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Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages

View ORCID ProfileR Gray Huffman, View ORCID ProfileAndrew Leduc, View ORCID ProfileChristoph Wichmann, View ORCID ProfileMarco di Gioia, View ORCID ProfileFrancesco Borriello, View ORCID ProfileHarrison Specht, View ORCID ProfileJason Derks, View ORCID ProfileSaad Khan, View ORCID ProfileEdward Emmott, View ORCID ProfileAleksandra A. Petelski, View ORCID ProfileDavid H Perlman, View ORCID ProfileJürgen Cox, View ORCID ProfileIvan Zanoni, View ORCID ProfileNikolai Slavov
doi: https://doi.org/10.1101/2022.03.16.484655
R Gray Huffman
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Andrew Leduc
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Christoph Wichmann
2Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Germany
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Marco di Gioia
3Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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Francesco Borriello
3Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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Harrison Specht
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Jason Derks
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Saad Khan
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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Edward Emmott
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
4Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute for Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
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Aleksandra A. Petelski
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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David H Perlman
5Merck Exploratory Sciences Center, Merck Sharp & Dohme Corp., 320 Bent St. Cambridge, MA 02141
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Jürgen Cox
2Computational Systems Biochemistry Research Group, Max Planck Institute of Biochemistry, Germany
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Ivan Zanoni
3Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
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Nikolai Slavov
1Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center, and Barnett Institute, Northeastern University, Boston, MA 02115, USA
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  • For correspondence: nslavov@northeastern.edu
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Abstract

Major aims of single-cell proteomics include increasing the consistency, sensitivity, and depth of protein quantification, especially for proteins and modifications of biological interest. To simultaneously advance all of these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE ensures duty-cycle time for analyzing prioritized peptides across all single cells (thus increasing data consistency) while analyzing identifiable peptides at full duty-cycle, thus increasing proteome depth. These strategies increased the quantified data points for challenging peptides and the overall proteome coverage about 2-fold. pSCoPE enabled quantifying proteome polarization in primary mouse macrophages and linking it to phenotypic variability in endocytic activity. Proteins annotated to phagosome maturation and proton transport showed concerted variation for both untreated and lipopolysaccharide-treated macrophages, indicating a conserved axis of polarization. pSCoPE further quantified proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is easily accessible and likely to benefit many applications, especially mechanistic analysis seeking to focus on proteins of interest without sacrificing proteome coverage.

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Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ∈ Data, code & protocols: scp.slavovlab.net/pSCoPE

  • https://scp.slavovlab.net/pSCoPE

  • https://scp.slavovlab.net/Huffman_et_al_2022

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 March 18, 2022.
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Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages
R Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco di Gioia, Francesco Borriello, Harrison Specht, Jason Derks, Saad Khan, Edward Emmott, Aleksandra A. Petelski, David H Perlman, Jürgen Cox, Ivan Zanoni, Nikolai Slavov
bioRxiv 2022.03.16.484655; doi: https://doi.org/10.1101/2022.03.16.484655
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Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages
R Gray Huffman, Andrew Leduc, Christoph Wichmann, Marco di Gioia, Francesco Borriello, Harrison Specht, Jason Derks, Saad Khan, Edward Emmott, Aleksandra A. Petelski, David H Perlman, Jürgen Cox, Ivan Zanoni, Nikolai Slavov
bioRxiv 2022.03.16.484655; doi: https://doi.org/10.1101/2022.03.16.484655

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