Figure 2

The manifestation of protein complexes in Y2H and AP-MS data. AP-MS experiments measure complex co-membership, and the fact that a prey is found by a certain bait means that there is either a direct physical interaction or an indirect physical interaction mediated by a protein complex. The set of proteins pulled down by a particular bait cannot therefore be equated with a single complex: if the bait is part of several different complexes, then the set of prey will be the union of all proteins in all complexes. (a) Protein B is involved in three different multiprotein complexes. In two of these it directly interacts with C, which itself can also interact with proteins F, G or H, whereas in the third complex, B interacts with D and E. (b) Assuming there are no other interactions under the conditions of the experiment, the bipartite graph between proteins B, ... H and complexes 1, 2, and 3 will look like this. (c,d) The result of a hypothetical AP-MS experiment with no false positives and no false negatives when (c) B is used as a bait and (e) F is used as a bait. (e,f) Result from a hypothetical Y2H experiment with a genome-wide set of preys and with no false positives and false negatives when (d) B is used as a bait and (f) F is used as a bait. (g,h) The results of (g) an ideal AP-MS experiment and (h) an ideal Y2H experiment if all proteins were used as baits. The Y2H data in (e,f,h) identifies the direct interactions, but it does not contain information on the number and architecture of the complexes. The maximal cliques identified by the AP-MS experiment in (g) correspond to the complexes in (a). However, the AP-MS data do not contain information on the topology of the direct interactions within each complex.