Advanced

PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

Bodenmiller, Bernd; Malmström, Johan LU ; Gerrits, Bertran; Campbell, David; Lam, Henry; Schmidt, Alexander; Rinner, Oliver; Mueller, Lukas N; Shannon, Paul T and Pedrioli, Patrick G A, et al. (2007) In Molecular Systems Biology 3.
Abstract

The ability to analyze and understand the mechanisms by which cells process information is a key question of systems biology research. Such mechanisms critically depend on reversible phosphorylation of cellular proteins, a process that is catalyzed by protein kinases and phosphatases. Here, we present PhosphoPep, a database containing more than 10 000 unique high-confidence phosphorylation sites mapping to nearly 3500 gene models and 4600 distinct phosphoproteins of the Drosophila melanogaster Kc167 cell line. This constitutes the most comprehensive phosphorylation map of any single source to date. To enhance the utility of PhosphoPep, we also provide an array of software tools that allow users to browse through phosphorylation sites on... (More)

The ability to analyze and understand the mechanisms by which cells process information is a key question of systems biology research. Such mechanisms critically depend on reversible phosphorylation of cellular proteins, a process that is catalyzed by protein kinases and phosphatases. Here, we present PhosphoPep, a database containing more than 10 000 unique high-confidence phosphorylation sites mapping to nearly 3500 gene models and 4600 distinct phosphoproteins of the Drosophila melanogaster Kc167 cell line. This constitutes the most comprehensive phosphorylation map of any single source to date. To enhance the utility of PhosphoPep, we also provide an array of software tools that allow users to browse through phosphorylation sites on single proteins or pathways, to easily integrate the data with other, external data types such as protein-protein interactions and to search the database via spectral matching. Finally, all data can be readily exported, for example, for targeted proteomics approaches and the data thus generated can be again validated using PhosphoPep, supporting iterative cycles of experimentation and analysis that are typical for systems biology research.

(Less)
Please use this url to cite or link to this publication:
author
, et al. (More)
(Less)
publishing date
type
Contribution to journal
publication status
published
keywords
Amino Acids, Animals, Cell Line, Drosophila Proteins, Drosophila melanogaster, Phosphopeptides, Phosphoproteins, Phosphoric Monoester Hydrolases, Protein Kinases, Proteome, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Review
in
Molecular Systems Biology
volume
3
publisher
Nature Publishing Group
external identifiers
  • scopus:35348839586
ISSN
1744-4292
DOI
10.1038/msb4100182
language
English
LU publication?
no
id
e19e5607-3bf5-4964-8c99-0a7c434e0d58
date added to LUP
2017-09-04 17:22:10
date last changed
2017-10-22 05:35:36
@article{e19e5607-3bf5-4964-8c99-0a7c434e0d58,
  abstract     = {<p>The ability to analyze and understand the mechanisms by which cells process information is a key question of systems biology research. Such mechanisms critically depend on reversible phosphorylation of cellular proteins, a process that is catalyzed by protein kinases and phosphatases. Here, we present PhosphoPep, a database containing more than 10 000 unique high-confidence phosphorylation sites mapping to nearly 3500 gene models and 4600 distinct phosphoproteins of the Drosophila melanogaster Kc167 cell line. This constitutes the most comprehensive phosphorylation map of any single source to date. To enhance the utility of PhosphoPep, we also provide an array of software tools that allow users to browse through phosphorylation sites on single proteins or pathways, to easily integrate the data with other, external data types such as protein-protein interactions and to search the database via spectral matching. Finally, all data can be readily exported, for example, for targeted proteomics approaches and the data thus generated can be again validated using PhosphoPep, supporting iterative cycles of experimentation and analysis that are typical for systems biology research.</p>},
  articleno    = {139},
  author       = {Bodenmiller, Bernd and Malmström, Johan and Gerrits, Bertran and Campbell, David and Lam, Henry and Schmidt, Alexander and Rinner, Oliver and Mueller, Lukas N and Shannon, Paul T and Pedrioli, Patrick G A and Panse, Christian and Lee, Hoo-Keun and Schlapbach, Ralph and Aebersold, Ruedi},
  issn         = {1744-4292},
  keyword      = {Amino Acids,Animals,Cell Line,Drosophila Proteins,Drosophila melanogaster,Phosphopeptides,Phosphoproteins,Phosphoric Monoester Hydrolases,Protein Kinases,Proteome,Journal Article,Research Support, N.I.H., Extramural,Research Support, Non-U.S. Gov't,Review},
  language     = {eng},
  publisher    = {Nature Publishing Group},
  series       = {Molecular Systems Biology},
  title        = {PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells},
  url          = {http://dx.doi.org/10.1038/msb4100182},
  volume       = {3},
  year         = {2007},
}