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

PloS One
Alessandro TancaSergio Uzzau

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 UniProtKB/TrEMBL, parsed at different taxonomic levels) to analyze the metaproteomic dataset. First, a quantitative comparison in terms of number and overlap of peptide identifications was carried out among all databases. As a result, only 35% of peptides were common to all database classes; moreover, genus/species-specific databases provided up to 17% more identifications compared to databases with generic taxonomy, while the metagenomic database ena...Continue Reading

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Methods Mentioned

BETA
electrophoresis
PCR
chip
Acetylation
SGA
an
SGA-PA

Software Mentioned

TrEMBL
Percolator
Meta
Venn Diagram Plotter
PA
BFV
Proteome Discoverer
MEGAN
Velvet
Unipept

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