Activity-based protein profiling (ABPP) is a robust technique enabling the user to explore the functional implications of disease and pathology on key protein effectors. As such, a variety of activity-based probes have been developed and applied broadly to study virus-host interactions and the consequences of essential noncoding RNAs, like microRNAs, which viruses exploit for their propagation. The following protocol describes the process of infecting and transfecting cells for ABPP and covers the main ways in which ABPP can be used to study infection: in-gel fluorescence, western blotting, and mass spectrometry. Taken together, the findings of these experiments can be used to identify new therapeutic targets and to test novel antiviral inhibitors.