Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell

Yu Wang, Zhi-Ying Guan, Shao-Wen Shi, Yi-Rong Jiang, Jie Zhang, Yi Yang, Qiong Wu, Jie Wu, Jian-Bo Chen, Wei-Xin Ying, Qin-Qin Xu, Qian-Xi Fan, Hui-Feng Wang, Li Zhou, Ling Wang, Jin Fang, Jian-Zhang Pan and Qun Fang ()
Additional contact information
Yu Wang: Zhejiang University
Zhi-Ying Guan: Zhejiang University
Shao-Wen Shi: ZJU-Hangzhou Global Scientific and Technological Innovation Center
Yi-Rong Jiang: Zhejiang University
Jie Zhang: China Medical University
Yi Yang: Zhejiang University
Qiong Wu: Zhejiang University
Jie Wu: Zhejiang University
Jian-Bo Chen: Zhejiang University
Wei-Xin Ying: Zhejiang University
Qin-Qin Xu: Zhejiang University
Qian-Xi Fan: Zhejiang University
Hui-Feng Wang: ZJU-Hangzhou Global Scientific and Technological Innovation Center
Li Zhou: Shanghai Omicsolution Co.
Ling Wang: Shanghai Omicsolution Co.
Jin Fang: China Medical University
Jian-Zhang Pan: Zhejiang University
Qun Fang: Zhejiang University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of ~1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a mammalian cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 2449–3500, 2278–3257 and 1621–2904 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27) under the DIA (MBR) mode, respectively. Benefiting from the flexible cell picking-up ability, we study HeLa cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.

Date: 2024
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DOI: 10.1038/s41467-024-45659-4

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