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A database of mass spectrometric assays for the yeast proteome

Nature Methods volume 5, pages 913–914 (2008)Cite this article

To the editor:

The current most widely used mass spectrometry (MS)-based proteomic methods sample the available proteome in a quasi-random manner. In each analysis only a subset of the proteins contained in a sample are measured, and replicate analyses sample partly overlapping proteome segments. In addition, these analyses are biased toward abundant proteins1,2. This limits the feasibility of consistently and comprehensively measuring defined sets of proteins (such as proteins constituting signaling or metabolic networks) across different samples, thus precluding the generation of complete datasets to support mathematical modeling of biological processes.

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Figure 1: Categorization of the yeast proteins represented in MRMAtlas by function and cellular abundance.

References

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Acknowledgements

We acknowledge C.H. Wong, V. Lange and L. Reiter for valuable assistance and insightful discussions; C. Miller and K. Miller, and N. Selevsek for testing the SRM assays developed in this study on Agilent and Thermo Fischer Scientific QQQ mass spectrometers, respectively; and R. Costenoble for valuable input and suggestions. This project was funded in part by the Swiss Federal Institute of Technology Zuerich, the Swiss National Science Foundation, with funds from the US National Heart, Lung, and Blood Institute, National Institutes of Health (N01-HV-28179) and by SystemsX.ch, the Swiss Initiative in Systems Biology. P.P. is the recipient of a Marie Curie Intra-European fellowship.

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Author notes

  1. Henry Lam

    Present address: Present address: Department of Chemical and Biomolecular Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,

  2. Paola Picotti, Henry Lam and David Campbell: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, Eidgenössische Technische Hochschule Zuerich, Wolfgang Pauli Str. 16, Zuerich, CH-8093, Switzerland

    Paola Picotti, Bruno Domon & Ruedi Aebersold

  2. Institute of Systems Biology, 1441 North 34th Street, Seattle, 98103, Washington, USA

    Henry Lam, David Campbell, Eric W Deutsch, Hamid Mirzaei, Jeff Ranish & Ruedi Aebersold

  3. Faculty of Science, University of Zuerich, Winterthurerstr. 190, Zuerich, CH-8057, Switzerland

    Ruedi Aebersold

  4. Competence Center for Systems Physiology and Metabolic Diseases, Schafmattstr. 18, Zuerich, CH-8093, Switzerland

    Ruedi Aebersold

Authors
  1. Paola Picotti
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Supplementary Methods, Supplementary Discussion, Supplementary Note (PDF 1327 kb)

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Picotti, P., Lam, H., Campbell, D. et al. A database of mass spectrometric assays for the yeast proteome. Nat Methods 5, 913–914 (2008). https://doi.org/10.1038/nmeth1108-913

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