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Current Organism:
D. melanogaster


PROJECT OVERVIEW

PhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms. Currently there is data from the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae). The experimental data was collected and analyzed by the Aebersold group at the Swiss Federal Institute of Technology (ETH) in collaboration with the Functional Genomics Center ( FGCZ ) in Zurich, Switzerland, and the Institute for Systems Biology (ISB) in Seattle, Washington USA.

The tabs below show details about the data collected from each organism, and link to this information in the database. PhosphoPep offers different software tools which allow users to browse through single proteins, through pathways, and importantly to integrate the data with information from external sources, like protein-protein interaction data. Finally all data can be readily exported e.g. for a targeted proteomics approach and the generated data can be again validated using PhosphoPep, enabling systems biology signaling research.

 

D. melanogaster was the first organism to be presented in PhosphoPep, and was obtained from the analysis Kc167 cells. Phosphopeptides were enriched using 3 complementary methods, as described in Nature Molecular Systems Biology . The current Drosophila PhosphoPep contains over 10,000 high quality phosphorylation sites mapping to nearly 4,600 phosphoproteins (3,500 gene models) of D. melanogaster Kc167 cells and thus being the most comprehensive phosphorylation map in any system to date.

Data on human phosphopeptides were obtained primarily from the publications of Cell Signaling and the Gygi lab. Overall the dataset consists of 3,980 phosphorylation sites.

C. elegans is a model organism whose development and genetics are very well characterized. Phosophopeptides were isolated from digested C. elegans whole organism lysates and analyzed using LTQ-FT and LTQ-Orbtitrap MS instruments.

Saccharomyces cerevisiae is a widely-used model organism whose popularity is enhanced with the release of the yeast deletion collection. This dataset contains nearly 9,000 identified phosphorylation sites, including over 5,800 with unambiguous phosphosite location. Most sites were identified from peptides which were separated according to their isoelectric point and analyzed using LTQ-FT and LTQ-Orbtitrap MS instruments.


ISB Phosphopep