Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics.

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Alterations in ECM organization or composition and excessive ECM deposition have been observed in diseases such as fibrosis, cardiovascular diseases, and cancer. We provide here optimized protocols to solubilize ECM proteins from normal or tumor tissues, digest the proteins into peptides, analyze ECM peptides by mass spectrometry, and interpret the mass spectrometric data. In addition, we present here two novel R-script-based web tools allowing rapid annotation and relative quantification of ECM proteins, peptides, and intensity/abundance in mass spectrometric data output files. We illustrate this protocol with ECMs obtained from two pairs of tissues, which differ in ECM content and cellularity: triple-negative breast cancer and adjacent mammary tissue, and omental metastasis from high-grade serous ovarian cancer and normal omentum. The complete proteomics data set generated in this study has been deposited to the public repository ProteomeXchange with the data set identifier: PXD005554.", "claims": [{"id": "claim-target-result", "statement": "The paper reports no statistical method or numerical result for the registered target; its source-data route is the ProteomeXchange data set PXD005554.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:28675934", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We provide here optimized protocols to solubilize ECM proteins from normal or tumor tissues, digest the proteins into peptides, analyze ECM peptides by mass spectrometry, and interpret the mass spectrometric data."}, {"asset": "source:pmid:28675934", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The complete proteomics data set generated in this study has been deposited to the public repository ProteomeXchange with the data set identifier: PXD005554."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper reports no statistical method or numerical result for the registered target; its source-data route is the ProteomeXchange data set PXD005554.", "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:28675934"], "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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