title: PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.
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.
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Bernd
authors.initials: B
authors.lastname: Bodenmiller
authors.forename: Johan
authors.initials: J
authors.lastname: Malmstrom
authors.forename: Bertran
authors.initials: B
authors.lastname: Gerrits
authors.forename: David
authors.initials: D
authors.lastname: Campbell
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmidt
authors.forename: Oliver
authors.initials: O
authors.lastname: Rinner
authors.forename: Lukas N
authors.initials: LN
authors.lastname: Mueller
authors.forename: Paul T
authors.initials: PT
authors.lastname: Shannon
authors.forename: Patrick G
authors.initials: PG
authors.lastname: Pedrioli
authors.forename: Christian
authors.initials: C
authors.lastname: Panse
authors.forename: Hoo-Keun
authors.initials: HK
authors.lastname: Lee
authors.forename: Ralph
authors.initials: R
authors.lastname: Schlapbach
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D000818:Animals; D002460:Cell Line; D029721:Drosophila Proteins / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D010748:Phosphopeptides / Q000235:genetics / Q000378:metabolism; D010750:Phosphoproteins; D010744:Phosphoric Monoester Hydrolases / Q000235:genetics; D011494:Protein Kinases / Q000235:genetics; D020543:Proteome
chemical_list: D000596:Amino Acids; D029721:Drosophila Proteins; D010748:Phosphopeptides; D010750:Phosphoproteins; D020543:Proteome; D011494:Protein Kinases; D010744:Phosphoric Monoester Hydrolases