MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database

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.

微生物群落研究在农业、环境与人类健康等多个研究领域中受到了日益广泛的关注。近年来，宏蛋白质组学（metaproteomics）已成为一种强有力的研究工具，可通过探测微生物的表达蛋白来解析群落成员的功能。然而，由于缺乏高效的生物信息学工具，以基因组分辨率开展宏蛋白质组数据集分析仍颇具挑战。本研究开发了MetaLab-MAG——一款专为基于宏基因组组装基因组（metagenome-assembled genomes, MAG）数据库解析微生物组而设计的工具。研究人员通过分析多个人类肠道微生物组数据集对MetaLab-MAG进行了性能评估，结果显示其表现可与直接搜索基因目录蛋白数据库的方法相媲美，甚至更胜一筹。MetaLab-MAG可实现基因组水平的微生物组组成定量，并支持无标记（label-free）与基于同量异位标记的两种定量策略。该工具扫清了宏蛋白质组数据分析的障碍，可为研究人员提供关于微生物组的深入且全面的研究信息。