Inferring direct interactions from actual AP-MS dataset. Overlap between the Y2 H interaction network of Yu et al. and various AP-MS-based networks: (a) High-confidence set of interactions from Krogan et al. (b) Set of 164 highest scoring interactions from Krogan et al. (c) Set of 164 interactions predicted as direct interactions by our algorithms, based on the AP-MS data from Krogan et al.