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Proteomics to study genes and genomes

Nature volume 405, pages 837–846 (2000)Cite this article

Abstract

Proteomics, the large-scale analysis of proteins, will contribute greatly to our understanding of gene function in the post-genomic era. Proteomics can be divided into three main areas: (1) protein micro-characterization for large-scale identification of proteins and their post-translational modifications; (2) ‘differential display’ proteomics for comparison of protein levels with potential application in a wide range of diseases; and (3) studies of protein–protein interactions using techniques such as mass spectrometry or the yeast two-hybrid system. Because it is often difficult to predict the function of a protein based on homology to other proteins or even their three-dimensional structure, determination of components of a protein complex or of a cellular structure is central in functional analysis. This aspect of proteomic studies is perhaps the area of greatest promise. After the revolution in molecular biology exemplified by the ease of cloning by DNA methods, proteomics will add to our understanding of the biochemistry of proteins, processes and pathways for years to come.

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Figure 1: A strategy for mass spectrometric identification of proteins and post-translational modifications.
Figure 2: Cell lysate from Escherichia coli analysed by FTICR.
Figure 3: A schematic showing the two-dimensional gel approach.
Figure 4: A schematic showing use of arrays for proteomic analysis.
Figure 5: A generic strategy to isolate interacting proteins.
Figure 6: Characterization of the multi-protein spliceosome complex.
Figure 7: The yeast two-hybrid system.

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Acknowledgements

We thank B. Blagoev and M. Fernandez for their expert assistance with cell culture and immunoprecipitation experiments. We thank all other members of the Protein Interaction Laboratory for valuable discussions and comments on the manuscript and A. King, Protana A/S, for obtaining the data for the new spliceosomal protein. O. N. Jensen and A. Stensballe are acknowledged for their contributions in the analysis of phosphopeptides. A.P. was supported by the Howard Temin Award from the National Cancer Institute. This work was funded in part by a grant from the Danish National Research Foundation to M.M.'s laboratory (http://www.pil.sdu.dk) at the Center for Experimental BioInformatics (CEBI).

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  1. Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, 02142, Massachusetts

    Akhilesh Pandey & Matthias Mann

  2. Department of Pathology, Brigham and Women's Hospital, Boston, 02115, Massachusetts, USA

    Akhilesh Pandey & Matthias Mann

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Pandey, A., Mann, M. Proteomics to study genes and genomes. Nature 405, 837–846 (2000). https://doi.org/10.1038/35015709

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