We employ an atomic-scale theory within the framework of nonaffine lattice dynamics to uncover the origin of the Johari-Goldstein (JG) $\beta$-relaxation in metallic glasses (MGs). Combining simulation and experimental data with our theoretical approach, we reveal that the large mass asymmetry between the elements in a La$_{60}$Ni$_{15}$Al$_{25}$ MG leads to a clear separation in the respective relaxation time scales, giving strong evidence that JG relaxation is controlled by the lightest atomic species present. Moreover, we show that only qualitative features of the vibrational density of states determine the overall observed mechanical response of the glass, paving the way for a possible unified theory of secondary relaxations in glasses.