The analytical tools for protein ubiquitination have been quickly established in recent years in parallel with the development of modern MS. These high-throughput methods have expanded the fields of proteins modified by different members in the Ub super-family. It is believed that thousands of proteins in eukaryotic cells are regulated by protein ubiquitination. MS analyses have also revealed the surprisingly complexity of polyUb topologies that might provide difficult signals for the downstream events. The analysis of other components in ubiquitination, such as E3 ligase complexes, DUBs, and Ub receptors, are benefited from the advance of proteomics as well.

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