Two β-lactoglobulin (BLG) isoforms, BLGA and BLGB, were used as a test bed for the differentiation of proteins using electrostatics. In these studies, the BLGA and BLGB binding to a highly charged, cationic gold nanoparticle (GNP) modified surface was investigated by atomic force microscopy (AFM) and surface plasmon resonance (SPR) spectroscopy. The binding affinity, and more importantly, the selectivity of this surface towards these two almost identical protein isoforms were both significantly increased on the cationic GNP surface array relative to the values measured with the same free cationic GNP in solution. While protein recognition is traditionally achieved almost exclusively via orientation dependent short-range interactions such as hydrogen bonds and hydrophobic interactions, our results show the potential of protein recognition platforms based on enhanced electrostatic interactions.