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

Research output: Contribution to journalArticle

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 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.

Details

Authors
  • Bernd Bodenmiller
  • Johan Malmström
  • Bertran Gerrits
  • David Campbell
  • Henry Lam
  • Alexander Schmidt
  • Oliver Rinner
  • Lukas N Mueller
  • Paul T Shannon
  • Patrick G A Pedrioli
  • Christian Panse
  • Hoo-Keun Lee
  • Ralph Schlapbach
  • Ruedi Aebersold
External organisations
  • ETH Zürich
Research areas and keywords

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
Original languageEnglish
Article number139
JournalMolecular Systems Biology
Volume3
Publication statusPublished - 2007
Publication categoryResearch
Peer-reviewedYes
Externally publishedYes