Nanopore-based resistive pulse sensing with biological nanopores has traditionally been applied to biopolymer analysis, but more recently, interest has grown in applying the technique to characterizing water-soluble metallic clusters. This paper reports on the use of alpha-hemolysin (alpha HL) for detecting a variety of thiolate-capped gold nanoclusters. The ligands studied here are p-mercaptobenzoic acid (p-MBA), tiopronin (TP), and thiolated PEG(7) (S-PEG(7)). Individual clusters trapped in the cis-side of an alpha HL pore for extended periods (>10 s) exhibit fluctuations between numerous substates. We compare these current steps between the three different ligands and find that they scale with the mass of the corresponding ligand, which suggests that nanopore sensing could be used to characterize intraparticle surface modifications.