title: Proteomic techniques to probe the ubiquitin landscape.
abstract: Protein ubiquitination is a powerful modulator of cellular functions. Classically linked to the degradation of proteins, it also plays a role in intracellular localization, DNA damage response, vesicle fusion events, and the immune and transcriptional responses. Ubiquitin is versatile and can code for several distinct signals, either by adding a single ubiquitin or forming a chain of ubiquitins on the target protein. The enzymatic cascade associated with the cellular process determines the nature of the modification. Numerous efforts have been made for the identification of ubiquitin acceptor sites in the target proteins using genetic, biochemical or MS-based proteomic methods, such as affinity-based enrichment of ubiquitinated proteins, and antibody-based enrichment of modified peptides. Modern instrumentation enables quantitative MS strategies to identify and characterize hundreds of ubiquitin substrates in a single analysis making it the dominant method for ubiquitin site detection. Characterization of the interubiquitin connectivity in ubiquitin polymers has also moved into focus, with the field of targeted proteomics techniques proving invaluable for identifying and quantifying linkage types found in such polyubiquitin chains. This review seeks to provide an overview of the many MS-based proteomics techniques available for exploring this dynamic field.
authors.affiliation: Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Beaudette
authors.affiliation: Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Popp
authors.affiliation: Department of Mass Spectrometry, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Dittmar
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D006801:Humans; D008969:Molecular Sequence Data; D040901:Proteomics; D025801:Ubiquitin / Q000737:chemistry* / Q000502:physiology; D057149:Ubiquitinated Proteins / Q000737:chemistry / Q000378:metabolism; D054875:Ubiquitination
chemical_list: D025801:Ubiquitin; D057149:Ubiquitinated Proteins
keywords: Mass spectrometry; Technology; Ubiquitin; Ubiquitin chain; Ubiquitination