The NA60 experiment has studied low-mass muon pair production in proton-nucleus collisions with a system of Be, Cu, In, W, Pb and U targets using a 400 GeV/$c$ proton beam at the CERN SPS. The mass spectrum is well described by the superposition of the two-body and Dalitz decays of the light neutral mesons $eta$, $rho$, $omega$, $eta$ and $phi$. A new high-precision measurement of the electromagnetic transition form factors of the $eta$ and $omega$ mesons is presented, complemented with a measurement of the temperature parameter of the $rho$ meson in cold nuclear matter. The $pt$ spectra for the $omega$ and $phi$ mesons are extracted in the full $pt$ range accessible, up to $pt = 2$ GeV/$c$. The nuclear dependence of the production cross sections for the $eta$, $omega$ and $phi$ mesons has been investigated in terms of the power law $sigma_mathrm{pA} propto mathrm{A}^alpha$, and the $alpha$ parameter was studied as a function of $pt$.