→ Slides doi:10.7490/f1000research.1112753.1
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 (Jagtap et al 2015; doi: 10.1002/pmic.201500074). The workflow output results are compatible with tools for taxonomic and functional characterization (Unipept and MEGAN5). MEGAN5 was used to generate functional characterization of the metaproteome using Inter2Pro pathway analysis. These workflows enable new discoveries from diverse communities such as dental plaques (Rudney et al 2015, doi: 10.1186/s40168-015-0136-z), bronchoalveolar lavage fluid (BALF), lung tissue, and cervical-vaginal fluid (CVF). Our results demonstrate the power of discovery metaproteomics to add functional understanding to microbiomes, beyond what is possible using traditional metagenomic approaches.