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ProvinceMass SpectrometryBottom-up proteomicsData-independent acquisitionNot availableRetina pigment epitheliumOatLiverProteomicsOrnithine aminotransferaseGyrate atrophyRetinaOrnithineMetabolismhttps://www.ebi.ac.uk/pride/archive/projects/PXD063614Retinal Pigment Epithelium Cell LineLiverRetinaTotal protein from each sample was reduced, alkylated, and purified by chloroform/methanol extraction prior to digestion with sequencing grade modified porcine trypsin (Promega). Tryptic peptides were then separated by reverse phase XSelect CSH C18 2.5 um resin (Waters) on an in-line 150 x 0.075 mm column using an UltiMate 3000 RSLCnano system (Thermo). Peptides were eluted using a 60 min gradient from 98:2 to 65:35 buffer A:B ratio. Eluted peptides were ionized by electrospray (2.2 kV) followed by mass spectrometric analysis on an Orbitrap Exploris 480 mass spectrometer (Thermo). To assemble a chromatogram library, six gas-phase fractions were acquired on the Orbitrap Exploris with 4 m/z DIA spectra (4 m/z precursor isolation windows at 30,000 resolution, normalized AGC target 100%, maximum inject time 66 ms) using a staggered window pattern from narrow mass ranges using optimized window placements. Precursor spectra were acquired after each DIA duty cycle, spanning the m/z range of the gas-phase fraction (i.e. 496-602 m/z, 60,000 resolution, normalized AGC target 100%, maximum injection time 50 ms). For wide-window acquisitions, the Orbitrap Exploris was configured to acquire a precursor scan (385-1015 m/z, 60,000 resolution, normalized AGC target 100%, maximum injection time 50 ms) followed by 50x 12 m/z DIA spectra (12 m/z precursor isolation windows at 15,000 resolution, normalized AGC target 100%, maximum injection time 33 ms) using a staggered window pattern with optimized window placements. Precursor spectra were acquired after each DIA duty cycle. Buffer A = 0.1% formic acid, 0.5% acetonitrile Buffer B = 0.1% formic acid, 99.9% acetonitrilePrideFollowing data acquisition, data were searched using an empirically corrected library against the UniProt Mus musculus database (February 2023) and a quantitative analysis was performed to obtain a comprehensive proteomic profile. Proteins were identified and quantified using EncyclopeDIA (Searle et al.) and visualized with Scaffold DIA using 1% false discovery thresholds at both the protein and peptide level. Protein MS2 exclusive intensity values were assessed for quality using ProteiNorm (Graw et al.). The data was normalized using Cyclic Loess (Ritchie et al) and analyzed using proteoDA to perform statistical analysis using Linear Models for Microarray Data (limma) with empirical Bayes (eBayes) smoothing to the standard errors (Thurman et al, Ritchie et al). Proteins with an FDR adjusted p-value < 0.05 and a fold change > 2 were considered significant. Acknowledgement: IDeA National Resource for Quantitative Proteomics and NIH/NIGMS grant R24GM137786.ProteomicsJianhai DuAssociate Professor, Department of Biochemistry and Molecular Medicine, West Virginia UniversityCOMPLETEMus Musculus (mouse)42373003 Puja A, Xu R, Mascari I, Ngo T, Zhang Y, Wang Q, Saravanan M, Du J. Early proteomic and metabolic signatures of liver and eye in OAT-deficient mice. Exp Eye Res. 2026 271:111140 10.1016/j.exer.2026.111140dprovince@uams.eduUAMSUnited States10.6019/PXD063614falseProteomic characterization of infant and adult ornithine aminotransferase-deficient miceThe deficiency of ornithine aminotransferase (OAT) cause gyrate atrophy, a progressive chorioretinal degeneration disease culminating in blindness. This project investigates age- and tissue-specific proteomic changes in the retina, retinal pigment epithelium (RPE), and liver of OAT-deficient mice to uncover the role of the enzyme in these tissues and the mechanisms underlying the eye damage.2026-07-062025-05-05PXD063614NEWT:1773NEWT:3555NEWT:38783NEWT:8727NEWT:1182590NEWT:8726NEWT:2NEWT:157546NEWT:10090NEWT:935293NEWT:749200NEWT:35554NEWT:4120NEWT:5693NEWT:9417NEWT:347515NEWT:8724NEWT:1216979NEWT:307972NEWT:92867NEWT:8723NEWT:990346NEWT:544496NEWT:5334NEWT:145953NEWT:257309NEWT:5180NEWT:284812NEWT:115104NCBITaxon:1313NEWT:1081927NEWT:43330NEWT:67825NEWT:44544NEWT:13076NEWT:373995NEWT:544404NEWT:3702NEWT:8839NEWT:376741NEWT:4232NEWT:990119NEWT:1736309NEWT:4113NEWT:7227NEWT:11298NEWT:7469NEWT:885318NEWT:171101NEWT:876138NEWT:4081NEWT:554NEWT:5691NEWT:98334NEWT:408170NEWT:260710NEWT:3708NEWT:106592NEWT:237561NEWT:9913NEWT:10036NEWT:4100NEWT:7574NEWT:1351NEWT:1076NEWT:6763NEWT:7215NEWT:803NEWT:8030NEWT:380394NEWT:272563NEWT:507601NEWT:1639NEWT:188229NEWT:4909NCBITaxon:79857NEWT:95648NEWT:746360NEWT:6239NEWT:1589NEWT:135588NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:95486NEWT:3880NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:1911079NEWT:1000589NEWT:145943NEWT:1902NEWT:85962NEWT:160488NEWT:317447NEWT:3635NEWT:7955NCBITaxon:2NEWT:235443NEWT:985076NEWT:7959NEWT:2261NEWT:3197NEWT:9615NEWT:884019NEWT:4565NEWT:1264690NEWT:169963NCBITaxon:38727NEWT:36329NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:9606NEWT:367830NEWT:157295NEWT:243230NEWT:931281NEWT:373153NEWT:7029NEWT:1283300NEWT:334747NEWT:470NCBITaxon:79824NCBITaxon:4563NEWT:3218NEWT:5759NEWT:9838NCBITaxon:9615NEWT:1736231NEWT:1193501NEWT:6287NEWT:2242NEWT:6326NEWT:9796NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:260707NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:29760NEWT:260705NEWT:80863NEWT:1148NEWT:4932NEWT:70448NEWT:9825NEWT:3603NEWT:698936NEWT:2759NEWT:39946NEWT:11676NEWT:9823NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:7370NEWT:573NEWT:6282NEWT:7091NEWT:1134506423730030000-0002-9850-632X