We show two effects as a result of considering the second-order correction to the spectrum of a nanomechanical resonator electrostatically coupled to a Cooper-pair box. The spectrum of the Cooper-pair box is modified in a way which depends on the Fock state of the resonator. Similarly, the frequency of the resonator becomes dependent on the state of the Cooper-pair box. We consider whether these frequency shifts could be utilized to prepare the nanomechanical resonator in a Fock state, to perform a quantum non-demolition measurement of the resonator Fock state, and to distinguish the phase states of the Cooper-pair box.