the characteristic periodic motion in the FT analyzer is calculated for one or more ion species of interest based on the intensities of adjacent (closely m/z-spaced) ion species. If the estimated frequency shift(s) for the one or more ion species exceeds a threshold, then a target ion population for an FT analyzer scan is adjusted downwardly to a value that produces a shift of acceptable value. An analytical scan of a second ion group is performed at the adjusted target ion population.