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Genome Biol. 2018 Oct 22;19(1):161. doi: 10.1186/s13059-018-1547-5.

SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation.

Author information

1
MSPRL, FAS Division of Science, Harvard University, Cambridge, MA, 02138, USA. bbudnik@mcb.harvard.edu.
2
Department of Biology, Northeastern University, Boston, MA, 02115, USA.
3
Department of Biology, Northeastern University, Boston, MA, 02115, USA. nslavov@alum.mit.edu.
4
Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA. nslavov@alum.mit.edu.

Abstract

Some exciting biological questions require quantifying thousands of proteins in single cells. To achieve this goal, we develop Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) and validate its ability to identify distinct human cancer cell types based on their proteomes. We use SCoPE-MS to quantify over a thousand proteins in differentiating mouse embryonic stem cells. The single-cell proteomes enable us to deconstruct cell populations and infer protein abundance relationships. Comparison between single-cell proteomes and transcriptomes indicates coordinated mRNA and protein covariation, yet many genes exhibit functionally concerted and distinct regulatory patterns at the mRNA and the protein level.

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