The untapped potential of metaproteomics in microbial systems ecology

As a direct readout of protein presence and abundance in complex microbiomes, metaproteomics has become central to uncovering functionality across diverse microbial ecosystems. Recent collaborative efforts within the research community have driven methodological advances, computational innovations, and diverse applications. With the advancing maturity of metaproteomics techniques, we highlight the Proteome-level Microbial Systems Ecology (ProMiSE) framework as a complementary framework for the next phase, providing a conceptual lens to interpret metaproteomics data with a bottom-up perspective that extends beyond functional profile and taxonomic composition to the quantitative assessment of system properties, processes, and dynamics. Building on existing metrics such as β-diversity and functional redundancy, future work can further develop quantitative approaches for resilience, exergy, and functional energy landscapes, thereby enabling a deeper systems-level understanding of microbiome dynamics and opening new avenues for the precise functional regulation of microbiomes. SIGNIFICANCE: This Perspective reviews the development of metaproteomics-particularly in the Journal of Proteomics-and envisions it as a transformative tool in microbial systems ecology, introducing the ProMiSE framework to integrate protein-resolved data with ecological theory and properties such as redundancy, resilience, and functional energy landscapes for the future of precise microbiome modulation.