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Navigating the Landscape of Cytometry-Based Single-Cell Proteomics: Quantification, Annotation, and Resources.
Yangbo Dai1, Ziqiang Liu1, Bing Liu2
1State Key Laboratory for Organic Electronics and Information Displays, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China.
International Journal of Molecular Sciences
|May 4, 2026
Summary
Cytometry-based single-cell proteomics (CySCP) offers deep insights into cellular heterogeneity by analyzing protein expression. This review details CySCP quantification, processing, and analysis strategies for biological discovery.
Area of Science:
- Biotechnology
- Proteomics
- Cell Biology
Background:
- Single-cell proteomics is crucial for understanding cellular heterogeneity.
- Existing literature lacks comprehensive summaries of Cytometry-based single-cell proteomics (CySCP) data handling.
Purpose of the Study:
- To provide a comprehensive review of CySCP, covering quantification, data processing, analysis, and resource platforms.
- To serve as a guide for researchers utilizing CySCP for single-cell protein-level biological insights.
Main Methods:
- Discussion of CySCP detection platforms, including their strengths and limitations.
- Detailed description of data processing steps: compensation, transformation, normalization, batch effect correction, signal cleaning, and removal of unwanted events (doublets, debris, dead cells).
- Illustration of various cell type annotation strategies: manual gating, unsupervised clustering, supervised/semi-supervised classification, and automated approaches.
Main Results:
- Strengths and limitations of CySCP detection platforms are discussed.
- Comprehensive data processing workflows for CySCP are detailed.
- Multiple cell annotation strategies are presented, from manual to automated.
- Emerging CySCP databases are summarized as critical resources for antibody validation, panel optimization, and data sharing.
Conclusions:
- This review offers a comprehensive guide to CySCP, empowering researchers to gain novel biological insights.
- Effective data processing and annotation are key to maximizing the potential of CySCP for understanding cellular heterogeneity at the protein level.
