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PhosphoPep—a database of protein phosphorylation sites in model organisms

Nature Biotechnology volume 26, pages 1339–1340 (2008)Cite this article

To the editor:

Reversible protein phosphorylation is a universal process that is involved in the control of most biological processes. The comprehensive and quantitative analysis of the protein phosphorylation patterns of cells at different states is therefore of considerable and general interest. Over the past years, mass spectrometry has become the method of choice for the analysis of protein phosphorylation and impressive gains have been realized in the isolation of phosphorylated peptides from complex samples as well as their mass spectrometric and computational analysis. In such studies, hundreds to thousands of phosphopeptides and phosphorylation sites are now routinely identified.

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Figure 1: Analysis of phosphorylation site conservation.

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Acknowledgements

We acknowledge Steve Gygi, Sean Beausoleil and Cell Signaling Technology for providing us with phosphorylation data as published6,7,8,9. We also thank the Functional Genomics Center Zurich for generous support with mass spectrometry resources. This project has been funded in part by ETH Zurich, the Swiss National Science Foundation under grant No. 31000-10767, with Federal (US) funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, under contract no. N01-HV-28179, and by the Center for Model Organism Proteomics of SystemsX.ch, the Swiss initiative for systems biology. Work at the FGCZ has been supported by the University Research Priority Program Systems Biology and Functional Genomics of the University of Zurich. R.A. was supported in part by a grant from F. Hoffmann-La Roche (Basel) provided to the Competence Center for Systems Physiology and Metabolic Disease. B.B. is the recipient of a fellowship from the Boehringer Ingelheim Fonds.

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Author notes

  1. Bernd Bodenmiller, David Campbell and Bertran Gerrits: These authors contributed equally to this work. aebersold@imsb.biol.ethz.ch

Authors and Affiliations

  1. Institute of Molecular Systems Biology, ETH Zurich, Zurich, 8093, Switzerland

    Bernd Bodenmiller, Paola Picotti & Ruedi Aebersold

  2. Zurich PhD Program in Molecular Life Sciences, Zurich, 8057, Switzerland

    Bernd Bodenmiller & Marko Jovanovic

  3. Institute for Systems Biology, Seattle, 98103, Washington, USA

    David Campbell, Henry Lam & Ruedi Aebersold

  4. Functional Genomics Center Zurich, UZH/ETH Zurich, Zurich, 8057, Switzerland

    Bertran Gerrits & Ralph Schlapbach

  5. Institute of Molecular Biology, University of Zurich, Zurich, 8057, Switzerland

    Marko Jovanovic

  6. Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, Zurich, 8093, Switzerland

    Ruedi Aebersold

  7. Faculty of Science, University of Zurich, Zurich, 8057, Switzerland

    Ruedi Aebersold

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Figure 1, Materials and Methods (PDF 696 kb)

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Bodenmiller, B., Campbell, D., Gerrits, B. et al. PhosphoPep—a database of protein phosphorylation sites in model organisms. Nat Biotechnol 26, 1339–1340 (2008). https://doi.org/10.1038/nbt1208-1339

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