Differently sized dodecanethiol capped Au and Ag nanoparticles have been investigated using synchrotron radiation based photoelectron spectroscopy (PES). Comparative measurements were also performed on self-assembled monolayers (SAMs) of dodecanethiol at vacuum evaporated Au and Ag surfaces. The series of experiments display important differences in the surface electronic and molecular structure between the different kinds of materials. Specifically, the changes measured in binding energies are discussed with respect to initial and final state effects. Also, a broadening is observed for metal-core levels in the smaller nanoparticles. Thus, surface atoms in a different chemical state than the rest of the surface atoms are detected. In valence-level spectra, the matching between the orbitals centered at the surface-coating molecule and the orbitals centered on the core materials are discussed.