Metaproteomics is a rapidly developing field that provides unique insights into the taxonomic composition and functional activity of microbial communities and their impact on host physiology. To date, data-dependent acquisition (DDA) mass spectrometry (MS) has been used to identify and quantify peptides in metaproteomics. However, this has been associated with well-known limitations in terms of depth, sensitivity and reproducibility. Methodological improvements were therefore needed to better characterise the protein landscape of microbiomes and their interactions with the host.

The paper describes a new state-of-the-art methodology for the characterisation of host-microbiome interactions under pathophysiological conditions. The researchers present an optimised proteomic workflow that uses the information acquired by Parallel Accumulation-Serial Fragmentation (PASEF) mass spectrometry for comprehensive metaproteomic studies.

The researchers tested this new method in mice, studying the interactions between gut bacteria and mice with neuropathic pain. They found changes in specific bacteria and metabolic activities associated with chronic pain. The study also revealed how proteins in the immune system and gut bacteria communicate during pain. This research advances our knowledge of microbial systems. It has implications for several scientific fields.

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