RT Journal Article
SR Electronic
T1 Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.03.16.484655
DO 10.1101/2022.03.16.484655
A1 R Gray Huffman
A1 Andrew Leduc
A1 Christoph Wichmann
A1 Marco di Gioia
A1 Francesco Borriello
A1 Harrison Specht
A1 Jason Derks
A1 Saad Khan
A1 Edward Emmott
A1 Aleksandra A. Petelski
A1 David H Perlman
A1 Jürgen Cox
A1 Ivan Zanoni
A1 Nikolai Slavov
YR 2022
UL http://biorxiv.org/content/early/2022/03/18/2022.03.16.484655.abstract
AB 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. Competing Interest StatementThe authors have declared no competing interest.