Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid.

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The retinal pigment epithelium and choroid (RPE/choroid) are essential in supporting the retina and absorbing light energy that enters the eye. Proteins were extracted from iris, ciliary body, and RPE/choroid tissues of eyes from five individuals and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. In iris, ciliary body, and RPE/choroid, we identified 2959, 2867, and 2755 nonredundant proteins with peptide and protein false-positive rates of <0.1% and <1%, respectively. Forty-three unambiguous protein isoforms were identified in iris, ciliary body, and RPE/choroid. Four \"missing proteins\" were identified in ciliary body based on ≥2 proteotypic peptides. The mass spectrometric proteome database of the human iris, ciliary body, and RPE/choroid may serve as a valuable resource for future investigations of the eye in health and disease. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001424 and PXD002194.", "claims": [{"id": "claim-target-result", "statement": "The study used SDS-PAGE fractionation and LC-MS/MS with peptide and protein false-positive rates of <0.1% and <1%, respectively, and deposited its source data through the ProteomeXchange Consortium via PRIDE under PXD001424 and PXD002194.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:26834087", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Proteins were extracted from iris, ciliary body, and RPE/choroid tissues of eyes from five individuals and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer."}, {"asset": "source:pmid:26834087", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In iris, ciliary body, and RPE/choroid, we identified 2,959, 2,867, and 2,755 non-redundant proteins with peptide and protein false positive rates of <0.1% and <1%, respectively."}, {"asset": "source:pmid:26834087", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001424 and PXD002194."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study used SDS-PAGE fractionation and LC-MS/MS with peptide and protein false-positive rates of <0.1% and <1%, respectively, and deposited its source data through the ProteomeXchange Consortium via PRIDE under PXD001424 and PXD002194.", "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:26834087"], "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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