The isolation of proteome subsets on the basis of the interactions of small molecules with proteins is an emerging paradigm in proteomics. Depending on the nature of the small molecule used as a bait, entire protein families can be monitored in biological samples, or new functions can be attributed to previously uncharacterized proteins. With pharmaceutical compounds as baits, drug targets and toxicity-relevant off-targets can be discovered in an unbiased proteomic screen. At the heart of this strategy are synthetic bi- or trifunctional small molecule probes. These probes carry the small molecules of interest as baits (selectivity function), as well as a sorting function for the isolation of small molecule-protein complexes or conjugates from complex protein mixtures. In some designs, a covalent linkage of the bound protein to the probe is established through a separate reactivity function or a combined selectivity/reactivity function. The covalent linkage allows for isolation or detection of probe-protein conjugates also under harsh or denaturing conditions. Ultimately, specifically isolated proteins are commonly identified by mass spectrometry. This review summarizes probe designs, workflows, and published applications of the three dominant approaches in the field, namely affinity pulldown, activity-based protein profiling, and Capture Compound Mass Spectrometry.
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