iDIA-QC: AI-empowered data-independent acquisition mass spectrometry-based quality control.

Journal: Nature communications
PMID:

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.

Authors

  • Huanhuan Gao
    Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
  • Yi Zhu
    2State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong China.
  • Dongxue Wang
    School of Sport Medicine and Rehabilitation, Beijing Sport University, Beijing, China.
  • Zongxiang Nie
    Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China.
  • He Wang
    Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, China International Neuroscience Institute, Beijing, China.
  • Guibin Wang
    State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
  • Shuang Liang
  • Yuting Xie
    Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
  • Yingying Sun
    NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Molecular Imaging Research Center (MIRC), Harbin Medical University, Harbin, Heilongjiang, China.
  • Wenhao Jiang
    YIWEI Medical Technology Co., Ltd, Room 1001, MAI KE LONG Building, Nanshan, ShenZhen, 518000, China.
  • Zhen Dong
    Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
  • Liqin Qian
    Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
  • Xufei Wang
    Two Sigma Investments, New York, New York 10013, United States.
  • Mengdi Liang
    State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China.
  • Min Chen
    School of Computer Science and TechnologyHuazhong University of Science and Technology Wuhan 430074 China.
  • Houqi Fang
    Luming Biotechnology Co., Ltd, Shanghai, China.
  • Qiufang Zeng
    Shanghai Applied Protein Technology Co., Ltd, Shanghai, China.
  • Jiao Tian
    Shanghai Applied Protein Technology Co., Ltd, Shanghai, China.
  • Zeyu Sun
    Deepwise AI lab, Beijing 100080, China.
  • Juan Xue
    Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.
  • Shan Li
    College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao 266061, China; Artificial Intelligence and Biomedical Big Data Research Center, Qingdao University of Science and Technology, Qingdao 266061, China. Electronic address: lishan5600@163.com.
  • Chen Chen
    The George Institute for Global Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
  • Xiang Liu
    College of Agricultural Science and Engineering, Hohai University, Nanjing 210098, China; Anhui Provincial Key Laboratory of Environmental Pollution Control and Resource Reuse, Anhui Jianzhu University, Hefei 230009, China.
  • Xiaolei Lyu
    SCIEX, Shanghai, China.
  • Zhenchang Guo
    Thermo Fisher Scientific, Shanghai, China.
  • Yingzi Qi
    Thermo Fisher Scientific, Shanghai, China.
  • Ruoyu Wu
  • Xiaoxian Du
    Bruker Daltonics, Shanghai, China.
  • Tingde Tong
    Thermo Fisher Scientific, Shanghai, China.
  • Fengchun Kong
    SCIEX, Shanghai, China.
  • Liming Han
    Bruker Daltonics, Shanghai, China.
  • Minghui Wang
    College of Chemistry and Material Science, Shandong Agricultural University, Tai'an 271018, PR China.
  • Yang Zhao
    The George Institute for Global Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
  • Xinhua Dai
    West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
  • Fuchu He
    Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China.
  • Tiannan Guo
    Institute of Basic Medical Sciences, School of Life Science, Westlake University, Hangzhou 310024, China.