The orbital trap mass analyzer provides a number of unique analytical features along with inevitable limitations as an electrostatic instrument operating in high space charge regimes resulting in systematic measured frequency errors as an effect of stored ion clouds on the trap field and each other effect of non-ideal machining the trap electrodes, effect of injection slot, effect of real versus theoretical trap dimensions, etc. This paper deals with determining the influence of the space charge effect and imperfection of the electrostatic field on the motion of ion ensembles in the orbital trap. We examine effects of theoretically modeled non-harmonicity of the electrostatic potential and the number of confined ions on stability of coherent ion motion in the trap that determines the frequency shifts of axial ion oscillation. Three different Orbitrap geometries were considered: geometry close to preproduction Orbitrap, close to standard Orbitrap, close to high field Orbitrap. Frequency shifts for m/z = 500 and for charge state +23 of cytochrome c isotopic cluster particles with 10(4)-6*10(6) elemental charges in the trap were considered. Refined spectra were calculated using the filter diagonalization method proposed by Mandelshtam et al. and applied to mass spectrometry by O'Connor and Aizikov.