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Visual proteomics of the human pathogen Leptospira interrogans

Nature Methods volume 6, pages 817–823 (2009)Cite this article

Abstract

Systems biology conceptualizes biological systems as dynamic networks of interacting elements, whereby functionally important properties are thought to emerge from the structure of such networks. Owing to the ubiquitous role of complexes of interacting proteins in biological systems, their subunit composition and temporal and spatial arrangement within the cell are of particular interest. 'Visual proteomics' attempts to localize individual macromolecular complexes inside of intact cells by template matching reference structures into cryo-electron tomograms. Here we combined quantitative mass spectrometry and cryo-electron tomography to detect, count and localize specific protein complexes in the cytoplasm of the human pathogen Leptospira interrogans. We describe a scoring function for visual proteomics and assess its performance and accuracy under realistic conditions. We discuss current and general limitations of the approach, as well as expected improvements in the future.

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Figure 1: An integrated workflow for visual proteomics.
Figure 2: Stress response of L. interrogans cells in the context of the protein complexes selected as templates for template matching.
Figure 3: Generation of in silico test data and development of a scoring function for template matching in cryo-electron tomograms.
Figure 4: Template matching in subvolumes of L. interrogans cells.

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Acknowledgements

This project has been funded in part by ETH Zurich, the Swiss National Science Foundation (grant 31000-10767), federal funds from the US National Heart, Lung, and Blood Institute, the US National Institutes of Health (contract N01-HV-28179), by SystemsX.ch the Swiss initiative for systems biology, in part by the proteomics in time and space (PROSPECTS) European network of excellence, and with funds from the European Research Council project 'Proteomics V3.0'. M.B. was supported by a long-term fellowship of the European Molecular Biology Organization and a Marie Curie fellowship of the European Commission; J.A.M. was supported by a fellowship from the Swedish society for medical research (SSMF); and A.S. and V.L. were supported by the Competence Center for Systems Physiology and Metabolic Diseases. We thank O. Medalia, W. Baumeister, members of the electron microscopy facility of ETH Zurich (EMEZ) for continued support and F. Förster for critical reading of the manuscript.

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Author notes

  1. Martin Beck and Johan A Malmström: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Molecular Systems Biology, The Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland

    Martin Beck, Johan A Malmström, Vinzenz Lange, Alexander Schmidt & Ruedi Aebersold

  2. Institute for Systems Biology, Seattle, Washington, USA

    Eric W Deutsch & Ruedi Aebersold

  3. Faculty of Science, University of Zurich, Zurich, Switzerland

    Ruedi Aebersold

  4. Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland

    Ruedi Aebersold

Authors
  1. Martin Beck
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  2. Johan A Malmström
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  3. Vinzenz Lange
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  4. Alexander Schmidt
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  5. Eric W Deutsch
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  6. Ruedi Aebersold
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Contributions

J.A.M. and M.B. planned the experiments, performed the experimental work and data analysis and wrote the manuscript. A.S. and V.L. participated in the experimental work and the data analysis. E.W.D. assembled the PeptideAtlas build. R.A. was the project leader and wrote the manuscript.

Corresponding author

Correspondence to Ruedi Aebersold.

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Supplementary Figures 1–7, Supplementary Tables 1–3 and Supplementary Results (PDF 3539 kb)

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Beck, M., Malmström, J., Lange, V. et al. Visual proteomics of the human pathogen Leptospira interrogans. Nat Methods 6, 817–823 (2009). https://doi.org/10.1038/nmeth.1390

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