Advanced search
1 file | 3.44 MB

The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events

Niklaas Colaert (UGent), Davy Maddelein (UGent), Francis Impens (UGent), Petra Van Damme (UGent), Kim Plasman (UGent), Kenny Helsens (UGent), Niels Hulstaert (UGent), Joël Vandekerckhove (UGent), Kris Gevaert (UGent) and Lennart Martens (UGent)
(2013) NUCLEIC ACIDS RESEARCH. 41(D1). p.D333-D337
Author
Organization
Project
Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
LIBRARY, REVEALS, GRANZYME, PROTEASES, SUBSTRATE, IDENTIFICATION, CELL-DEATH, PROTEOMICS

Downloads

  • D333.full.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 3.44 MB

Citation

Please use this url to cite or link to this publication:

Chicago
Colaert, Niklaas, Davy Maddelein, Francis Impens, Petra Van Damme, Kim Plasman, Kenny Helsens, Niels Hulstaert, Joël Vandekerckhove, Kris Gevaert, and Lennart Martens. 2013. “The Online Protein Processing Resource (TOPPR) : a Database and Analysis Platform for Protein Processing Events.” Nucleic Acids Research 41 (D1): D333–D337.
APA
Colaert, N., Maddelein, D., Impens, F., Van Damme, P., Plasman, K., Helsens, K., Hulstaert, N., et al. (2013). The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events. NUCLEIC ACIDS RESEARCH, 41(D1), D333–D337.
Vancouver
1.
Colaert N, Maddelein D, Impens F, Van Damme P, Plasman K, Helsens K, et al. The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events. NUCLEIC ACIDS RESEARCH. 2013;41(D1):D333–D337.
MLA
Colaert, Niklaas, Davy Maddelein, Francis Impens, et al. “The Online Protein Processing Resource (TOPPR) : a Database and Analysis Platform for Protein Processing Events.” NUCLEIC ACIDS RESEARCH 41.D1 (2013): D333–D337. Print.
@article{3117281,
  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.},
  author       = {Colaert, Niklaas and Maddelein, Davy and Impens, Francis and Van Damme, Petra and Plasman, Kim and Helsens, Kenny and Hulstaert, Niels and Vandekerckhove, Jo{\"e}l and Gevaert, Kris and Martens, Lennart},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {LIBRARY,REVEALS,GRANZYME,PROTEASES,SUBSTRATE,IDENTIFICATION,CELL-DEATH,PROTEOMICS},
  language     = {eng},
  number       = {D1},
  pages        = {D333--D337},
  title        = {The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events},
  url          = {http://dx.doi.org/10.1093/nar/gks998},
  volume       = {41},
  year         = {2013},
}

Altmetric
View in Altmetric
Web of Science
Times cited: