Silver nanoparticles with mixed ligand self-assembled monolayers were synthesized from dodecanethiol and another ligand from a homologous series of alkanethiols (butanethiol, pentanethiol, heptanethiol, octanethiol, nonanethiol, decanethiol, undecanethiol, or dodecanethiol[D25]). These were hypothesized to exhibit ligand phase separation that increases with degree of physical mismatch between the ligands based on the difference in the number of carbons in the two ligands. Dodecanethiol/dodecanethiol[D25] was expected to exhibit minimal phase separation as the ligands have only isotopic differences, while dodecanethiol/butanethiol was hypothesized to exhibit the most phase separation due to the difference in chain length. Phase separation of all other ligand mixtures was expected to fall between these two extremes. Matrix-assisted laser desorption ionization (MALDI) mass spectroscopy provided a value for ligand phase separation by comparison with a binomial (random) model and subsequent calculation of the sum-of-squares error (SSR). These nanoparticle systems were also modeled using the Scheutjens and Fleer self-consistent mean-field theory (SCFT), which determined the most thermodynamically favorable arrangement of ligands on the surface. From MALDI, it was found that dodecanethiol/dodecanethiol[D25] formed a well-mixed monolayer with SSR = 0.002, and dodecanethiol/butanethiol formed a microphase separated monolayer with SSR = 0.164; in intermediate dodecanethiol/alkanethiol mixtures, SSR increased with increasing ligand length difference as expected. For comparison with experiment, an effective SSR value was calculated from SCFT simulations. The SSR values obtained by experiment and theory show good agreement and provide strong support for the validity of SCFT predictions of monolayer structure. These approaches represent robust methods of characterization for ligand phase separation on silver nanoparticles.