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Multiplexed single-cell proteomics using SCoPE2

View ORCID ProfileAleksandra A. Petelski, View ORCID ProfileEdward Emmott, View ORCID ProfileAndrew Leduc, View ORCID ProfileR. Gray Huffman, View ORCID ProfileHarrison Specht, David H. Perlman, View ORCID ProfileNikolai Slavov
doi: https://doi.org/10.1101/2021.03.12.435034
Aleksandra A. Petelski
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Edward Emmott
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
3Centre for Proteome Research, Department of Biochemistry & Systems Biology, University of Liverpool, Liverpool, L69 7ZB, UK
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Andrew Leduc
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
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R. Gray Huffman
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Harrison Specht
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
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David H. Perlman
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
5Merck Exploratory Sciences Center, Merck Sharp & Dohme Corp., 320 Bent St. Cambridge, MA 02141
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Nikolai Slavov
1Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
2Barnett Institute, Northeastern University, Boston, MA 02115, USA
4Department of Biology, Northeastern University, Boston, MA 02115, USA
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  • For correspondence: nslavov@alum.mit.edu nslavov@northeastern.edu
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Abstract

Many biological systems are composed of diverse single cells. This diversity necessitates functional and molecular single-cell analysis. Single-cell protein analysis has long relied on affinity reagents, but emerging mass-spectrometry methods (either label-free or multiplexed) have enabled quantifying over 1,000 proteins per cell while simultaneously increasing the specificity of protein quantification. Isobaric carrier based multiplexed single-cell proteomics is a scalable, reliable, and cost-effective method that can be fully automated and implemented on widely available equipment. It uses inexpensive reagents and is applicable to any sample that can be processed to a single-cell suspension. Here we describe an automated Single Cell ProtEomics (SCoPE2) workflow that allows analyzing about 200 single cells per 24 hours using only standard commercial equipment. We emphasize experimental steps and benchmarks required for achieving quantitative protein analysis.

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Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ∈ Data & analysis code: scope2.slavovlab.net

  • https://scope2.slavovlab.net

  • https://scope2.slavovlab.net/mass-spec/protocol

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 04, 2021.
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Multiplexed single-cell proteomics using SCoPE2
Aleksandra A. Petelski, Edward Emmott, Andrew Leduc, R. Gray Huffman, Harrison Specht, David H. Perlman, Nikolai Slavov
bioRxiv 2021.03.12.435034; doi: https://doi.org/10.1101/2021.03.12.435034
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Multiplexed single-cell proteomics using SCoPE2
Aleksandra A. Petelski, Edward Emmott, Andrew Leduc, R. Gray Huffman, Harrison Specht, David H. Perlman, Nikolai Slavov
bioRxiv 2021.03.12.435034; doi: https://doi.org/10.1101/2021.03.12.435034

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