In this contribution the emission of gold-molecule cluster ions from self-assembled monolayers (SAMs) of alkanethiols on gold is investigated using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Layers of alkanethiols [CH 3(CH 2) n SH] with various chain lengths ( n=8, 12, 16) have been chosen because they form well-ordered molecular monolayers on gold. First, we compare and interpret the yields and energy spectra of gold-thiolate cluster ions, obtained for different thiol sizes. Our results show that the unimolecular dissociation of larger aggregates in the acceleration section of the spectrometer constitutes a significant formation channel for gold-molecule clusters. Second, we present preliminary results of molecular dynamics simulations performed in order to improve our understanding of the cluster emission processes. These calculations have been conducted using 8 keV projectiles and a long-range term in the hydrocarbon potential in order to account for the van der Waals forces between the thiol chains.