Hydroxylamine Chemical Digestion for Insoluble Extracellular Matrix Characterization.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28971683", "kind": "science-record", "revision": 5, "content_hash": "sha256:bb9dbcf773f8660032608ee80a1d54a8f1d68b0d15022b7854d1896470b50eec", "created_at": "2026-11-01T15:40:28Z", "updated_at": "2026-11-01T18:49:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Hydroxylamine Chemical Digestion for Insoluble Extracellular Matrix Characterization.", "doi": "10.1021/acs.jproteome.7b00527", "pmid": "28971683", "authors": ["Alexander S Barrett", "Matthew J Wither", "Ryan C Hill", "Monika Dzieciatkowska", "Angelo D'Alessandro", "Julie A Reisz", "Kirk C Hansen"], "journal": "Journal of proteome research", "year": 2017, "abstract": "The extracellular matrix (ECM) is readily enriched by decellularizing tissues with nondenaturing detergents to solubilize and deplete the vast majority of cellular components. This approach has been used extensively to generate ECM scaffolds for regenerative medicine technologies and in 3D cell culture to model how the ECM contributes to disease progression. A highly enriched ECM fraction can then be generated using a strong chaotrope buffer that is compatible with downstream bottom-up proteomic analysis or 3D cell culture experiments after extensive dialysis. With most tissues, an insoluble pellet remains after chaotrope extraction that is rich in structural ECM components. Previously, we showed that this understudied fraction represented approximately 80% of total fibrillar collagen from the lung and other ECM fiber components that are known to be covalently cross-linked. Here, we present a hydroxylamine digestion approach for chaotrope-insoluble ECM analysis with comparison to an established CNBr method for matrisome characterization. Because ECM characteristics vary widely among tissues, we chose five tissues that represent unique and diverse ECM abundances, composition, and biomechanical properties. Hydroxylamine digestion is compatible with downstream proteomic workflows, yields high levels of ECM peptides from the insoluble ECM fraction, and reduces analytical variability when compared to CNBr digestion. Data are available via ProteomeXchange with identifier PXD006428.", "claims": [{"id": "claim-target-result", "statement": "NH2OH digestion followed by trypsin yielded higher protein abundance than CNBr digestion followed by trypsin, with cellular proteins averaging 2.5-fold higher and collagens, glycoproteins, and proteoglycans averaging 1.6-, 2.8-, and 2.2-fold higher, respectively. The paper used principal component analysis as a statistical method, and the underlying proteomics data are publicly available through PRIDE under submission #185523.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28971683", "locator": "sections[16] \"Comparison of quantitative yield, protein and peptide identifications between CNBr and NH2OH digestion approaches\" paragraph 2", "quote": "In general, NH2OH digestion followed by trypsin yielded a higher protein abundance than CNBr followed by trypsin."}, {"asset": "source:pmid:28971683", "locator": "sections[16] \"Comparison of quantitative yield, protein and peptide identifications between CNBr and NH2OH digestion approaches\" paragraph 2", "quote": "More specifically, cellular proteins quantified across the tissues tested were on average 2.5 fold higher in NH2OH preparations compared to CNBr."}, {"asset": "source:pmid:28971683", "locator": "sections[16] \"Comparison of quantitative yield, protein and peptide identifications between CNBr and NH2OH digestion approaches\" paragraph 2", "quote": "Along these same lines, collagens, glycoproteins and proteoglycans were found to be 1.6, 2.8 and 2.2-fold higher in NH2OH preparations, on average, for all tissues tested (Supplementary Table S3)."}, {"asset": "source:pmid:28971683", "locator": "sections[16] \"Comparison of quantitative yield, protein and peptide identifications between CNBr and NH2OH digestion approaches\" paragraph 2", "quote": "These differences are largely driven by variations in basement membrane (i.e. Col4a2, Lama2) and cytoskeletal (i.e. Act) component abundance between methods as discovered by performing principal component analysis (not shown) despite these proteins having fewer Asn-Gly motifs than Met residues."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "NH2OH digestion followed by trypsin yielded higher protein abundance than CNBr digestion followed by trypsin, with cellular proteins averaging 2.5-fold higher and collagens, glycoproteins, and proteoglycans averaging 1.6-, 2.8-, and 2.2-fold higher, respectively. The paper used principal component analysis as a statistical method, and the underlying proteomics data are publicly available through PRIDE under submission #185523.", "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:28971683"], "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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