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
{"title":"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。","authors":"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","doi":"10.1080/14789450.2025.2537210","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Research design and methods: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":50463,"journal":{"name":"Expert Review of Proteomics","volume":" ","pages":"307-314"},"PeriodicalIF":2.8000,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Repurposing proteomic nanoLC-MS platforms for untargeted metabolomics: evaluating DIA and polarity switching performance in human plasma.\",\"authors\":\"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\",\"doi\":\"10.1080/14789450.2025.2537210\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>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.</p><p><strong>Research design and methods: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>\",\"PeriodicalId\":50463,\"journal\":{\"name\":\"Expert Review of Proteomics\",\"volume\":\" \",\"pages\":\"307-314\"},\"PeriodicalIF\":2.8000,\"publicationDate\":\"2025-08-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Expert Review of Proteomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1080/14789450.2025.2537210\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2025/7/24 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMICAL RESEARCH METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Expert Review of Proteomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1080/14789450.2025.2537210","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/7/24 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
Repurposing proteomic nanoLC-MS platforms for untargeted metabolomics: evaluating DIA and polarity switching performance in human plasma.
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.
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.
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