Abstract
Metaproteomics is a powerful approach for characterizing the functional metabolic activities of complex microbiome systems. For example, clinical metaproteomics provides details about how the human microbiome affects/responds to clinical conditions, whereas environmental metaproteomics provides information on how the microbiome affects/responds to the ecosystem. Metaproteomics is still under rapid development, with a few standardized methods and approaches even among the experienced practitioners.To better understand and enhance the overall power of metaproteomics, the Metaproteomics Initiative [1] has launched a series of Critical Assessment of Metaproteome Investigations, termed "CAMPI." The first campaign, CAMPI-1, compared experimental and bioinformatic workflows across international laboratories, demonstrating a strong correlation in microbial functionals [2]. Building on this, two new CAMPI projects are currently in progress. CAMPI-2, involving 11 labs, focuses on evaluating a variety of sample preparation protocols for fecal or soil microbiomes to enable sample shipment at ambient temperatures. CAMPI-3, meanwhile, is evaluating bioinformatic tools for protein assignments and inferring taxonomic assignments using metaproteomic raw data from a synthetic community (with a known representation) and a complex fecal sample. Over 20 labs participated, revealing a wide variety of strategies and accuracies in the analysis. These findings are being compiled into a manuscript that will provide critical insights and propose best practices. Future CAMPI projects are being prioritized to address key challenges in metaproteomics, driving the field forward to become an essential tool for tackling global challenges in microbiome research.References[1] Van Den Bossche, T., Arntzen, M.Ø., Becher, D. et al. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. Microbiome 9, 243 (2021). https://doi.org/10.1186/s40168-021-01176-w[2] Van Den Bossche, T., Kunath, B.J., Schallert, K. et al. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun 12, 7305 (2021). https://doi.org/10.1038/s41467-021-27542-8