Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics

Huffman, R Gray, Leduc, Andrew, Wichmann, Christoph, Di Gioia, Marco, Borriello, Francesco, Specht, Harrison, Derks, Jason, Khan, Saad, Khoury, Luke, Emmott, Edward ORCID: 0000-0002-3239-8178
et al (show 5 more authors) (2023) Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. NATURE METHODS, 20 (5). pp. 714-722.

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Major aims of single-cell proteomics include increasing the consistency, sensitivity and depth of protein quantification, especially for proteins and modifications of biological interest. Here, 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 maximizing instrument time spent analyzing identifiable peptides, thus increasing proteome depth. These strategies increased the sensitivity, data completeness and proteome coverage over twofold. 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, similarly across both treatment conditions. This covariation is 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 .

Item Type: Article
Uncontrolled Keywords: Macrophages, Peptides, Proteome, Proteomics, Mass Spectrometry
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User: Symplectic Admin
Date Deposited: 17 Apr 2023 09:45
Last Modified: 26 May 2023 05:50
DOI: 10.1038/s41592-023-01830-1
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