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Published on: December 9, 2022
EasySCP unveils extensive liver zonation at single-cell proteomics resolution
Bingbing Hao1,2, Jinghui Wei3,4,5, Jiaen Xu3
1State Key Laboratory of Metabolic Dysregulation & Prevention and Treatment of Esophageal Cancer, Tianjian Laboratory of Advanced Biomedical Sciences, School of Convergence Medicine, Zhengzhou University, Zhengzhou, China. bbhao@zzu.edu.cn.
Nature Communications
|June 16, 2026
Summary
We developed EasySCP, a high-throughput single-cell proteomics method. This accessible tool analyzes cellular heterogeneity and reconstructs liver zonation, bridging transcriptomics and proteomics.
Area of Science:
- Proteomics
- Cell Biology
- Systems Biology
Background:
- Single-cell proteomics (SCP) application is limited by complex workflows and specialized equipment.
- High-throughput, accessible methods are needed to analyze cellular heterogeneity at the proteomic level.
Purpose of the Study:
- Introduce EasySCP, a high-throughput method for single-cell proteomics.
- Enable dissection of cellular heterogeneity and functional proteomics.
- Develop a tool for reconstructing liver zonation patterns.
Main Methods:
- Integrated FACS-based single-cell sorting, single-step digestion in 384-well plates, and mass spectrometry.
- Applied EasySCP to HEK293 cells and female murine liver.
- Developed hepatocyte spatial status score (HSS) using conserved zonation markers.
Main Results:
- Identified nearly 5000 proteins from individual HEK293 cells.
- Achieved spatially informed proteomics profiling of murine liver hepatocytes, detecting ~3500 proteins per cell.
- Uncovered zonation patterns for 3277 out of 5267 quantified proteins.
- Demonstrated HSS enables reconstruction of liver zonation across datasets.
Conclusions:
- EasySCP is a broadly accessible tool for single-cell proteomics.
- Facilitates the study of cellular heterogeneity in healthy and disease states.
- Bridges the gap between transcriptomics and functional proteomics.
