title: Deciphering the ubiquitin proteome: Limits and advantages of high throughput global affinity purification-mass spectrometry approaches.
abstract: Ubiquitination is a posttranslational modification of proteins that involves the covalent attachment of ubiquitin, either as a single moiety or as polymers. This process controls almost every cellular metabolic pathway through a variety of combinations of linkages. Mass spectrometry now allows high throughput approaches for the identification of the thousands of ubiquitinated proteins and of their ubiquitination sites. Despite major technological improvements in mass spectrometry in terms of sensitivity, resolution and acquisition speed, the use of efficient purification methods of ubiquitinated proteins prior to mass spectrometry analysis is critical to achieve an efficient characterization of the ubiquitome. This critical step is achieved using different approaches that possess advantages and pitfalls. Here, we discuss the limits that can be encountered when deciphering the ubiquitome. This article is part of a Directed Issue entitled: Molecular basis of muscle wasting.
authors.affiliation: INRA, UMR 1019, UNH, CRNH Auvergne, F-63122 Saint Genès Champanelle, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Polge
authors.forename: Sandrine
authors.initials: S
authors.lastname: Uttenweiler-Joseph
authors.forename: Roza
authors.initials: R
authors.lastname: Leulmi
authors.forename: Anne-Elisabeth
authors.initials: AE
authors.lastname: Heng
authors.forename: Odile
authors.initials: O
authors.lastname: Burlet-Schiltz
authors.forename: Didier
authors.initials: D
authors.lastname: Attaix
authors.forename: Daniel
authors.initials: D
authors.lastname: Taillandier
mesh_terms: D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000737:chemistry* / Q000378:metabolism*; D025801:Ubiquitin / Q000737:chemistry* / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D020543:Proteome; D025801:Ubiquitin
keywords: 19S RC; 19S regulatory complex; E1; E2; E3; MS; Mass spectrometry; PTM; Post Translational Modification; UBD; UPS; Ub; Ubiquitin; Ubiquitin Binding Domain; Ubiquitin Proteasome System; Ubiquitin chain linkage; Ubiquitin proteasome system; mass spectrometry; ubiquitin; ubiquitin-activating enzyme; ubiquitin-conjugating enzyme; ubiquitin-protein ligase