ArticleNucleic acids research2013
The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Serpina3k lactylation protects from cardiac ischemia reperfusion injury.Nature communications · 2025Article
- Extracellular Alterations in pH and K+ Modify the Murine Brain Endothelial Cell Total and Phospho-Proteome.Pharmaceutics · 2022Article
- The carboxy-terminus, a key regulator of protein function.Critical reviews in biochemistry and molecular biology · 2019Review
- Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors.Nucleic acids research · 2016Article
- Exploring the potential of public proteomics data.Proteomics · 2016Review
- N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men.Molecular & cellular proteomics : MCP · 2014Article
- MEROPS: the database of proteolytic enzymes, their substrates and inhibitors.Nucleic acids research · 2014Article
- Proteolytic post-translational modification of proteins: proteomic tools and methodology.Molecular & cellular proteomics : MCP · 2013Review
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Authors and funding
10 authors.
Funding
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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.
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