title: Ubiquitinated proteome: ready for global?
abstract: Ubiquitin (Ub) is a small and highly conserved protein that can covalently modify protein substrates. Ubiquitination is one of the major post-translational modifications that regulate a broad spectrum of cellular functions. The advancement of mass spectrometers as well as the development of new affinity purification tools has greatly expedited proteome-wide analysis of several post-translational modifications (e.g. phosphorylation, glycosylation, and acetylation). In contrast, large-scale profiling of lysine ubiquitination remains a challenge. Most recently, new Ub affinity reagents such as Ub remnant antibody and tandem Ub binding domains have been developed, allowing for relatively large-scale detection of several hundreds of lysine ubiquitination events in human cells. Here we review different strategies for the identification of ubiquitination site and discuss several issues associated with data analysis. We suggest that careful interpretation and orthogonal confirmation of MS spectra is necessary to minimize false positive assignments by automatic searching algorithms.
authors.affiliation: Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Shi
authors.forename: Ping
authors.initials: P
authors.lastname: Xu
authors.forename: Jun
authors.initials: J
authors.lastname: Qin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry; D020543:Proteome / Q000737:chemistry*; D015203:Reproducibility of Results; D057149:Ubiquitinated Proteins / Q000737:chemistry*; D054875:Ubiquitination
chemical_list: D010446:Peptide Fragments; D020543:Proteome; D057149:Ubiquitinated Proteins