Journal
PROTEOMICS
Volume 13, Issue 18-19, Pages 2786-2804Publisher
WILEY
DOI: 10.1002/pmic.201200566
Keywords
Bioinformatics; Data mining; High-throughput proteomics; Microbiology
Funding
- European Community [FP7-KBBE-2009-245226, FP7-KBBE-2008-226977, FP7-KBBE-2010-266473, FP7-KBBE-CALL 6-312139]
- Deutsche Forschungsgemeinschaft [SPP1319, FOR 1530]
- BMBF IFB Adiposity Disease
- Helmholtz Impulse and Networking Fund through Helmholtz Interdisciplinary Graduate School for Environmental Research (HIGRADE)
- Spanish Ministry of Economy and Competitiveness [CSD2007-00005, BIO2011-25012, BFU2008-04501-E]
- European Regional Development Fund (ERDF) funds
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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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