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

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40794857", "kind": "science-record", "revision": 2, "content_hash": "sha256:16abe5324b1c43a121f4e1746b046226490293d5d9b825f5ba89042e176ea390", "created_at": "2026-11-01T20:30:53Z", "updated_at": "2026-11-01T21:35:36Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "PEELing: an integrated and user-centric platform for spatially resolved proteomics data analysis.", "doi": "10.1093/bioinformatics/btaf439", "pmid": "40794857", "authors": ["Xi Peng", "Jody Clements", "Zuzhi Jiang", "Shuo Han", "Stephan Preibisch", "Jiefu Li"], "journal": "Bioinformatics (Oxford, England)", "year": 2025, "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.\nAVAILABILITY 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).", "claims": [{"id": "claim-method", "statement": "PEELing uses a ratiometric strategy as previously described (Hung et al. 2014) in which the labeled-to-control ratio of each protein reflects whether this protein is cell-surface enriched or not.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40794857", "locator": "sections[2] \"2 Implementation, benchmarks, and results\" paragraph 2", "quote": "PEELing uses a ratiometric strategy as previously described (Hung et al. 2014) in which the labeled-to-control ratio of each protein reflects whether this protein is cell-surface enriched or not."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All datasets used for benchmarking are included as Files 1–17, available as supplementary data at Bioinformatics online.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40794857", "locator": "sections[9] \"Data availability\" paragraph 2", "quote": "All datasets used for benchmarking are included as Files 1–17, available as supplementary data at Bioinformatics online."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This is further illustrated by a receiver operating characteristic (ROC) curve bending toward the left-upper corner and exhibiting an area under the curve (AUC) of 0.79 (Fig. 1e).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40794857", "locator": "sections[2] \"2 Implementation, benchmarks, and results\" paragraph 3", "quote": "This is further illustrated by a receiver operating characteristic (ROC) curve bending toward the left-upper corner and exhibiting an area under the curve (AUC) of 0.79 (Fig. 1e)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "This is further illustrated by a receiver operating characteristic (ROC) curve bending toward the left-upper corner and exhibiting an area under the curve (AUC) of 0.79 (Fig. 1e).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:40794857"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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