Development and application of GlycanDIA workflow for glycomic analysis
Abstract Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat on cells called the glycocalyx. The changes in glycosylation have been linked to the initiation and progression of many diseases. Herein, we report a DIA-based glycomic workflow, termed GlycanDIA, to ide...
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61473-y |
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| author | Yixuan Xie Xingyu Liu Li Yi Shunyang Wang Zongtao Lin Chenfeng Zhao Siyu Chen Faith M. Robison Benson M. George Carlito B. Lebrilla Ryan A. Flynn Benjamin A. Garcia |
| author_facet | Yixuan Xie Xingyu Liu Li Yi Shunyang Wang Zongtao Lin Chenfeng Zhao Siyu Chen Faith M. Robison Benson M. George Carlito B. Lebrilla Ryan A. Flynn Benjamin A. Garcia |
| author_sort | Yixuan Xie |
| collection | DOAJ |
| description | Abstract Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat on cells called the glycocalyx. The changes in glycosylation have been linked to the initiation and progression of many diseases. Herein, we report a DIA-based glycomic workflow, termed GlycanDIA, to identify and quantify glycans with high sensitivity and precision. The GlycanDIA workflow combines higher energy collisional dissociation (HCD)-MS/MS and staggered windows for glycomic analysis, which facilitates the sensitivity in identification and precision in quantification compared to conventional glycomic methods. To facilitate its use, we also develop a generic search engine, GlycanDIA Finder, incorporating an iterative decoy searching for confident glycan identification from DIA data. Our results demonstrate that GlycanDIA can distinguish glycan composition and isomers from N-glycans, O-glycans, and human milk oligosaccharides (HMOs), while it also reveals information on low-abundant modified glycans. With the improved sensitivity and precision, we perform experiments to profile N-glycans from RNA samples, which have been underrepresented due to their low abundance. Using this integrative workflow to unravel the N-glycan profile in cellular and tissue glycoRNA samples, we find that RNA-glycans have different abundant forms as compared to protein-glycans and there are also tissue-specific differences, suggesting their distinct functions in biological processes. |
| format | Article |
| id | doaj-art-40b3656be06e4d7680e0976597c950ab |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-40b3656be06e4d7680e0976597c950ab2025-08-20T04:03:01ZengNature PortfolioNature Communications2041-17232025-08-0116111310.1038/s41467-025-61473-yDevelopment and application of GlycanDIA workflow for glycomic analysisYixuan Xie0Xingyu Liu1Li Yi2Shunyang Wang3Zongtao Lin4Chenfeng Zhao5Siyu Chen6Faith M. Robison7Benson M. George8Carlito B. Lebrilla9Ryan A. Flynn10Benjamin A. Garcia11State Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Institutes of Biomedical Sciences, Fudan UniversityDepartment of Biochemistry and Molecular Biophysics, Washington University School of MedicineState Key Laboratory of Genetic Engineering, Greater Bay Area Institute of Precision Medicine (Guangzhou), School of Life Sciences and Institutes of Biomedical Sciences, Fudan UniversityDepartment of Chemistry, University of California, Davis, DavisDepartment of Biochemistry and Molecular Biophysics, Washington University School of MedicineDepartment of Computer Science & Engineering, Washington UniversityDepartment of Chemistry, University of California, Davis, DavisDepartment of Biochemistry and Molecular Biophysics, Washington University School of MedicineStem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, BostonDepartment of Biochemistry and Molecular Biophysics, Washington University School of MedicineStem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, BostonDepartment of Biochemistry and Molecular Biophysics, Washington University School of MedicineAbstract Glycans modify protein, lipid, and even RNA molecules to form the regulatory outer coat on cells called the glycocalyx. The changes in glycosylation have been linked to the initiation and progression of many diseases. Herein, we report a DIA-based glycomic workflow, termed GlycanDIA, to identify and quantify glycans with high sensitivity and precision. The GlycanDIA workflow combines higher energy collisional dissociation (HCD)-MS/MS and staggered windows for glycomic analysis, which facilitates the sensitivity in identification and precision in quantification compared to conventional glycomic methods. To facilitate its use, we also develop a generic search engine, GlycanDIA Finder, incorporating an iterative decoy searching for confident glycan identification from DIA data. Our results demonstrate that GlycanDIA can distinguish glycan composition and isomers from N-glycans, O-glycans, and human milk oligosaccharides (HMOs), while it also reveals information on low-abundant modified glycans. With the improved sensitivity and precision, we perform experiments to profile N-glycans from RNA samples, which have been underrepresented due to their low abundance. Using this integrative workflow to unravel the N-glycan profile in cellular and tissue glycoRNA samples, we find that RNA-glycans have different abundant forms as compared to protein-glycans and there are also tissue-specific differences, suggesting their distinct functions in biological processes.https://doi.org/10.1038/s41467-025-61473-y |
| spellingShingle | Yixuan Xie Xingyu Liu Li Yi Shunyang Wang Zongtao Lin Chenfeng Zhao Siyu Chen Faith M. Robison Benson M. George Carlito B. Lebrilla Ryan A. Flynn Benjamin A. Garcia Development and application of GlycanDIA workflow for glycomic analysis Nature Communications |
| title | Development and application of GlycanDIA workflow for glycomic analysis |
| title_full | Development and application of GlycanDIA workflow for glycomic analysis |
| title_fullStr | Development and application of GlycanDIA workflow for glycomic analysis |
| title_full_unstemmed | Development and application of GlycanDIA workflow for glycomic analysis |
| title_short | Development and application of GlycanDIA workflow for glycomic analysis |
| title_sort | development and application of glycandia workflow for glycomic analysis |
| url | https://doi.org/10.1038/s41467-025-61473-y |
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