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