title: Current trends and challenges in proteomic identification of protease substrates.
abstract: Proteolytic cleavage is a ubiquitous, irreversible, posttranslational modification that changes protein structure and function and plays an important role in numerous physiological and pathological processes. Over the last decade, proteases have become increasingly important clinical targets because many of their inhibitors are already used in the clinic or in various stages of clinical testing. Therefore, a better understanding of protease action and their repertoires of physiological substrates can not only provide an important insight into their mechanisms of action but also open a path toward novel drug design. Historically, proteases and their substrates were mainly studied on a case-by-case basis, but recent advancements in mass spectrometry-based proteomics have enabled proteolysis studies on a global scale. Because there are many different types of proteases that can operate in various cellular contexts, multiple experimental approaches for their degradomic characterization had to be developed. The present paper reviews the mass spectrometry-based approaches for determining the proteolytic events in complex biological samples. The methodologies for substrate identification and the determination of protease specificity are discussed, with a special focus on terminomic strategies, which combine peptide labeling and enrichment.
authors.affiliation: Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.
authors.forename: Matej
authors.initials: M
authors.lastname: Vizovišek
authors.affiliation: Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; International Postgraduate School Jožef Stefan, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.
authors.forename: Robert
authors.initials: R
authors.lastname: Vidmar
authors.affiliation: Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia. Electronic address: marko.fonovic@ijs.si.
authors.forename: Marko
authors.initials: M
authors.lastname: Fonović
authors.affiliation: Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia; Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva cesta 5, SI-1000 Ljubljana, Slovenia. Electronic address: boris.turk@ijs.si.
authors.forename: Boris
authors.initials: B
authors.lastname: Turk
mesh_terms: D000818:Animals; D015180:Electrophoresis, Gel, Two-Dimensional; D006801:Humans; D013058:Mass Spectrometry; D010447:Peptide Hydrolases / Q000378:metabolism*; D010455:Peptides / Q000378:metabolism; D059748:Proteolysis; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics / Q000379:methods* / Q000639:trends*; D013379:Substrate Specificity
chemical_list: D010455:Peptides; D020543:Proteome; D010447:Peptide Hydrolases
keywords: Degradomics; Proteases; Proteomics; Substrates; Terminomics