Capture and mass spectrometry analysis of effector-substrate complexes using genetically incorporated photo-crosslinkers in host cells

Interactions between effectors and their host targets are often weak or transient, making them difficult to identify. We describe a protocol for covalent capture of effector substrates in living cells using genetic code expansion technology. The effector-substrate complexes are captured by the crosslinker and subsequently purified with tandem chromatography. We detail steps for mass spectrum analysis and substrate verification. While the steps here are specific for substrates of enteropathogenic E. coli in HEK293T cells, the protocol has broader applications. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).¹.