Protein-protein interactions, whether desirable or not, can have direct effects on protein separations. The most obvious of these are interactions between similar molecules, which determine the thermodynamic properties and phase behavior of protein solutions. Interactions between dissimilar molecules also affect the properties and phase behavior of protein mixtures and, therefore, protein separations. Here, we seek to quantify these effects by comparing precipitation behavior from binary solutions with direct measurements of protein-protein interactions using cross-interaction chromatography, which is a variant of affinity chromatography that provides data that can be interpreted in terms of the virial cross-coefficient. First, the effects of pH, ionic strength, different precipitants and the initial protein concentrations and their ratio on the binary precipitation of lysozyme and ovalbumin were investigated. Next, self- and cross-interaction measurements were used to suggest the optimal precipitation conditions for separating lysozyme from ovalbumin. The results show that protein interactions can explain anomalies and inconsistencies that frequently confound the extraction of meaningful general trends in separations analyses.