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 (proteome extraction from enzymatic labeling data), 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.
Manuscript preprint: https://www.biorxiv.org/content/10.1101/2023.04.21.537871
Please note that this bioRxiv preprint will be updated as we add new functionalities to PEELing.
http://peeling.janelia.org/tutorial
PEELing also provides a command line program. Please refer to this repo.