Chemistry-driven strategies for modifying, controlling and monitoring protein function in vitro and in vivo have attracted widespread interest among chemists in recent years. Several strategies have now emerged that complement standard genetics-based approaches, and they are being increasingly adopted by biologists to address issues in relevant contexts from cells to animals. With the development of these chemical biology tools, we might be approaching a time when detailed quantitative analysis of protein function, to a degree previously available only in reconstituted systems, is attainable in an in vivo setting.