Dynamic Organellar Maps, a Tool to Study Proteome‐Wide Subcellular Localization Changes

Abstract

Most biological process involve changes in protein subcellular localization that are critical for cellular function. However, there is currently no method for monitoring such translocation events on a systems‐wide level. We have combined subcellular fractionation with mass‐spectrometry based proteomics in a robust workflow for the reliable determination of protein subcellular localization. Using this method, we have localized ~8,700 proteins in cultured cells to 14 different subcellular compartments, making it the largest repository of human protein subcellular localization of a single system. The method is robust enough to apply the maps comparatively, which we assessed using EGF signaling as a model system. We captured ligand‐induced movement of EGFR from the plasma membrane to the endosome, as well as accompanying known and novel translocation events, validating the method for use in dynamic studies. We then investigated localization changes induced during treatment with several small molecules, leading us to a rapid understanding of the molecular mechanism of these compounds. In conclusion, we have generated an extensive resource for protein subcellular localization, and developed a method for determining protein subcellular localization changes at the proteome‐wide level. This method adds a novel dimension to the systems biologist handbook. It provides a powerful tool in drug discovery, and will also grant unprecedented insights into processes such as cell signaling, trafficking, and cellular differentiation. Support or Funding Information Max Planck Society

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