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

doi:10.1038/s41467-024-54871-1

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

Nat Commun. 2025 Jan 21;16(1):892. doi: 10.1038/s41467-024-54871-1.

Authors

Huanhuan Gao^#^{1

2

3}, Yi Zhu^#^{4

5

6}, Dongxue Wang^#^{7

8}, Zongxiang Nie^#⁹, He Wang^#^{1

2

3}, Guibin Wang⁷, Shuang Liang¹⁰, Yuting Xie^{1

2

3}, Yingying Sun^{1

2

3}, Wenhao Jiang^{1

2

3}, Zhen Dong^{1

2

3}, Liqin Qian^{1

2

3}, Xufei Wang¹¹, Mengdi Liang¹¹, Min Chen¹², Houqi Fang¹², Qiufang Zeng¹³, Jiao Tian¹³, Zeyu Sun¹⁴, Juan Xue^{15

16}, Shan Li^{15

16}, Chen Chen¹⁷, Xiang Liu¹⁷, Xiaolei Lyu¹⁷, Zhenchang Guo¹⁸, Yingzi Qi¹⁸, Ruoyu Wu¹⁹, Xiaoxian Du¹⁹, Tingde Tong¹⁸, Fengchun Kong¹⁷, Liming Han¹⁹, Minghui Wang¹⁹, Yang Zhao²⁰, Xinhua Dai²⁰, Fuchu He^{21

22}, Tiannan Guo^{23

24

25}

Affiliations

¹ Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China.
² Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang province, China.
³ Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang province, China.
⁴ Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China. [email protected].
⁵ Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang province, China. [email protected].
⁶ Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang province, China. [email protected].
⁷ State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
⁸ International Academy of Phronesis Medicine, Guangzhou, Guangdong, China.
⁹ Westlake Omics (Hangzhou) Biotechnology Co., Ltd., Hangzhou, China.
¹⁰ State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
¹¹ State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China.
¹² Luming Biotechnology Co., Ltd, Shanghai, China.
¹³ Shanghai Applied Protein Technology Co., Ltd, Shanghai, China.
¹⁴ 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, Hangzhou, Zhejiang, China.
¹⁵ Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.
¹⁶ College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, China.
¹⁷ SCIEX, Shanghai, China.
¹⁸ Thermo Fisher Scientific, Shanghai, China.
¹⁹ Bruker Daltonics, Shanghai, China.
²⁰ Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100029, China.
²¹ State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China. [email protected].
²² International Academy of Phronesis Medicine, Guangzhou, Guangdong, China. [email protected].
²³ Affiliated Hangzhou First People's Hospital, State Key Laboratory of Medical Proteomics, School of Medicine, Westlake University, Hangzhou, Zhejiang Province, China. [email protected].
²⁴ Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang province, China. [email protected].
²⁵ Research Center for Industries of the Future, School of Life Sciences, Westlake University, Hangzhou, Zhejiang province, China. [email protected].

^# Contributed equally.

PMID: 39837863
DOI: 10.1038/s41467-024-54871-1

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.

MeSH terms

Animals
Chromatography, Liquid / methods
Liver* / chemistry
Mass Spectrometry / methods
Mice
Proteomics* / methods
Proteomics* / standards
Quality Control*
Software*
Tandem Mass Spectrometry* / methods