Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

TL;DR

This paper introduces SCoPE-MS, a mass spectrometry-based method for quantifying proteome heterogeneity in single mammalian cells, revealing insights into cell differentiation and regulatory mechanisms.

Contribution

The study develops and validates a novel single-cell proteomics technique, SCoPE-MS, enabling detailed analysis of proteome heterogeneity during cell differentiation.

Findings

SCoPE-MS quantifies over a thousand proteins in single cells.

Single-cell proteomes reveal cell population structures and protein relationships.

Post-transcriptional regulation significantly influences proteome remodeling.

Abstract

Cellular heterogeneity is important to biological processes, including cancer and development. However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To alleviate these limitations, we developed Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS), and validated its ability to identify distinct human cancer cell types based on their proteomes. We used SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem (ES) cells. The single-cell proteomes enabled us to deconstruct cell populations and infer protein abundance relationships. Comparison between single-cell proteomes and transcriptomes indicated coordinated mRNA and protein covariation. Yet many genes exhibited functionally concerted and distinct regulatory patterns at the mRNA and the protein levels, suggesting that post-transcriptional regulatory mechanisms contribute to proteome remodeling during lineage specification, especially for developmental genes. SCoPE-MS is broadly applicable to measuring proteome configurations of single cells and linking them to functional phenotypes, such as cell type and differentiation potentials.