PEELing: an integrated and user-centric platform for cell-surface proteomics analysis

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Bioinformatics. 2025 Aug 06;. doi: 10.1093/bioinformatics/btaf439

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PEELing: an integrated and user-centric platform for cell-surface proteomics analysis Li LabScientific Computing

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

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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).

Contact: Technical support for PEELing: peeling@janelia.hhmi.org.

bioRxiv Preprint: https://doi.org/10.1101/2023.04.21.537871