metaproteomic

Metaproteomics is the large-scale study of the complete set of proteins expressed by a microbial community in a given environment or host-associated sample. It aims to characterize functional activity by identifying and quantifying proteins and linking them to organisms, pathways, and ecological processes. The approach complements metagenomics and metatranscriptomics by providing direct evidence of expressed functions rather than potential capabilities.

The workflow typically begins with sample collection and preservation, followed by cell lysis and protein extraction. Proteins are digested into peptides and analyzed by mass spectrometry, often using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Spectral data are searched against protein sequence databases, frequently constructed from sample-specific metagenomic data (metaproteogenomics), to improve identification. Quantification can be label-free or use chemical labels such as TMT or iTRAQ. Results are mapped to functional annotations (GO, KEGG, COG) and assigned to taxa when possible, enabling pathway-level and community-level interpretation.

Challenges include the complexity of mixed communities, wide dynamic range of protein abundances, incomplete reference databases, and ambiguity in assigning peptides to proteins or taxa. Additional issues include host protein contamination, post-translational modifications, and the need for robust computational tools and standardized workflows.

Applications span human microbiome research, environmental and soil microbiology, biogeochemical cycling, agriculture, and biotechnology. Emerging methods, such as data-independent acquisition and integration with metagenomics (metaproteogenomics), continue to improve depth, quantification, and interpretability of the metaproteome.