ArticleNature methods2023
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed.
- Proteomic investigation of signaling dynamics: from static maps to network rewiring.Bioscience reports · 2026Review
- SoftHybrid: A Hybrid Imputation Algorithm Optimized for Single-Cell Proteomics Data.Journal of proteome research · 2026Article
- Aspiration Patch Proteomics Enables CE-ESI-MS Proteotyping of Identified Single Neurons in Intact Brain Tissue.Analytical chemistry · 2026Article
- Article
- Single-Cell Proteomic Technologies: Tools in the Quest for Principles.Annual review of biophysics · 2026Review
- A nature-inspired ion trap for parallel manipulation of ions on a massive scale.Science advances · 2026Article
- Single-molecule peptide sequencing through reverse translation of peptides into DNA.Nature biotechnology · 2026Article
- Single-Cell Proteomics of Human Peripheral Blood Mononuclear Cells Exceeding 600 Cells per Day.bioRxiv : the preprint server for biology · 2026Article
- Resolving Single-Cell Gene Expression by Pseudotemporal Integration of Transcriptomic and Proteomic Datasets.Molecular & cellular proteomics : MCP · 2026Article
- Article
- The pursuit of ultrasensitive phosphoproteomics to unravel signalling in rare cells.Communications biology · 2025Review
- Review
- Real-Time Eco-AI, Electrophoresis-Correlative Data-Dependent Acquisition with AI-Based Data Processing Broadens Access to Single-Cell Mass Spectrometry Proteomics.Angewandte Chemie (International ed. in English) · 2025Article
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Alternate RNA decoding results in stable and abundant proteins in mammals.bioRxiv : the preprint server for biology · 2025Article
- Single-cell proteomics using mass spectrometry.Cell genomics · 2025Review
- Plasma-Derived Extracellular Vesicle Proteomics.Journal of proteome research · 2025Review
- Liquid Chromatographic and Mass Spectrometric Methods for Quantitative Proteomic Analysis from Single-Cell and Nanogram-Level Samples.Analytical chemistry · 2025Article
- scplainer: using linear models to understand mass spectrometry-based single-cell proteomics data.Genome biology · 2025Article
- Sensitive neoantigen discovery by real-time mutanome-guided immunopeptidomics.Nature communications · 2025Article
4 more citing papers are in PubMed but not listed here.
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15 authors.
Funding
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. 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 http://scp.slavovlab.net/pSCoPE .
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