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

MSPRL, FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
Department of Biology, Northeastern University, Boston, MA, USA
Department of Bioengineering, Northeastern University, Boston, MA, USA
Subject Areas
Biochemistry, Cell Biology, Computational Biology, Developmental Biology, Molecular Biology
mass-spectrometry, stem cells, single-cell, proteomics, differentiation, cell classification, cancer
© 2017 Budnik et al.
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Cite this article
Budnik B, Levy E, Slavov N. 2017. Mass-spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. PeerJ Preprints 5:e2767v1


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.

Author Comment

This is a version 1 of a preprint submission to PeerJ