Protein complexes: the forest and the trees

Figures & data

Figure 1. The forest (Y2H) and the trees (AP-MS).

High-throughput Y2H measurements provide data akin to an aerial view of a forest. A dense canopy obscures information on individual trees. Ground-level data from AP-MS provides a detailed view of a few trees, but is less amenable to systems-level measurements.

AP-MS: Affinity purification followed by mass spectrometry; Y2H: Yeast-two-hybrid.

Figure 2. Protein–protein interactions, Y2H and AP-MS.

Proteome-scale Y2H representation of cellular protein interactions (top). In this view, each edge represents a binary protein–protein interaction. Y2H interactions do not translate to all cell states and do not account for post-translational modifications (middle). AP-MS provides for the detection of protein complexes assembled under physiological conditions (bottom). Although more detailed in terms of dynamics and modifications, relative throughput is low for AP-MS and low-affinity interactions may be missed.

AP-MS: Affinity purification followed by mass spectrometry; Y2H: Yeast-two-hybrid.