Ghent University Academic Bibliography

Advanced

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

Niklaas Colaert UGent, Davy Maddelein, Francis Impens UGent, Petra Van Damme UGent, Kim Plasman, Kenny Helsens UGent, Niels Hulstaert UGent, Joël Vandekerckhove, Kris Gevaert UGent and Lennart Martens UGent (2013) NUCLEIC ACIDS RESEARCH. 41(D1). p.D333-D337
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
LIBRARY, REVEALS, GRANZYME, PROTEASES, SUBSTRATE, IDENTIFICATION, CELL-DEATH, PROTEOMICS
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
41
issue
D1
pages
D333 - D337
Web of Science type
Article
Web of Science id
000312893300047
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
8.808 (2013)
JCR rank
22/291 (2013)
JCR quartile
1 (2013)
ISSN
0305-1048
DOI
10.1093/nar/gks998
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
3117281
handle
http://hdl.handle.net/1854/LU-3117281
date created
2013-01-31 14:21:52
date last changed
2017-05-05 11:01:00
@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},
}

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.