Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

Abstract

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Single-cell technologies are revolutionizing biology but are today mainly limited to imaging and deep sequencing. However, proteins are the main drivers of cellular function and in-depth characterization of individual cells by mass spectrometry (MS)based proteomics would thus be highly valuable and complementary. Chemical labeling-based single-cell approaches introduce hundreds of cells into the MS, but direct analysis of single cells has not yet reached the necessary sensitivity, robustness and quantitative accuracy to answer biological questions. Here, we develop a robust workflow combining miniaturized sample preparation, very-low flow-rate chromatography and a novel trapped ion mobility mass spectrometer, resulting in a more than ten-fold improved sensitivity. We accurately and robustly quantify proteomes and their changes in single, FACS-isolated cells. Arresting cells at defined stages of the cell cycle by drug treatment retrieves expected key regulators such as CDK2NA, E2 ubiquitin ligases such as UBE2S and highlights potential novel ones. Comparing the variability in more than 420 single-cell proteomes to transcriptome data revealed a stable core proteome despite perturbation. Our technology can readily be applied to ultra-high sensitivity analysis of tissue material, including post-translational modifications and to small molecule studies.