Repurposing proteomic nanoLC-MS platforms for untargeted metabolomics: evaluating DIA and polarity switching performance in human plasma.

IF 2.8 3区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Expert Review of Proteomics Pub Date : 2025-08-01 Epub Date: 2025-07-24 DOI:10.1080/14789450.2025.2537210

Frederico G Pinto, Alexander D Giddey, Nesrin Mohamed, Rauda S B Almarri, Munazza Murtaza, Nasna Nassir, Omer S Alkhnbashi, Mohammed J Uddin, Nelson C Soares

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引用次数: 0

Abstract

Background: Many of the advanced MS methods applied in proteomics such as nanoflow LC-MS with data-independent acquisition have yet to be verified and/or optimized on metabolomics applications.

Research design and methods: This study evaluates the feasibility of repurposing a proteomics-optimized nanoLC-MS platform for untargeted metabolomics. Using NIST SRM 1950 reference human plasma, we compared the performance of polarity switching and separate polarity modes under DIA conditions, focusing on metabolite coverage, annotation, and response linearity.

Results: We observed, in the separate polarity and switching polarity runs 669 and 353 features in (+) mode and 558 and 446 features in (-) mode, respectively. A total of 233 metabolites were annotated using the (±) separate polarities and 179 using the (±) switching polarity based on MassBank of North America (MoNA) public MS library and filtered with the Human Metabolome Database (HMDB). Both switching and separate polarity methods performed well regarding response linearities which were investigated by spiking some amino acid compounds into plasma matrix.

Conclusions: The polarity switching DIA approach for metabolomics reduced sample consumption and analysis time, but led to fewer detected features and annotations compared to separate polarity runs. These findings support the use of unified nanoLC-MS platforms for integrated multi-omics analysis.

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重新利用蛋白质组学纳米质谱平台进行非靶向代谢组学：评估人血浆中的介质和极性切换性能。

背景：许多应用于蛋白质组学的先进的质谱方法，如具有数据独立采集的纳米流LC-MS，尚未在代谢组学应用中得到验证和/或优化。研究设计和方法：本研究评估了将蛋白质组学优化的纳米lc - ms平台重新用于非靶向代谢组学的可行性。使用NIST SRM 1950参考人血浆，我们比较了DIA条件下极性切换和分离极性模式的性能，重点关注代谢物覆盖率、注释和响应线性。结果：我们观察到，在分离极性和切换极性中，分别有669和353个特征处于（+）模式，558和446个特征处于（-）模式。基于北美MassBank （MoNA）公共质谱库，用（±）分离极性注释了233种代谢物，用（±）切换极性注释了179种代谢物，并用Human Metabolome Database （HMDB）进行了过滤。开关法和分离极性法均表现出良好的响应线性，通过将一些氨基酸化合物注入等离子体基质来研究。结论：代谢组学的极性切换DIA方法减少了样品消耗和分析时间，但与单独极性运行相比，检测到的特征和注释更少。这些发现支持使用统一的纳米色谱-质谱平台进行综合多组学分析。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Expert Review of Proteomics 生物-生化研究方法

CiteScore

7.60

自引率

0.00%

发文量

审稿时长

6-12 weeks

期刊介绍： Expert Review of Proteomics (ISSN 1478-9450) seeks to collect together technologies, methods and discoveries from the field of proteomics to advance scientific understanding of the many varied roles protein expression plays in human health and disease. The journal coverage includes, but is not limited to, overviews of specific technological advances in the development of protein arrays, interaction maps, data archives and biological assays, performance of new technologies and prospects for future drug discovery. The journal adopts the unique Expert Review article format, offering a complete overview of current thinking in a key technology area, research or clinical practice, augmented by the following sections: Expert Opinion - a personal view on the most effective or promising strategies and a clear perspective of future prospects within a realistic timescale Article highlights - an executive summary cutting to the author''s most critical points.