BACKGROUND There is an important need for the development of fast and robust methods to quantify the diversity and temporal dynamics of microbial communities in complex environmental samples. Because tandem mass spectrometry allows rapid inspection of protein content, metaproteomics is increasingly used for the phenotypic analysis of microbiota across many fields, including biotechnology, environmental ecology, and medicine. RESULTS Here, we present a new method for identifying the biomass contribution of any given organism based on a signature describing the number of peptide sequences shared with all other organisms, calculated by mathematical modeling and phylogenetic relationships. This so-called "phylopeptidomics" principle allows for the calculation of the relative ratios of peptide-specified taxa by the linear combination of such signatures applied to an experimental metaproteomic dataset. We illustrate its efficiency using artificial mixtures of two closely related pathogens of clinical interest, and with more complex microbiota models. CONCLUSIONS This approach paves the way to a new vision of taxonomic changes and accurate label-free quantitative metaproteomics for fine-tuned functional characterization. Video abstract.

中文翻译：

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使用“ phylepteptidomics”估算微生物群中生物的相对生物量。

背景技术迫切需要开发快速和鲁棒的方法以量化复杂环境样品中微生物群落的多样性和时间动态。由于串联质谱法可以快速检测蛋白质含量，因此元蛋白质组学越来越多地用于包括生物技术，环境生态学和医学在内的许多领域的微生物群表型分析。结果在这里，我们提出了一种新的方法，该方法基于签名，该签名描述了与所有其他生物共享的肽序列数量，该签名是通过数学建模和系统发育关系计算得出的。这就是所谓的“系统肽组学” 原理允许通过将这样的特征标记的线性组合应用于实验性元蛋白质组学数据集来计算特定肽类的相对比率。我们说明了使用两种密切相关的临床感兴趣病原体的人工混合物以及更复杂的微生物群模型的效率。结论该方法为分类学变化和精确的无标记定量元蛋白质组学的新视野铺平了道路，以进行微调的功能表征。录像摘要。结论该方法为分类学变化和精确的无标记定量元蛋白质组学的新视野铺平了道路，以进行微调的功能表征。录像摘要。结论该方法为分类学变化和精确的无标记定量元蛋白质组学的新视野铺平了道路，以进行微调的功能表征。录像摘要。