Metaproteomics is a key methodology for understanding the function of microbiomes by efficiently connecting genomic and metabolic information. Through the large-scale characterization of the entire protein complement of microbiota and the functional dynamics of the microbiome, metaproteomics has the potential to unravel the mechanistic details of microbial interactions with the host/environment. Functional characterization offers numerous advantages over nucleic acid-based methods that primarily measure taxonomic composition. However, while the techniques in current use for metaproteomics are fundamentally the same as those used for single-organism proteomics, there are a number of key differences in terms of sample preparation, analysis and data processing/interpretation that require specialized expertise for success in metaproteomics experiments.