Functionalized nanoparticles provide a wide range of potential applications for Biological Mass Spectrometry (MS). Particularly, we have studied the effects of chromophore activity on the performance of gold nanoparticles (AuNPs) capped with substituted azo (-N=N-) dyes for analyte ion production in Laser Desorption Ionization Mass Spectrometry (LDI-MS) conditions. A series of aromatic thiol compounds were used as Self-Assembled Monolayers (SAM) to functionalize the surface of the AuNPs. Results indicate that AuNPs functionalized with molecules having an active azo chromophore provide enhanced analyte ion yields than the nanoparticles capped with the hydrazino analogs or simple substituted aromatic thiols. We have also conducted experiments using the azo SAM molecules on 2, 5, 20, 30, and 50 nm AuNPs exploring the changes of Relative Ion Yield (RIY) with increased AuNP diameters. Our results indicate that the role of the SAM to drive energy deposition decreases as the size of the AuNP increases. It was determined that 5 nm is the optimum size to exploit the benefits of the SAM on the ionization and selectivity of the AuNPs.