MassIVE MSV000082077

Partial Public PXD008985

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


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 thousands of 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. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: stem cells ; cancer ; single cell ; low input ; TMT


Principal Investigators: Nikolai Slavov, Northeastern University, USA
Submitting User: nnslavov


Budnik B., Levy E., Harmange G., Slavov N.
Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation.

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