The Galaxy platform for metaproteomic characterization of microbiomes

Metaproteomics analysis is emerging as an effective approach for identifying microorganisms and functional role of the microbiome in response to environment or host-physiology. Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism. Mass spectrometry (MS)-based metaproteomics has catalyzed new discoveries into the functional dynamics of microbiomes (Wilmes et al 2015, doi: 10.1002/pmic.201500183). Metaproteomic informatics is distinctly challenging due to the large databases and complex processing steps involved. This challenge limits widespread use of metaproteomics. Through modular workflows, we demonstrate the use of the Galaxy bioinformatics framework as a metaproteomic informatics solution. Our results demonstrate the power of discovery metaproteomics to add functional understanding to microbiomes, beyond what is possible using traditional metagenomic approaches.