Comprehensive spectral libraries for various rabbit eye tissue proteomes.

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Various rabbit ocular disease models, such as dry eye, age-related macular degeneration, and glaucoma, have been established. Despite the growing application of proteomics in vision research using rabbit ocular models, there is no spectral assay library for rabbit eye proteome publicly available. Here, we generated spectral assay libraries for rabbit eye compartments, including conjunctiva, cornea, iris, retina, sclera, vitreous humor, and tears using fractionated samples and ion mobility separation enabling deep proteome coverage. The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides. We present the data as a freely available community resource for proteomic studies in the vision field. Instrument data and spectral libraries are available via ProteomeXchange with identifier PXD031194.", "claims": [{"id": "claim-method", "statement": "False identifications are controlled by FDR estimation at three levels: peptide-spectrum match (PSM), peptide, and protein group level.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35351915", "locator": "sections[11] \"Technical Validation\" paragraph 2", "quote": "False identifications are controlled by FDR estimation at three levels: peptide-spectrum match (PSM), peptide, and protein group level."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Software used in the generation of this project is third-party software as described in the Data Records section, i.e., Spectronaut and DIALib-QC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35351915", "locator": "sections[17] \"Code availability\" paragraph 2", "quote": "Software used in the generation of this project is third-party software as described in the Data Records section, i.e., Spectronaut and DIALib-QC."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35351915", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The rabbit eye spectral assay library includes 9,830 protein groups and 113,593 peptides.", "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:35351915"], "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": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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