School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada.
J Proteome Res. 2023 Feb 3;22(2):387-398. doi: 10.1021/acs.jproteome.2c00554. Epub 2022 Dec 12.
The studies of microbial communities have drawn increased attention in various research fields such as agriculture, environment, and human health. Recently, metaproteomics has become a powerful tool to interpret the roles of the community members by investigating the expressed proteins of the microbes. However, analyzing the metaproteomic data sets at genome resolution is still challenging because of the lack of efficient bioinformatics tools. Here we develop MetaLab-MAG, a specially designed tool for the characterization of microbiomes from metagenome-assembled genomes databases. MetaLab-MAG was evaluated by analyzing various human gut microbiota data sets and performed comparably or better than searching the gene catalog protein database directly. MetaLab-MAG can quantify the genome-level microbiota compositions and supports both label-free and isobaric labeling-based quantification strategies. MetaLab-MAG removes the obstacles of metaproteomic data analysis and provides the researchers with in-depth and comprehensive information from the microbiomes.
微生物群落的研究在农业、环境和人类健康等各个研究领域引起了越来越多的关注。最近，宏蛋白质组学通过研究微生物表达的蛋白质，成为解释群落成员作用的有力工具。然而，由于缺乏有效的生物信息学工具，在基因组分辨率上分析宏蛋白质组数据集仍然具有挑战性。在这里，我们开发了 MetaLab-MAG，这是一种专门用于从宏基因组组装基因组数据库中表征微生物组的工具。MetaLab-MAG 通过分析各种人类肠道微生物组数据集进行了评估，其性能可与直接搜索基因目录蛋白数据库相媲美，甚至更好。MetaLab-MAG 可以定量基因组水平的微生物组组成，并支持无标记和基于等压标记的定量策略。MetaLab-MAG 消除了宏蛋白质组数据分析的障碍，为研究人员提供了来自微生物组的深入和全面的信息。
