A theoretical approach to investigate the effects of the breakdown of the Born-Oppenheimer approximation in vibration-rotational spectra of polyatomic molecules in their electronic ground state is developed. The treatment is based on the derivation of an effective nuclear Hamiltonian in a space-fixed frame including adiabatic and non-adiabatic terms involving isotopically invariant functions of internuclear distances. At the stage of the transformation of this Hamiltonian into the molecular frame, the treatment is restricted to linear molecules, and adiabatic and non-adiabatic corrections to the potential and vibration-rotational kinetic energies respectively are calculated in the triatomic case. The advantages of this approach relative to that formerly used for diatomic molecules from the point of view of deriving mass independent spectroscopic parameters are discussed.