High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

Jongmin Woo, Sarah M. Williams, Lye Meng Markillie, Song Feng, Chia-Feng Tsai, Victor Aguilera-Vazquez, Ryan L. Sontag, Ronald J. Moore, Dehong Hu, Hardeep S. Mehta, Joshua Cantlon-Bruce, Tao Liu, Joshua N. Adkins, Richard D. Smith, Geremy C. Clair, Ljiljana Pasa-Tolic and Ying Zhu ()
Additional contact information
Jongmin Woo: Pacific Northwest National Laboratory
Sarah M. Williams: Pacific Northwest National Laboratory
Lye Meng Markillie: Pacific Northwest National Laboratory
Song Feng: Pacific Northwest National Laboratory
Chia-Feng Tsai: Pacific Northwest National Laboratory
Victor Aguilera-Vazquez: Pacific Northwest National Laboratory
Ryan L. Sontag: Pacific Northwest National Laboratory
Ronald J. Moore: Pacific Northwest National Laboratory
Dehong Hu: Pacific Northwest National Laboratory
Hardeep S. Mehta: Pacific Northwest National Laboratory
Joshua Cantlon-Bruce: Scienion AG
Tao Liu: Pacific Northwest National Laboratory
Joshua N. Adkins: Pacific Northwest National Laboratory
Richard D. Smith: Pacific Northwest National Laboratory
Geremy C. Clair: Pacific Northwest National Laboratory
Ljiljana Pasa-Tolic: Pacific Northwest National Laboratory
Ying Zhu: Pacific Northwest National Laboratory

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract Global quantification of protein abundances in single cells could provide direct information on cellular phenotypes and complement transcriptomics measurements. However, single-cell proteomics is still immature and confronts many technical challenges. Herein we describe a nested nanoPOTS (N2) chip to improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip reduces reaction volume to 240 single cells on a single microchip. The tandem mass tag (TMT) pooling step is simplified by adding a microliter droplet on the nested nanowells to combine labeled single-cell samples. In the analysis of ~100 individual cells from three different cell lines, we demonstrate that the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal membrane protein markers. Our analyses also reveal low protein abundance variations, suggesting the single-cell proteome profiles are highly stable for the cells cultured under identical conditions.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-26514-2

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DOI: 10.1038/s41467-021-26514-2

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