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

Xi Peng·Jody Clements·Zuzhi Jiang·Shuo Han·Stephan Preibisch·Jiefu Li
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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).

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Xi Peng, Jody Clements, Zuzhi Jiang, Shuo Han, Stephan Preibisch, Jiefu Li. 2025-08-02. PEELing: an integrated and user-centric platform for spatially resolved proteomics data analysis.. https://doi.org/10.1093/bioinformatics%2Fbtaf439

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