PT  - JOURNAL ARTICLE
AU  - R Gray Huffman
AU  - Andrew Leduc
AU  - Christoph Wichmann
AU  - Marco di Gioia
AU  - Francesco Borriello
AU  - Harrison Specht
AU  - Jason Derks
AU  - Saad Khan
AU  - Luke Khoury
AU  - Edward Emmott
AU  - Aleksandra A. Petelski
AU  - David H Perlman
AU  - Jürgen Cox
AU  - Ivan Zanoni
AU  - Nikolai Slavov
TI  - Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages
AID  - 10.1101/2022.03.16.484655
DP  - 2022 Jan 01
TA  - bioRxiv
PG  - 2022.03.16.484655
4099  - http://biorxiv.org/content/early/2022/09/26/2022.03.16.484655.short
4100  - http://biorxiv.org/content/early/2022/09/26/2022.03.16.484655.full
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 these aims, we developed prioritized Single Cell ProtEomics (pSCoPE). pSCoPE consistently analyzes thousands of prioritized peptides across all single cells (thus increasing data completeness) while analyzing identifiable peptides at full duty-cycle, thus increasing proteome depth. These strategies increased the sensitivity, data completeness, and proteome coverage over 2-fold. The gains enabled quantifying protein variation in untreated and lipopolysaccharide-treated primary macrophages. Within each condition, proteins covaried within functional sets, including phagosome maturation and proton transport. This protein covariation within a treatment condition was similar across the treatment conditions and coupled to phenotypic variability in endocytic activity. pSCoPE also enabled quantifying proteolytic products, suggesting a gradient of cathepsin activities within a treatment condition. pSCoPE is freely available and widely applicable, especially for analyzing proteins of interest without sacrificing proteome coverage. Support for pSCoPE is available at: scp.slavovlab.net/pSCoPECompeting Interest StatementThe authors have declared no competing interest.