Structural representation of an activity-based probe (ABP), which is comprised of a targeting sequence that directs the probe to the targeted enzyme, a reactive chemical warhead which binds irreversibly to the enzyme’s catalytic residues, and a tag for identification or visualization of probe-bound enzymes. Biotin-tagged ABPs can be used for affinity purification and mass spectrometry-based identification of probe targets, as well as for visualization of these targets by streptavidin affinity blotting. Radiolabeled and fluorescent ABPs can be used to visualize target proteins by in-gel fluorescence. Additionally, cell-permeable fluorescent ABPs can be used to monitor enzyme activity in living cells or tissue samples via fluorescence microscopy.