Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy
Abstract A dereplication strategy was developed for the screening of secondary metabolites from Sophora flavescens. The strategy consisted of 4 procedures. First, the extract of the Sophora flavescens root was subjected to LC–MS/MS analysis with both data-independent acquisition (DIA) mode and data-...
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Nature Portfolio
2025-03-01
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| Online Access: | https://doi.org/10.1038/s41598-025-94958-3 |
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| author | Hua Wang Hui Ding |
| author_facet | Hua Wang Hui Ding |
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| description | Abstract A dereplication strategy was developed for the screening of secondary metabolites from Sophora flavescens. The strategy consisted of 4 procedures. First, the extract of the Sophora flavescens root was subjected to LC–MS/MS analysis with both data-independent acquisition (DIA) mode and data-dependent acquisition (DDA) mode. Then the DIA results were used to construct a molecular networking (MN) according to the GNPS workflow and consequently obtain annotations. In parallel, the DDA results were projected to both MN analysis and direct databases matching to obtain annotations. Finally, the isomers were discriminated and annotated by their extracted ion chromatogram. Through the combination of these approaches, a total of 51 compounds were annotated and dereplicated in the Sophora flavescens samples. The annotation results showed DIA and DDA approach are complementary to each other. MN on GNPS can overcome the challenges of trace compound identification compared to direct DB matching. This strategy provides a powerful tool for the dereplication study in plant chemistry. |
| format | Article |
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| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-03-01 |
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| spelling | doaj-art-ff3b49fa303343488e1d5220f76fff8f2025-08-20T03:40:44ZengNature PortfolioScientific Reports2045-23222025-03-0115111010.1038/s41598-025-94958-3Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategyHua Wang0Hui Ding1Instrumental Analysis Center, Yancheng Teachers UniversitySchool of Pharmacy, Yancheng Teachers UniversityAbstract A dereplication strategy was developed for the screening of secondary metabolites from Sophora flavescens. The strategy consisted of 4 procedures. First, the extract of the Sophora flavescens root was subjected to LC–MS/MS analysis with both data-independent acquisition (DIA) mode and data-dependent acquisition (DDA) mode. Then the DIA results were used to construct a molecular networking (MN) according to the GNPS workflow and consequently obtain annotations. In parallel, the DDA results were projected to both MN analysis and direct databases matching to obtain annotations. Finally, the isomers were discriminated and annotated by their extracted ion chromatogram. Through the combination of these approaches, a total of 51 compounds were annotated and dereplicated in the Sophora flavescens samples. The annotation results showed DIA and DDA approach are complementary to each other. MN on GNPS can overcome the challenges of trace compound identification compared to direct DB matching. This strategy provides a powerful tool for the dereplication study in plant chemistry.https://doi.org/10.1038/s41598-025-94958-3Sophora flavescensMetabolitesDereplicationMolecular networkingAlkaloidsFlavonoids |
| spellingShingle | Hua Wang Hui Ding Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy Scientific Reports Sophora flavescens Metabolites Dereplication Molecular networking Alkaloids Flavonoids |
| title | Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy |
| title_full | Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy |
| title_fullStr | Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy |
| title_full_unstemmed | Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy |
| title_short | Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy |
| title_sort | dereplication of secondary metabolites from sophora flavescens using an lc ms ms based molecular networking strategy |
| topic | Sophora flavescens Metabolites Dereplication Molecular networking Alkaloids Flavonoids |
| url | https://doi.org/10.1038/s41598-025-94958-3 |
| work_keys_str_mv | AT huawang dereplicationofsecondarymetabolitesfromsophoraflavescensusinganlcmsmsbasedmolecularnetworkingstrategy AT huiding dereplicationofsecondarymetabolitesfromsophoraflavescensusinganlcmsmsbasedmolecularnetworkingstrategy |