November 21, 2021
Journal Article

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

Abstract

Global quantification of protein abundances in single cells would provide more direct information on cellular function phenotypes and complement transcriptomics measurements. However, single-cell proteomics (scProteomics) is still immature and confronts technical challenges, including limited proteome coverage, poor reproducibility, as well as low throughput. Here we describe a nested nanowell (N2) chip to dramatically improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip allows reducing cell digestion volume to 240 single cells in one microchip. In the analysis of ~100 individual cells from three different cell lines, we demonstrate the N2 chip-based scProteomics platform can robustly quantify ~1500 proteins and reveal functional differences. Our analysis also reveals low protein abundance variations (median CVs

Published: November 21, 2021

Citation

Woo J., S.M. Williams, L. Markillie, S. Feng, C. Tsai, V. Aguilera-Vazquez, and R.L. Sontag, et al. 2021. "High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip." Nature Communications 12. PNNL-SA-159977. doi:10.1038/s41467-021-26514-2