Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture.

ABSTRACT: Metaproteomics enables the investigation of the protein repertoire expressed by complex microbial communities. However, to unleash its full potential, refinements in bioinformatic approaches for data analysis are still needed. In this context, sequence databases selection represents a major challenge. This work assessed the impact of different databases in metaproteomic investigations by using a mock microbial mixture including nine diverse bacterial and eukaryotic species, which was subjected to shotgun metaproteomic analysis. Then, both the microbial mixture and the single microorganisms were subjected to next generation sequencing to obtain experimental metagenomic- and genomic-derived databases, which were used along with public databases (namely, NCBI, UniProtKB/SwissProt and UniProtK

SUBMITTER: Tanca A 

PROVIDER: S-EPMC3857319 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature