PEELing：一个用于空间分辨蛋白质组学数据分析的集成式且以用户为中心的平台。

PEELing: an integrated and user-centric platform for spatially resolved proteomics data analysis.

作者信息

Peng Xi, Clements Jody, Jiang Zuzhi, Han Shuo, Preibisch Stephan, Li Jiefu

机构信息

Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, United States.

Yuanpei College, Peking University, Beijing 100871, China.

出版信息

Bioinformatics. 2025 Aug 2;41(8). doi: 10.1093/bioinformatics/btaf439.

DOI:10.1093/bioinformatics/btaf439

PMID:40794857

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12343102/

Abstract

SUMMARY

Molecular compartmentalization is vital for cellular physiology. Spatially resolved proteomics allows biologists to survey protein composition and dynamics with subcellular resolution. Here, we present PEELing, an integrated package and user-friendly web service for analyzing spatially resolved proteomics data. PEELing assesses data quality using curated or user-defined references, performs cutoff analysis to remove contaminants, connects to databases for functional annotation, and generates data visualizations-providing a streamlined and reproducible workflow to explore spatially resolved proteomics data.

AVAILABILITY AND IMPLEMENTATION

PEELing and its tutorial are publicly available at https://peeling.janelia.org/ (Zenodo DOI: 10.5281/zenodo.15692517). A Python package of PEELing is available at https://github.com/JaneliaSciComp/peeling/ (Zenodo DOI: 10.5281/zenodo.15692434).

摘要

分子区室化对细胞生理学至关重要。空间分辨蛋白质组学使生物学家能够以亚细胞分辨率研究蛋白质组成和动态变化。在此，我们介绍了PEELing，这是一个用于分析空间分辨蛋白质组学数据的集成软件包和用户友好的网络服务。PEELing使用经过整理的或用户定义的参考来评估数据质量，进行截止分析以去除污染物，连接数据库进行功能注释，并生成数据可视化结果，从而提供了一个简化且可重复的工作流程来探索空间分辨蛋白质组学数据。

可用性和实现方式

PEELing及其教程可在https://peeling.janelia.org/ （Zenodo DOI：10.5281/zenodo.15692517）上公开获取。PEELing的Python软件包可在https://github.com/JaneliaSciComp/peeling/ （Zenodo DOI：10.5281/zenodo.15692434）上获取。