Figure 3.

Interaction proteomics. To detect specific binders to a tagged protein of interest (e.g., GFP, green sphere on target protein), abundance of potential interaction partners is compared with the abundance of the same protein from a mock purification expressing only untagged versions of the proteins. For example, extracts from “heavy” SILAC-labeled cells expressing tagged proteins (left) or control extracts (right) are subjected to affinity chromatography. The resulting eluates from target and mock purification are mixed and analyzed by the proteomics pipeline. Background binders are present in equal amounts in both purifications (circles in the plot), whereas proteins specifically binding to the bait have high ratios reflecting their specific enrichment from the heavy SILAC-labeled sample (rectangles in the plot).