Nonspecific protein labeling of photoaffinity linkers correlates with their molecular shapes in living cells

Herein we report molecular shape-dependent nonspecific labeling of photoaffinity linkers (PLs) in the cellular proteome. Linear PLs have a greater tendency to engage in nonspecific binding than branched PLs. Exploiting this property, we discovered a smaller branched diazirine-based PL as the best photoaffinity probe with minimal nonspecific binding characteristics from among 5 probes with different PLs.