Abstract
This chapter provides detailed methodology and materials required to profile deubiquitinases (DUBs) in a cellular matrix using specific activity-based probes, with immunoblotting and mass spectrometry proteomics-based readouts. Different types of activity-based protein profiling (ABPP) for studying the potency and selectivity of DUB inhibitors are outlined here, including the standard ABPP, the deep DUBome ABPP, and the ABPP-HT (high-throughput compatible).
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Acknowledgments
We thank members of the Kessler group for their helpful discussions. We are grateful to Roman Fischer and Iolanda Vendrell, leads of the Discovery Proteomics Facility, for expert help with mass spectrometry analysis. H.B.L.J. was supported by a Bristol Myers Squibb award to B.M.K. A.P.F. and B.M.K were supported by the Chinese Academy of Medical Sciences (CAMS) Innovation Fund for Medical Science (CIFMS), China (grant number: 2018-I2M-2-002), and by Pfizer.
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Jones, H.B.L., Heilig, R., Kessler, B.M., Pinto-Fernández, A. (2023). Activity-Based Protein Profiling (ABPP) for Cellular Deubiquitinase (DUB) and Inhibitor Profiling at Deep and High-Throughput Levels. In: Maupin-Furlow, J., Edelmann, M.J. (eds) Deubiquitinases. Methods in Molecular Biology, vol 2591. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2803-4_7
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DOI: https://doi.org/10.1007/978-1-0716-2803-4_7
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