Pick-up Single-Cell Proteomic Analysis for Quantifying up to 3000 Proteins in a Tumor Cell

Wang, Y.; Guan, Z.-Y.; Shi, S.-W.; Jiang, Y.-R.; Wu, Q.; Wu, J.; Chen, J.-B.; Ying, W.-X.; Xu, Q.-Q.; Fan, Q.-X.; Wang, H.-F.; Zhou, L.; Pan, J.-Z.; Fang, Q.

doi:10.1101/2022.06.28.498038

bioRxiv · 10.1101/2022.06.28.498038

Pick-up Single-Cell Proteomic Analysis for Quantifying up to 3000 Proteins in a Tumor Cell

Wang, Y.·Guan, Z.-Y.·Shi, S.-W.·Jiang, Y.-R.·Wu, Q.·Wu, J.·Chen, J.-B.·Ying, W.-X.·Xu, Q.-Q.·Fan, Q.-X.·Wang, H.-F.·Zhou, L.·Pan, J.-Z.·Fang, Q.

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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 tumor 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, 1804-3349, 1778-3049 and 1074-2487 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27), respectively. Benefiting from the flexible cell picking-up ability, we study tumor cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.

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Wang, Y., Guan, Z.-Y., Shi, S.-W., Jiang, Y.-R., Wu, Q., Wu, J., Chen, J.-B., Ying, W.-X., Xu, Q.-Q., Fan, Q.-X., Wang, H.-F., Zhou, L., Pan, J.-Z., Fang, Q.. 2022-06-30. Pick-up Single-Cell Proteomic Analysis for Quantifying up to 3000 Proteins in a Tumor Cell. https://doi.org/10.1101/2022.06.28.498038

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