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Using mass spectrometry to identify ubiquitin and ubiquitin‐like protein conjugation sites
Author(s) -
Jeram Stanley M.,
Srikumar Tharan,
Pedrioli Patrick G. A.,
Raught Brian
Publication year - 2009
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200800666
Subject(s) - ubiquitin , conjugate , computational biology , posttranslational modification , biochemistry , biomolecule , identification (biology) , proteomics , chemistry , biology , gene , enzyme , mathematical analysis , botany , mathematics
Ubiquitin (Ub) and the ubiquitin‐like proteins (Ubls) are polypeptides that are covalently conjugated to proteins and other biomolecules to modulate their turnover rate, localization, and/or function. The full range of Ubl functions is only beginning to be understood, and the wide variety of Ubl conjugates is only beginning to be identified. Moreover, how Ubl conjugation is regulated, and how Ubl conjugate populations change, e.g ., throughout the cell cycle, in response to hormones, nutrients, or stress, or in various disease states, remains largely enigmatic. MS represents a powerful tool for the characterization of PTMs. However, standard sample preparation and data search methods are not amenable to the identification of many types of Ubl conjugates. Here, we describe the challenges of identifying Ub/Ubl conjugates, and propose an improved workflow for identification of Ub/Ubl conjugation sites. Considering the importance of Ubls in normal cellular physiology, and their roles in disease etiology and progression, it will be critical to develop improved high‐throughput MS methods capable of efficiently identifying proteins and other biomolecules modified by these very interesting and important PTMs.