Multiomic studies are increasingly performed to gain a deeper understanding of molecular processes occurring in a biological system, such as the complex microbial communities (i.e., microbiota) that reside the distal gut. While a combination of metabolomics and proteomics is more commonly used, multiomics studies including peptidomcis characterization are less frequently undertaken. Here, we investigated three different extraction methods, chosen for their previous use in extracting metabolites, peptides, and proteins, and compared their ability to perform metabolomic, peptidomic, and proteomic analysis of mouse cecum content. The methanol/chloroform/water extraction performed the best for metabolomic and peptidomic analysis as it detected the largest number of small molecules and identified the largest number of peptides, but the acidified methanol extraction performed best for proteomics analysis as it had the highest number of protein identifications. The methanol/chloroform/water extraction was further analyzed by identifying metabolites with tandem mass spectrometry (MS/MS) analysis and by gene ontology analysis for the peptide and protein results to provide a multiomics analysis of the gut microbiota.

中文翻译：

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肠道菌群样品代谢组学、肽组学和蛋白质组学组合分析的提取优化


越来越多的多组学研究是为了更深入地了解生物系统中发生的分子过程，例如位于远端肠道的复杂微生物群落（即微生物群）。虽然代谢组学和蛋白质组学的组合更常用，但包括肽组学表征在内的多组学研究较少进行。在这里，我们研究了三种不同的提取方法，选择它们之前用于提取代谢物、肽和蛋白质，并比较它们对小鼠盲肠内容物进行代谢组学、肽组学和蛋白质组学分析的能力。甲醇/氯仿/水提取对于代谢组学和肽组学分析表现最佳，因为它检测到最多数量的小分子并鉴定了最多数量的肽，但酸化甲醇提取对于蛋白质组学分析表现最好，因为它具有最多数量的蛋白质身份证明。通过串联质谱 (MS/MS) 分析鉴定代谢物以及对肽和蛋白质结果进行基因本体分析，进一步分析甲醇/氯仿/水提取物，以提供肠道微生物群的多组学分析。