Holstein Tanja, Muth Thilo
Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany.
VIB-UGent Center for Medical Biotechnology, VIB and Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
Methods Mol Biol. 2024;2820:187-213. doi: 10.1007/978-1-0716-3910-8_16.
The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.
在过去几年中，微生物群落对生态和人类健康等领域的强大影响已得到广泛认可。因此，人们开发了各种用于研究微生物群落样本组成和功能的技术。元蛋白质组学，即对微生物群落中的蛋白质进行全面分析，不仅可以研究微生物群落的分类学，还可以研究其功能和定量组成。由于所研究群落的复杂性，为单一生物体蛋白质组学开发的方法不能直接应用于元蛋白质组学样本。为此，需要专门针对元蛋白质组学量身定制的方法。在这项工作中，对当前元蛋白质组学中的生物信息学解决方案和方案进行了详细概述。在介绍蛋白质组数据库搜索之后，详细解释了元蛋白质组学的后处理步骤。重点介绍了十种特定的生物信息学软件解决方案，涵盖了包括数据库驱动的鉴定和定量以及分类和功能分配在内的各个步骤。
