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Related Concept Videos

Proteomics01:33

Proteomics

8.9K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
8.9K

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Related Experiment Video

Updated: Nov 19, 2025

Proteomic Profiling of Macrophages by 2D Electrophoresis
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Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2.

Harrison Specht1, Edward Emmott2,3, Aleksandra A Petelski2

  • 1Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA. hms89@cornell.edu.

Genome Biology
|January 28, 2021
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Summary

Single-cell proteome analysis reveals macrophage heterogeneity even without external stimuli. The SCoPE2 method enables high-throughput protein quantification, uncovering continuous proteome states and regulatory interactions.

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Last Updated: Nov 19, 2025

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Area of Science:

  • Immunology
  • Proteomics
  • Cell Biology

Background:

  • Macrophages exhibit diverse phenotypes crucial for innate immunity.
  • Single-cell proteome analysis is limited in quantitative accuracy and throughput.
  • Understanding macrophage heterogeneity is essential but challenging.

Purpose of the Study:

  • To develop an advanced method for quantitative single-cell proteome analysis.
  • To investigate the emergence of macrophage heterogeneity during differentiation.
  • To explore regulatory interactions within single cells.

Main Methods:

  • Development of SCoPE2 (Single-cell Cơpe2) for automated and miniaturized sample preparation.
  • High-throughput quantification of over 3042 proteins in 1490 single monocytes and macrophages.
  • Parallel measurement of transcripts using 10× Genomics.

Main Results:

  • SCoPE2 significantly increases quantitative accuracy, throughput, and reduces cost and hands-on time.
  • Analysis revealed a continuous gradient of proteome states in macrophages, indicating heterogeneity emerges intrinsically.
  • Protein quantification revealed 20-fold more protein copies than RNA copies per gene, enabling better statistical analysis.
  • Exploration of regulatory interactions, including the p53 pathway.

Conclusions:

  • Macrophage proteomes are heterogeneous even in a homogeneous environment.
  • This heterogeneity correlates with the inflammatory axis of macrophage activation.
  • The developed methodology enables automated, quantitative single-cell proteomics and inference of gene regulation.