Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities

Authors

  • Jana Seifert,

    1. Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
    2. Institute of Animal Nutrition, University of Hohenheim, Stuttgart, Germany
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  • Florian-Alexander Herbst,

    1. Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
    2. Faculty of Biology, University of Freiburg, Freiburg, Germany
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  • Per Halkjær Nielsen,

    1. Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
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  • Francisco J. Planes,

    1. CEIT and TECNUN, University of Navarra, San Sebastian, Spain
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  • Nico Jehmlich,

    1. Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
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  • Manuel Ferrer,

    1. CSIC, Institute of Catalysis, Madrid, Spain
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  • Martin von Bergen

    Corresponding author
    1. Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark
    2. Department of Metabolomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
    • Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
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  • Colour Online: See the article online to view Figs. 1, 2, 4 and 6 in colour.

Correspondence: Dr. Martin von Bergen, Department of Proteomics, UFZ—Helmholtz Centre for Environmental Research, Permoserstrasse 15, D-04318 Leipzig, Germany

E-mail: martin.vonbergen@ufz.de

Fax: +49-235-454485

Abstract

Metaproteomics of microbial communities promises to add functional information to the blueprint of genes derived from metagenomics. Right from its beginning, the achievements and developments in metaproteomics were closely interlinked with metagenomics. In addition, the evaluation, visualization, and interpretation of metaproteome data demanded for the developments in bioinformatics. This review will give an overview about recent strategies to use genomic data either from public databases or organismal specific genomes/metagenomes to increase the number of identified proteins obtained by mass spectrometric measurements. We will review different published metaproteogenomic approaches in respect to the used MS pipeline and to the used protein identification workflow. Furthermore, different approaches of data visualization and strategies for phylogenetic interpretation of metaproteome data are discussed as well as approaches for functional mapping of the results to the investigated biological systems. This information will in the end allow a comprehensive analysis of interactions and interdependencies within microbial communities.

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