title: The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events.
abstract: We here present The Online Protein Processing Resource (TOPPR; http://iomics.ugent.be/toppr/), an online database that contains thousands of published proteolytically processed sites in human and mouse proteins. These cleavage events were identified with COmbinded FRActional DIagonal Chromatography proteomics technologies, and the resulting database is provided with full data provenance. Indeed, TOPPR provides an interactive visual display of the actual fragmentation mass spectrum that led to each identification of a reported processed site, complete with fragment ion annotations and search engine scores. Apart from warehousing and disseminating these data in an intuitive manner, TOPPR also provides an online analysis platform, including methods to analyze protease specificity and substrate-centric analyses. Concretely, TOPPR supports three ways to retrieve data: (i) the retrieval of all substrates for one or more cellular stimuli or assays; (ii) a substrate search by UniProtKB/Swiss-Prot accession number, entry name or description; and (iii) a motif search that retrieves substrates matching a user-defined protease specificity profile. The analysis of the substrates is supported through the presence of a variety of annotations, including predicted secondary structure, known domains and experimentally obtained 3D structure where available. Across substrates, substrate orthologs and conserved sequence stretches can also be shown, with iceLogo visualization provided for the latter.
authors.affiliation: Department of Medical Protein Research, VIB, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium.
authors.forename: Niklaas
authors.initials: N
authors.lastname: Colaert
authors.forename: Davy
authors.initials: D
authors.lastname: Maddelein
authors.forename: Francis
authors.initials: F
authors.lastname: Impens
authors.forename: Petra
authors.initials: P
authors.lastname: Van Damme
authors.forename: Kim
authors.initials: K
authors.lastname: Plasman
authors.forename: Kenny
authors.initials: K
authors.lastname: Helsens
authors.forename: Niels
authors.initials: N
authors.lastname: Hulstaert
authors.forename: Joël
authors.initials: J
authors.lastname: Vandekerckhove
authors.forename: Kris
authors.initials: K
authors.lastname: Gevaert
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D000818:Animals; D030562:Databases, Protein; D006801:Humans; D020407:Internet; D051379:Mice; D010447:Peptide Hydrolases / Q000378:metabolism*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000378:metabolism; D059748:Proteolysis; D013379:Substrate Specificity
chemical_list: D011506:Proteins; D010447:Peptide Hydrolases