Single Cell ProtEomics by Mass Spectrometry (SCoPE-MS) new technique for quantification proteomes of single mammalian cells
Bogdan Budnik1@, Ezra Levy2,John Neveu1,Harrison Specht3, Nikolai Slavov2;3
1MSPRL, FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA;
2Department of Biology, Northeastern University, Boston, MA 02115, USA;
3Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
Cellular heterogeneity is important to biological processes, including cancer1,2 and development3.However, proteome heterogeneity is largely unexplored because of the limitations of existing methods for quantifying protein levels in single cells. To overcome 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 hundreds of individual 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 good correspondence between mRNA and protein covariation and show that many proteins have been post translationally regulated.
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.
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3. Semrau, S. & van Oudenaarden, A. Studying lineage decision-making in vitro: emerging concepts and novel tools. Annual review of cell and developmental biology 31, 317–345 (2015).