Large-scale biochemical analysis of cell-specific signaling can be interrogated in cocultures of Eph receptor- and ephrin-expressing cells by combining proteomics analysis with cell-specific metabolic labeling. In this chapter, we describe how to perform such large-scale analysis, including the generation of cells stably expressing the receptors and ligands of interest, optimization steps for Eph–ephrin coculture, and the proteomics analysis. As the experimental details may vary depending on the specific system that is being interrogated, the goal of the chapter is mainly to provide sufficient experimental context for experienced researchers to set up and conduct these experiments.
