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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.

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|May 4, 2026
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Summary
This summary is machine-generated.

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.

Keywords:
cell type annotationdata processingflow cytometrysingle-cell proteomics

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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.