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Searching for a needle in a stack of needles: challenges in metaproteomics data analysis.

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Muth,  Thilo
Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Benndorf,  Dirk
Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Reichl,  Udo
Otto-von-Guericke-Universität Magdeburg;
Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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Rapp,  Erdmann
Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Max Planck Society;

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1752843_muth.pdf
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Citation

Muth, T., Benndorf, D., Reichl, U., Rapp, E., & Martens, L. (2013). Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. Molecular BioSystems, 9(4), 578-585. doi:10.1039/c2mb25415h.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0013-87EA-3
Abstract
In the past years the integral study of microbial communities of varying complexity has gained increasing research interest. Mass spectrometry-driven metaproteomics enables the analysis of such communities on the functional level, but this fledgling field still faces various technical and semantic challenges regarding experimental data analysis and interpretation. In the present review, we outline the hurdles involved and attempt to cover the most valuable methods and software implementations available to researchers in the field today. Beyond merely focusing on protein identification, we provide an overview on different data pre- and post-processing steps, such as metabolic pathway analysis, that can be useful in a typical metaproteomics workflow. Finally, we briefly discuss directions for future work. c The Royal Society of Chemistry 2013 [accessed 2013 March 13th]