Nature Communications (Jan 2025)
iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control
- 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
Affiliations
- Huanhuan Gao
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Yi Zhu
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Dongxue Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics
- Zongxiang Nie
- Westlake Omics (Hangzhou) Biotechnology Co., Ltd.
- He Wang
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Guibin Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics
- Shuang Liang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences
- Yuting Xie
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Yingying Sun
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Wenhao Jiang
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Zhen Dong
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Liqin Qian
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- Xufei Wang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University
- Mengdi Liang
- State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University
- Min Chen
- Luming Biotechnology Co., Ltd
- Houqi Fang
- Luming Biotechnology Co., Ltd
- Qiufang Zeng
- Shanghai Applied Protein Technology Co., Ltd
- Jiao Tian
- Shanghai Applied Protein Technology Co., Ltd
- Zeyu Sun
- State 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 University
- Juan Xue
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine
- Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine
- Chen Chen
- SCIEX
- Xiang Liu
- SCIEX
- Xiaolei Lyu
- SCIEX
- Zhenchang Guo
- Thermo Fisher Scientific
- Yingzi Qi
- Thermo Fisher Scientific
- Ruoyu Wu
- Bruker Daltonics
- Xiaoxian Du
- Bruker Daltonics
- Tingde Tong
- Thermo Fisher Scientific
- Fengchun Kong
- SCIEX
- Liming Han
- Bruker Daltonics
- Minghui Wang
- Bruker Daltonics
- Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology
- Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology
- Fuchu He
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics
- Tiannan Guo
- Affiliated Hangzhou First People’s Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University
- DOI
- https://doi.org/10.1038/s41467-024-54871-1
- Journal volume & issue
-
Vol. 16,
no. 1
pp. 1 – 13
Abstract
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.
