Proteomic diversity in bacteria: Insights and implications for bacterial identification.

IF 6.1 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS Molecular & Cellular Proteomics Pub Date : 2025-01-27 DOI:10.1016/j.mcpro.2025.100917

Miriam Abele, Armin Soleymaniniya, Florian P Bayer, Nina Lomp, Etienne Doll, Chen Meng, Klaus Neuhaus, Siegfried Scherer, Mareike Wenning, Nina Wantia, Bernhard Kuster, Mathias Wilhelm, Christina Ludwig

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Abstract

Mass spectrometry-based proteomics has revolutionized bacterial identification and elucidated many molecular mechanisms underlying bacterial growth, community formation, and drug resistance. However, most research has been focused on a few model bacteria, overlooking bacterial diversity. In this study, we present the most extensive bacterial proteomic resource to date, covering 303 species, 119 genera, and five phyla with over 636,000 unique expressed proteins, confirming the existence of over 38,700 hypothetical proteins. Accessible via the public resource ProteomicsDB, this dataset enables quantitative exploration of proteins within and across species. Additionally, we developed MS2Bac, a bacterial identification algorithm that queries NCBI's bacterial proteome space in two iterations. MS2Bac achieved over 99% species-level and 89% strain-level accuracy, surpassing methods like MALDI-TOF and FTIR, as demonstrated with food-derived bacterial isolates. MS2Bac also effectively identified bacteria in clinical samples, highlighting the potential of MS-based proteomics as a routine diagnostic tool.

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基于质谱的蛋白质组学彻底改变了细菌的鉴定，并阐明了细菌生长、群落形成和耐药性的许多分子机制。然而，大多数研究都集中在少数模式菌上，忽略了细菌的多样性。在这项研究中，我们展示了迄今为止最广泛的细菌蛋白质组资源，涵盖 303 个种、119 个属和 5 个门，有超过 636,000 个独特表达的蛋白质，证实了超过 38,700 个假定蛋白质的存在。该数据集可通过公共资源 ProteomicsDB 访问，可对物种内和物种间的蛋白质进行定量探索。此外，我们还开发了 MS2Bac，这是一种细菌鉴定算法，可通过两次迭代查询 NCBI 的细菌蛋白质组空间。MS2Bac 的物种级准确率超过 99%，菌株级准确率超过 89%，超过了 MALDI-TOF 和傅立叶变换红外光谱等方法。MS2Bac 还能有效鉴定临床样本中的细菌，凸显了基于 MS 的蛋白质组学作为常规诊断工具的潜力。

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来源期刊

Molecular & Cellular Proteomics 生物-生化研究方法

CiteScore

11.50

自引率

4.30%

发文量

131

审稿时长

84 days

期刊介绍： The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action. The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data. Scope: -Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights -Novel experimental and computational technologies -Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes -Pathway and network analyses of signaling that focus on the roles of post-translational modifications -Studies of proteome dynamics and quality controls, and their roles in disease -Studies of evolutionary processes effecting proteome dynamics, quality and regulation -Chemical proteomics, including mechanisms of drug action -Proteomics of the immune system and antigen presentation/recognition -Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease -Clinical and translational studies of human diseases -Metabolomics to understand functional connections between genes, proteins and phenotypes