Wu Qing, Ning Zhibin, Zhang Ailing, Zhang Xu, Sun Zhongzhi, Figeys Daniel
School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada.
Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada.
Anal Chem. 2025 May 13;97(18):9739-9747. doi: 10.1021/acs.analchem.4c06645. Epub 2025 May 2.
Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. One challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxon-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxon-Function (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX includes extensive statistical and visualization tools, establishing it as a robust platform for metaproteomics analysis. We validated MetaX by reanalyzing ex vivo gut microbiome metaproteomic data exposed to various sweeteners, yielding more detailed results than traditional protein analysis. Furthermore, using the peptide-centric approach and OTF, we observed that significantly responds to certain sweeteners, highlighting its role in modifying specific metabolic functions. With its intuitive, user-friendly interface, MetaX facilitates a detailed study of the complex interactions between microbial taxa and their functions in metaproteomics. It enhances our understanding of microbial roles in ecosystems and health.
元蛋白质组学通过识别肽段并将它们映射到最可能的蛋白质和分类群来分析微生物群落的功能动态。该领域的一个挑战在于无缝整合分类学和功能注释，以准确呈现各个微生物分类群对功能多样性的贡献。我们引入了MetaX，这是一个用于分析元蛋白质组学中分类群与功能关系的综合工具，它通过将肽段映射到其最近共同祖先并基于比例阈值分配功能，确保了准确的肽段水平映射。重要的是，MetaX引入了操作分类群-功能（OTF），这是一个用于探索生态系统内微生物角色和相互作用的新概念单元。此外，MetaX还包括广泛的统计和可视化工具，使其成为一个强大的元蛋白质组学分析平台。我们通过重新分析暴露于各种甜味剂的离体肠道微生物群落元蛋白质组学数据对MetaX进行了验证，得到了比传统蛋白质分析更详细的结果。此外，使用以肽段为中心的方法和OTF，我们观察到[具体内容缺失]对某些甜味剂有显著反应，突出了其在改变特定代谢功能中的作用。凭借其直观、用户友好的界面，MetaX有助于在元蛋白质组学中详细研究微生物分类群与其功能之间的复杂相互作用。它增进了我们对微生物在生态系统和健康中的作用的理解。
