Fecal metaproteomics is a useful approach to measure changes in microbial and host protein abundance and to infer which members of the gut microbiota are involved in specific functions and pathways. This chapter describes a protocol enabling analysis and characterization of fecal metaproteomes, successfully applied to human, mouse, and rat stool samples. The protocol combines mechanical and thermal treatments for protein extraction, a centrifugal filter-based procedure for cleanup and digestion, long-gradient liquid chromatography for peptide separation, and high-resolution mass spectrometry for peptide detection.
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