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Title (Primary) Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
Author Seifert, J.; Herbst, F.-A.; Nielsen, P.H.; Planes, F.J.; Ferrer, M.; von Bergen, M.;
Journal Proteomics
Year 2013
Department PROTEOM;
Volume 13
Issue 18-19
Language englisch;
POF III (all) F11; T41;
Keywords Bioinformatics; Data mining; High-throughput proteomics; Microbiology
UFZ wide themes RU3;
Abstract Metaproteomics of microbial communities bears the promise 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, visualisation 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 mass spectrometry pipeline and to the used protein identification workflow. Furthermore different approaches of data visualisation 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 to comprehensively analysing interactions and interdependencies within microbial communities.
ID 13675
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=13675
Seifert, J., Herbst, F.-A., Nielsen, P.H., Planes, F.J., Ferrer, M., von Bergen, M. (2013):
Bioinformatic progress and applications in metaproteogenomics for bridging the gap between genomic sequences and metabolic functions in microbial communities
Proteomics 13 (18-19), 2786 - 2804