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Photocaged, activity‐based ubiquitin (Ub) probes (Ub‐ABPs) have been developed for the time‐resolved probing of deubiquitinating enzyme (DUB) activities, but many Ub‐ABPs are still challenging to photocage because their warheads (e.g. propargylamide (PA) or dehydroalanine (Dha)) are difficult to temporally block and activate. Here, we describe a new C‐terminal backbone modification strategy for the construction of photocaged Ub‐ABPs in which a light‐sensitive group is placed at the backbone amide bond of the Ub Gly75. This strategy enabled the facile generation of cell‐permeable photocaged Ub‐PA and Dha probes that could be activated to capture DUBs after photo‐irradiation, and were used to profile DUBs in cells under specially designed conditions (e.g. in cells experiencing oxidative stress) or DUBs with isopeptide linkage selectivity. This backbone modification strategy is anticipated to provide a general solution for the development of photocaged Ub ABPs bearing any warheads for DUB profiling. [ABSTRACT FROM AUTHOR]

• Heterotypic Ub reagents were obtained by CAET strategy with high efficiency. • The reagents identify heterotypic Ub-interacting and modifying proteins simultaneously. • Sequential release of two groups of proteins was completed by using urea and reductant. • Proteomic profiling facilitates future investigations of heterotypic Ub chains. Heterotypic ubiquitin (Ub) chains have emerged as fundamental components in a wide range of cellular processes. The integrative identification of Ub-interacting proteins (readers) and Ub-modifying enzymes (writers and erasers) that selectively recognize and regulate heterotypic ubiquitination may provide crucial insights into these processes. In this study, we employed the bifunctional molecule-assisted (CAET) strategy to develop a type of disulfide bond-activated heterotypic Ub reagents, which allowed to enrich heterotypic Ub-interacting proteins and modifying enzymes simultaneously. The sequential release of readers which are non-covalently bound and writers or erasers which are covalently conjugated by using urea and reductant, respectively, combined with label-free quantitative (LFQ) MS indicated that these heterotypic Ub reagents would facilitate future investigations into functional roles played by heterotypic Ub chains. [ABSTRACT FROM AUTHOR]