The atomic masses of the proton, deuteron, triton and helion are regarded as fundamental constants and impact several areas of physics. In particular, a high-precision value for the mass difference between tritium and helium-3 is important for testing systematics in the ongoing KATRIN neutrino mass experiment, while the deuteron-proton mass ratio is important for interpreting the results of recent high-precision laser and teraherz spectroscopy of the HD+ molecular ion. At FSU we precisely measure mass ratios of ions from their cyclotron frequency ratios, trapping the two ions simultaneously in a Penning trap. For most of these measurements we alternated each ion between the center of the trap, where its cyclotron frequency was measured, and a large cyclotron “parking” orbit. Our measurements on mass-3 ions, besides providing an important datum for KATRIN, revealed significant error in previously accepted values for the masses of p, d and h. In the case of measurements of H₂+ against D+, we achieved sufficient resolution to distinguish different vibrational levels of H₂+ by their difference in mass, and also to observe Stark quenching of the vibrational motion. Recently, we have placed a H₂+ and D+ in a strongly coupled magnetron orbit and measured their cyclotron frequencies simultaneously. This suppresses the effect of variation in the magnetic field by several orders of magnitude. It also reduces uncertainty related to measurement of the ions’ axial frequencies. Using this technique we have partly resolved H₂+ rotational energy through the change in mass. This resulted in a value for m_d/m_p at 5 x 10^-12 and the first mp at 10^-11.