Patrick R. A. Zanon, Fengchao Yu, Patricia Z. Musacchio, Lisa Lewald, Michael Zollo, Kristina Krauskopf, Dario Mrdović, Patrick Raunft, Thomas E. Maher, Marko Cigler, Christopher J. Chang, Kathrin Lang, F. Dean Toste, Alexey I. Nesvizhskii, Stephan M. Hacker
Covalent inhibitors that do not rely on hijacking enzymatic activity have mainly been limited to those targeting cysteine residues. The development of such cysteine-directed covalent inhibitors has greatly profited from the use of competitive residue-specific proteomics to determine their proteome-wide selectivity. Several probes have been developed to monitor other amino acids using this technology, and many more electrophiles exist to modify proteins. Nevertheless, there has been a lack of direct, proteome-wide comparisons of the selectivity of diverse electrophiles. Here we developed an unbiased workflow to analyse electrophile selectivity proteome-wide and used it to directly compare 56 alkyne probes containing diverse reactive groups. In this way, we verified and identified probes to monitor a total of nine different amino acids, as well as the protein amino terminus, across the proteome.