LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics
Abstract Improving annotation accuracy, coverage, speed and depth of lipid profiles remains a significant challenge in traditional lipid annotation. We introduce LipidIN, an advanced framework designed for flash platform-independent annotation. LipidIN features a 168.5-million lipid fragmentation hi...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-05-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-59683-5 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849310323790577664 |
|---|---|
| author | Hao Xu Tianhang Jiang Yuxiang Lin Lei Zhang Huan Yang Xiaoyun Huang Ridong Mao Zhu Yang Changchun Zeng Shuang Zhao Lijun Di Wenbin Zhang Jun Zeng Zongwei Cai Shu-Hai Lin |
| author_facet | Hao Xu Tianhang Jiang Yuxiang Lin Lei Zhang Huan Yang Xiaoyun Huang Ridong Mao Zhu Yang Changchun Zeng Shuang Zhao Lijun Di Wenbin Zhang Jun Zeng Zongwei Cai Shu-Hai Lin |
| author_sort | Hao Xu |
| collection | DOAJ |
| description | Abstract Improving annotation accuracy, coverage, speed and depth of lipid profiles remains a significant challenge in traditional lipid annotation. We introduce LipidIN, an advanced framework designed for flash platform-independent annotation. LipidIN features a 168.5-million lipid fragmentation hierarchical library that encompasses all potential chain compositions and carbon-carbon double bond locations. The expeditious querying module achieves speeds exceeding one hundred billion queries per second across all mass spectral libraries. The lipid categories intelligence model is developed using three relative retention time rules, reducing false positive annotations and predicting unannotated lipids with a 5.7% estimated false discovery rate, covering 8923 lipids cross various species. More importantly, LipidIN integrates a Wide-spectrum Modeling Yield network for regenerating lipid fragment fingerprints to further improve accuracy and coverage with a 20% estimated recall boosting. We further demonstrate the utility of LipidIN in multiple tasks for lipid annotation and biomarker discovery in clinical cohorts. |
| format | Article |
| id | doaj-art-ee5faf47eb1e44a2a30af4f45b586e6f |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-ee5faf47eb1e44a2a30af4f45b586e6f2025-08-20T03:53:46ZengNature PortfolioNature Communications2041-17232025-05-0116111710.1038/s41467-025-59683-5LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomicsHao Xu0Tianhang Jiang1Yuxiang Lin2Lei Zhang3Huan Yang4Xiaoyun Huang5Ridong Mao6Zhu Yang7Changchun Zeng8Shuang Zhao9Lijun Di10Wenbin Zhang11Jun Zeng12Zongwei Cai13Shu-Hai Lin14The First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, XMU-HBN Skin Biomedical Research Center, Xiamen UniversityThe First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, XMU-HBN Skin Biomedical Research Center, Xiamen UniversityDepartment of Breast Surgery, Fujian Medical University Union HospitalThe First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, XMU-HBN Skin Biomedical Research Center, Xiamen UniversityThe First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, XMU-HBN Skin Biomedical Research Center, Xiamen UniversityCollege of Ocean Food and Biological Engineering, Jimei UniversityThe First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, XMU-HBN Skin Biomedical Research Center, Xiamen UniversityState Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist UniversityDepartment of General Medicine, Shenzhen Longhua District Central HospitalXiamen Meliomics Co., Ltd.Department of Biological Sciences, Faculty of Health Sciences, University of MacauDepartment of Occupational and Environmental Health and the Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Fourth Military Medical UniversityCollege of Ocean Food and Biological Engineering, Jimei UniversityState Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist UniversityThe First Affiliated Hospital of Xiamen University, State Key Laboratory of Cellular Stress Biology, School of Life Sciences, XMU-HBN Skin Biomedical Research Center, Xiamen UniversityAbstract Improving annotation accuracy, coverage, speed and depth of lipid profiles remains a significant challenge in traditional lipid annotation. We introduce LipidIN, an advanced framework designed for flash platform-independent annotation. LipidIN features a 168.5-million lipid fragmentation hierarchical library that encompasses all potential chain compositions and carbon-carbon double bond locations. The expeditious querying module achieves speeds exceeding one hundred billion queries per second across all mass spectral libraries. The lipid categories intelligence model is developed using three relative retention time rules, reducing false positive annotations and predicting unannotated lipids with a 5.7% estimated false discovery rate, covering 8923 lipids cross various species. More importantly, LipidIN integrates a Wide-spectrum Modeling Yield network for regenerating lipid fragment fingerprints to further improve accuracy and coverage with a 20% estimated recall boosting. We further demonstrate the utility of LipidIN in multiple tasks for lipid annotation and biomarker discovery in clinical cohorts.https://doi.org/10.1038/s41467-025-59683-5 |
| spellingShingle | Hao Xu Tianhang Jiang Yuxiang Lin Lei Zhang Huan Yang Xiaoyun Huang Ridong Mao Zhu Yang Changchun Zeng Shuang Zhao Lijun Di Wenbin Zhang Jun Zeng Zongwei Cai Shu-Hai Lin LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics Nature Communications |
| title | LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics |
| title_full | LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics |
| title_fullStr | LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics |
| title_full_unstemmed | LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics |
| title_short | LipidIN: a comprehensive repository for flash platform-independent annotation and reverse lipidomics |
| title_sort | lipidin a comprehensive repository for flash platform independent annotation and reverse lipidomics |
| url | https://doi.org/10.1038/s41467-025-59683-5 |
| work_keys_str_mv | AT haoxu lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT tianhangjiang lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT yuxianglin lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT leizhang lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT huanyang lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT xiaoyunhuang lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT ridongmao lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT zhuyang lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT changchunzeng lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT shuangzhao lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT lijundi lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT wenbinzhang lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT junzeng lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT zongweicai lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics AT shuhailin lipidinacomprehensiverepositoryforflashplatformindependentannotationandreverselipidomics |