This thesis reports on the setup of a new ion trap apparatus designed for experiments with single ⁴⁰Ca⁺ ions to perform molecular spectroscopy. The calcium ion is laser cooled, allowing for sympathetic cooling of the nonfluorescing molecular ion. The aim of these experiments is to explore loading and identifying molecular ions in RF-Paul traps, as well as developing new spectroscopic tools to measure transitions of molecular ions via the fluorescence of co-trapped ⁴⁰Ca⁺ ions. Ground state cooling of a mixed ion pair is implemented as a first step towards increasing the sensitivity of our technique to the level necessary to measure transitions with low scattering rates (like those present in molecular ions). Doppler cooling on the S(1/2)->P(1/2) transition of the calcium ion results in the formation of a Coulomb crystal, the behavior of which may be used to infer properties of the molecular ion. Following cooling, sideband spectroscopy on the narrow S(1/2)->D(5/2) quadrupole transition of calcium may be used to identify the mass of single molecular ions. This method is verified via a non-destructive measurement on ⁴⁰CaH⁺ and ⁴⁰Ca¹⁶O⁺. The normal modes of the Coulomb crystal can also be used to extract information from the target ion to the control ion. By driving the blue side of a transition, laser induced heating can be put into the two ion system, which leads to changes in fluorescence of the ⁴⁰Ca⁺ ion, first demonstrated with two Ca⁺ isotopes. Increasing the sensitivity of this technique requires ground state cooling of both the ⁴⁰Ca⁺ ion and the ion of interest, enabling the transfer of the ion's motional state into the ground state with high probability. This thesis demonstrates ground state cooling of the atomic ion and sympathetic cooling of a second ion (⁴⁴Ca⁺). Once in the ground state, heating of the Coulomb crystal by scattering photons off of the spectroscopy ion can be measured by monitoring the resolved motional sidebands of the S(1/2)->D(5/2) transition of ⁴⁰Ca⁺, allowing for spectral lines to be inferred. Future experiments will investigate this technique with molecular ions.