Metaproteomics defines the characterizing of the entire protein complement of a given microbiota. Generally, protein identification occurs by searching MS/MS spectra against protein databases. Most protein sequences in publicly available databases originate from model organisms and not necessarily from environmental relevant organisms that may be uncultured This imperfect match between sample and database results in a failure to allocate spectra making identification of divergent proteins. However, for the investigation of communities in the environment, it is crucial to identify potentially all proteins. In our study, we combine metaproteomics with metagenomics in order to obviate this problem as much as possible and apply this approach to a number of bacterial communities on plant leaves.
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