Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China.
ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 311200, Hangzhou, China.
NPJ Biofilms Microbiomes. 2023 Jan 24;9(1):4. doi: 10.1038/s41522-023-00373-9.
Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.
代谢蛋白质组学可以提供有价值的人类肠道微生物组（GM）功能见解，但由于 GM 的极端复杂性和异质性，这是一项具有挑战性的任务。数据非依赖性采集（DIA）质谱（MS）在常规蛋白质组学中是一种新兴的定量技术，但在代谢蛋白质组学领域仍处于早期发展阶段。在此，我们应用了无文库 DIA（directDIA）-基于代谢蛋白质组学的方法，并将 directDIA 与其他基于 MS 的代谢蛋白质组学定量技术进行了比较，用于模拟微生物群落和用已知比例细菌接种的粪便样本，通过全面考虑鉴定中的蛋白质组覆盖度以及定量的准确性和精密度，证明了 directDIA 的优越性能。我们在胰腺癌（PC）和轻度认知障碍（MCI）的两个临床粪便样本队列中对人类 GM 进行了表征。每个队列都定量了约 70000 个微生物蛋白，并对其进行了注释，以分析不同疾病中 GM 的分类和功能特征。我们的工作证明了 directDIA 在用于研究肠道微生物组及其相关疾病发病机制的定量代谢蛋白质组学中的实用性。
