iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control
Abstract Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collect 2754 files acquired by data independent acquisition (DIA) and paired 2638 DDA files from mouse liver digests using 21 mass spect...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-54871-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832585562161152000 |
|---|---|
| author | Huanhuan Gao Yi Zhu Dongxue Wang Zongxiang Nie He Wang Guibin Wang Shuang Liang Yuting Xie Yingying Sun Wenhao Jiang Zhen Dong Liqin Qian Xufei Wang Mengdi Liang Min Chen Houqi Fang Qiufang Zeng Jiao Tian Zeyu Sun Juan Xue Shan Li Chen Chen Xiang Liu Xiaolei Lyu Zhenchang Guo Yingzi Qi Ruoyu Wu Xiaoxian Du Tingde Tong Fengchun Kong Liming Han Minghui Wang Yang Zhao Xinhua Dai Fuchu He Tiannan Guo |
| author_facet | Huanhuan Gao Yi Zhu Dongxue Wang Zongxiang Nie He Wang Guibin Wang Shuang Liang Yuting Xie Yingying Sun Wenhao Jiang Zhen Dong Liqin Qian Xufei Wang Mengdi Liang Min Chen Houqi Fang Qiufang Zeng Jiao Tian Zeyu Sun Juan Xue Shan Li Chen Chen Xiang Liu Xiaolei Lyu Zhenchang Guo Yingzi Qi Ruoyu Wu Xiaoxian Du Tingde Tong Fengchun Kong Liming Han Minghui Wang Yang Zhao Xinhua Dai Fuchu He Tiannan Guo |
| author_sort | Huanhuan Gao |
| collection | DOAJ |
| description | Abstract Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collect 2754 files acquired by data independent acquisition (DIA) and paired 2638 DDA files from mouse liver digests using 21 mass spectrometers across nine laboratories over 31 months. Our data demonstrate that DIA-based LC-MS/MS-related consensus QC metrics exhibit higher sensitivity compared to DDA-based QC metrics in detecting changes in LC-MS status. We then prioritize 15 metrics and invite 21 experts to manually assess the quality of 2754 DIA files based on those metrics. We develop an AI model for DIA-based QC using 2110 training files. It achieves AUCs of 0.91 (LC) and 0.97 (MS) in the first validation dataset (n = 528), and 0.78 (LC) and 0.94 (MS) in an independent validation dataset (n = 116). Finally, we develop an offline software called iDIA-QC for convenient adoption of this methodology. |
| format | Article |
| id | doaj-art-491f92f49b0e42248a6dd291d575d01d |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-491f92f49b0e42248a6dd291d575d01d2025-01-26T12:41:19ZengNature PortfolioNature Communications2041-17232025-01-0116111310.1038/s41467-024-54871-1iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality controlHuanhuan Gao0Yi Zhu1Dongxue Wang2Zongxiang Nie3He Wang4Guibin Wang5Shuang Liang6Yuting Xie7Yingying Sun8Wenhao Jiang9Zhen Dong10Liqin Qian11Xufei Wang12Mengdi Liang13Min Chen14Houqi Fang15Qiufang Zeng16Jiao Tian17Zeyu Sun18Juan Xue19Shan Li20Chen Chen21Xiang Liu22Xiaolei Lyu23Zhenchang Guo24Yingzi Qi25Ruoyu Wu26Xiaoxian Du27Tingde Tong28Fengchun Kong29Liming Han30Minghui Wang31Yang Zhao32Xinhua Dai33Fuchu He34Tiannan Guo35Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityAffiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsWestlake Omics (Hangzhou) Biotechnology Co., Ltd.Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsState Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural SciencesAffiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityAffiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityAffiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityAffiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityAffiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityState Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical UniversityState Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical UniversityLuming Biotechnology Co., LtdLuming Biotechnology Co., LtdShanghai Applied Protein Technology Co., LtdShanghai Applied Protein Technology Co., LtdState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang UniversityInstitute of Infection and Immunity, Taihe Hospital, Hubei University of MedicineInstitute of Infection and Immunity, Taihe Hospital, Hubei University of MedicineSCIEXSCIEXSCIEXThermo Fisher ScientificThermo Fisher ScientificBruker DaltonicsBruker DaltonicsThermo Fisher ScientificSCIEXBruker DaltonicsBruker DaltonicsTechnology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of MetrologyTechnology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of MetrologyState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsAffiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake UniversityAbstract Quality control (QC) in mass spectrometry (MS)-based proteomics is mainly based on data-dependent acquisition (DDA) analysis of standard samples. Here, we collect 2754 files acquired by data independent acquisition (DIA) and paired 2638 DDA files from mouse liver digests using 21 mass spectrometers across nine laboratories over 31 months. Our data demonstrate that DIA-based LC-MS/MS-related consensus QC metrics exhibit higher sensitivity compared to DDA-based QC metrics in detecting changes in LC-MS status. We then prioritize 15 metrics and invite 21 experts to manually assess the quality of 2754 DIA files based on those metrics. We develop an AI model for DIA-based QC using 2110 training files. It achieves AUCs of 0.91 (LC) and 0.97 (MS) in the first validation dataset (n = 528), and 0.78 (LC) and 0.94 (MS) in an independent validation dataset (n = 116). Finally, we develop an offline software called iDIA-QC for convenient adoption of this methodology.https://doi.org/10.1038/s41467-024-54871-1 |
| spellingShingle | Huanhuan Gao Yi Zhu Dongxue Wang Zongxiang Nie He Wang Guibin Wang Shuang Liang Yuting Xie Yingying Sun Wenhao Jiang Zhen Dong Liqin Qian Xufei Wang Mengdi Liang Min Chen Houqi Fang Qiufang Zeng Jiao Tian Zeyu Sun Juan Xue Shan Li Chen Chen Xiang Liu Xiaolei Lyu Zhenchang Guo Yingzi Qi Ruoyu Wu Xiaoxian Du Tingde Tong Fengchun Kong Liming Han Minghui Wang Yang Zhao Xinhua Dai Fuchu He Tiannan Guo iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control Nature Communications |
| title | iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control |
| title_full | iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control |
| title_fullStr | iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control |
| title_full_unstemmed | iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control |
| title_short | iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control |
| title_sort | idia qc ai empowered data independent acquisition mass spectrometry based quality control |
| url | https://doi.org/10.1038/s41467-024-54871-1 |
| work_keys_str_mv | AT huanhuangao idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT yizhu idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT dongxuewang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT zongxiangnie idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT hewang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT guibinwang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT shuangliang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT yutingxie idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT yingyingsun idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT wenhaojiang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT zhendong idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT liqinqian idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT xufeiwang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT mengdiliang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT minchen idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT houqifang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT qiufangzeng idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT jiaotian idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT zeyusun idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT juanxue idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT shanli idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT chenchen idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT xiangliu idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT xiaoleilyu idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT zhenchangguo idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT yingziqi idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT ruoyuwu idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT xiaoxiandu idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT tingdetong idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT fengchunkong idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT liminghan idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT minghuiwang idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT yangzhao idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT xinhuadai idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT fuchuhe idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol AT tiannanguo idiaqcaiempowereddataindependentacquisitionmassspectrometrybasedqualitycontrol |