Studying the structure and function of microbiomes is an emerging research field. Metaproteomic approaches focusing on the characterization of expressed proteins and post-translational modifications (PTMs) provide a deeper understanding of microbial communities. Previous research has highlighted the value of examining microbiome-wide protein expression in studying the roles of the microbiome in human diseases. Nevertheless, the regulation of protein functions in complex microbiomes remains underexplored. This is mainly due to the lack of efficient bioinformatics tools to identify and quantify PTMs in the microbiome. We have developed comprehensive software termed MetaLab for the data analysis of metaproteomic data sets. Here, we build an open search workflow within MetaLab for unbiased identification and quantification of unmodified peptides as well as peptides with various PTMs from microbiome samples. This bioinformatics platform provides information about proteins, PTMs, taxa, functions, and pathways of microbial communities. The performance of the workflow was evaluated using conventional proteomics, metaproteomics from mouse and human gut microbiomes, and modification-specific enriched data sets. Superior accuracy and sensitivity were obtained simultaneously by using our method compared with the traditional closed search strategy.

中文翻译：

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MetaLab 2.0支持对元蛋白质组学进行准确的翻译后修饰分析。

研究微生物组的结构和功能是一个新兴的研究领域。专注于表达蛋白质表征和翻译后修饰（PTM）的元蛋白质组学方法可提供对微生物群落的更深入了解。先前的研究强调了检查微生物组全蛋白表达在研究微生物组在人类疾病中的作用的价值。然而，复杂微生物群中蛋白质功能的调控仍未得到充分研究。这主要是由于缺乏有效的生物信息学工具来识别和量化微生物组中的PTM。我们已经开发了称为MetaLab的综合软件，用于元蛋白质组数据集的数据分析。这里，我们在MetaLab中建立了一个开放的搜索工作流程，可对微生物组样品中未修饰的肽段以及具有各种PTM的肽段进行公正的鉴定和定量。该生物信息学平台提供有关蛋白质，PTM，生物分类，功能和微生物群落途径的信息。使用常规蛋白质组学，来自小鼠和人类肠道微生物组的元蛋白质组学以及修饰特定的丰富数据集来评估工作流程的性能。与传统的封闭搜索策略相比，使用我们的方法可以同时获得出色的准确性和灵敏度。使用常规蛋白质组学，来自小鼠和人类肠道微生物组的元蛋白质组学以及特定于修饰的丰富数据集来评估工作流程的性能。与传统的封闭搜索策略相比，使用我们的方法可以同时获得出色的准确性和灵敏度。使用常规蛋白质组学，来自小鼠和人类肠道微生物组的元蛋白质组学以及特定于修饰的丰富数据集来评估工作流程的性能。与传统的封闭搜索策略相比，使用我们的方法可以同时获得出色的准确性和灵敏度。