Deep Spectral Library of Mice Retina for Myopia Research: Proteomics Dataset generated by SWATH and DIA-NN.

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Recent advancements have introduced a library-independent approach for data-independent acquisition (DIA) analyses. This study demonstrates deep proteome identification and quantification in individual mice retinas during myopia development, with an average of 6,263 ± 86 unique protein groups. We anticipate that the use of a predicted retinal-specific spectral library combined with the robust quantification achieved within this dataset will contribute to a better understanding of the proteome complexity. Furthermore, a comprehensive mice retinal-specific spectral library was generated, encompassing a total identification of 9,401 protein groups, 70,041 peptides, 95,339 precursors, and 761,868 transitions acquired using SWATH-MS acquisition on a ZenoTOF 7600 mass spectrometer. This dataset surpasses the spectral library generated through high-pH reversed-phase fractionation by data-dependent acquisition (DDA). The data is available via ProteomeXchange with the identifier PXD046983. It will also serve as an indispensable reference for investigations in myopia research and other retinal or neurological diseases.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed using paired Student’s t-test with Prism software (ver. 9.5).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39389962", "locator": "sections[12] \"Reassembly of axial elongation during myopia progression\" paragraph 2", "quote": "Statistical analysis was performed using paired Student’s t-test with Prism software (ver. 9.5)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE39 partner repository with the dataset identifier PXD04698340.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39389962", "locator": "sections[10] \"Data Records\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE39 partner repository with the dataset identifier PXD04698340."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study demonstrates deep proteome identification and quantification in individual mice retinas during myopia development, with an average of 6,263 ± 86 unique protein groups.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39389962", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study demonstrates deep proteome identification and quantification in individual mice retinas during myopia development, with an average of 6,263 ± 86 unique protein groups."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study demonstrates deep proteome identification and quantification in individual mice retinas during myopia development, with an average of 6,263 ± 86 unique protein groups.", "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:39389962"], "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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Mass spectrometry sample preparation The protocol was adopted", "at. No. 23275, Thermo Fisher Scientific) for mass spectrometric analysis. Supplementary Materials Supplement"], "order_basis": "paper_text_order:14", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Methods Animals Black C57BL/6 J wild-type mice were obtained from The Jackson Laboratory (Farmin", "he Jackson Laboratory (Farmington, CT, USA). Mice were maintained as in-house breeding colonies at", "ux. Food and water were provided ad libitum. Mice were weaned on postnatal day 21 and housed until", "University. Animals were housed in standard mouse cages (Sealsafe Plus GM500, Tecniplast, Vare"], "order_basis": "paper_text_order:1372", "id": "assay:2"}]}