Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX2.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX1.mzid_DDA_VC_ORX1.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC5.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC4.mzid_DDA_VC_MC4.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC2.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX3.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX5.mzid_DDA_VC_ORX5.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX1.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC3.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC1.mzid_DDA_VC_MC1.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX3.mzid_DDA_VC_ORX3.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC4.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX4.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC1.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC5.mzid_DDA_VC_MC5.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC3.mzid_DDA_VC_MC3.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX4.mzid_DDA_VC_ORX4.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_MC2.mzid_DDA_VC_MC2.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX2.mzid_DDA_VC_ORX2.MGFftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080391/DDA_VC_ORX5.mzidprimary200OKLaszlo.Prokai@unthsc.eduLaszlo ProkaiMass SpectrometryBottom-up proteomicsAndrogen deprivation; bioinformatics; dhed; gonadectomy; neuroprotection; neuropro-teomics; mass spectrometry; oxidative stress; visual cortex.neuropro-teomicsAndrogen deprivationneuroprotectionbioinformaticsmass spectrometrygonadectomydhedoxidative stressvisual cortex.https://www.ebi.ac.uk/pride/archive/projects/PXD080391Visual CortexVacuum-dried peptides were reconstituted in 5% (v/v) aqueous acetonitrile (ACN) containing 0.1% (v/v) FA to a concentration equivalent to 1 μg/μL total protein. Data were collected in both DDA and DIA modes on a Thermo Exploris 480 mass spectrometer equipped with an Easy-SprayTM source (Thermo Fisher Scientific, San Jose, CA, USA) op-erating in positive polarity mode and coupled with a Vanquish Neo LC system. Briefly, 2 μL of reconstituted sample was subjected to separation by reverse-phase chromatography on an Acclaim PepMap Neo C18 column (150 mm × 75 μm i.d., 2 μm particle size, 100 Å pore size; Thermo Fisher Scientific) at a flow rate of 300 nL/min. For DDA, Peptides were eluted using a 90-min gradient using 0.1% FA in water and 0.1% FA in 80/20 v/v ACN/water (Solvent A and Solvent B, respectively). The gradient program for DDA con-sisted of an initial 1% B, ramping it up to 28% B for 90 mins, ending with column wash for 10 minutes with 99% B. DDA acquisition was performed using a full MS-ddMS2 method with the following parameters: S-lens radio frequency level, 5; MS1 scan range, 375−1475 m/z; full MS automatic gain control (AGC) target, 3 × 106; maximum injection time (IT), 50 ms. Full-scan mass spectra were obtained in profile mode at a nominal mass resolution of 120000 (defined at m/z 200) in the Orbitrap with the AGC target set to 400000. Da-ta-dependent MS2 scans for selected precursor ions with charges (z) of ≥ 2 were acquired using a 1.6 m/z isolation window with fragmentation performed by higher-energy colli-sional dissociation (HCD) at a normalized collision energy (NCE) of 30% and acquisitions in centroid mode at a nominal Orbitrap resolution of 120,000 (at m/z 200) and an AGC target of 400,000. nLC-MS/MS for DIA consisted of a 60 min gradient using the same sol-vent constitution as described for the DDA, The gradient program consisted of an initial 5% B, ramping it up to 25% B for 40 mins, further ramping up to 65% B for another 20 minutes ending with column wash for 10 minutes with 99% B.DIA acquisition was adopted from a previously described protocol [39], with the following parameters: MS1 scan range, 390–1010 m/z; Orbitrap resolution, 60000; maximum IT, auto; normalized AGC target 100% (1 × 106). MS1 data were acquired in centroid mode. For MS2 acquisi-tion, an 8 m/z variable window scheme was applied with an Orbitrap resolution of 15000, an AGC target of 100%, a loop count of 75, and a default charge state of 3. HCD fragmen-tation was performed at an NCE of 27 %. MS2 spectra were acquired in centroid modePrideAll searches relied on the same UniProtKB Rattus norvegicus protein database (spe-cies: Rattus norvegicus, 2025; 36,206 entries). Raw data files were processed assuming tryp-sin as the digestion enzyme, with a maximum of one missed cleavage and carbami-domethylation of cysteine as a fixed modification. A false discovery rate (FDR) of 1% was applied across all platforms unless otherwise stated. For DDA based discovery-driven proteomics, database searches were performed using Scaffold and Scaffold DDA (versions 5.3.3 and 6.5.0, respectively; Proteome Software, Portland, OR, USA), with their built-in MSFragger maintaining minimum protein probability of 99% by ProteinProphet and pep-tide probability of 95% by PeptideProphet, with at least two peptides per protein required for identification. Label-free quantification (LFQ) was performed using spectral counting, and statistical analysis was conducted using the software's built-in module. Differentially expressed proteins (DEPs) were identified using unpaired t-tests with Benja-mini-Hochberg (BH) correction for multiple testing, with significance set at p < 0.05. DIA data were analyzed using the AI-powered search algorithm CHIMERYS™ (MSAID GmbH, Garching b. München, Germany), incorporating deep learning-based fragmenta-tion prediction (inferys_4.7.0) and integrated within Proteome Discoverer (version 3.2). Fragment mass tolerance was set at 20 ppm and target FDR at 1%. Protein quantification was performed using the MS2 Apex method of the software with significance assessed through Proteome Discoverer's internal algorithm relying on unpaired t-tests (p < 0.05) with BH correction for multiple testing. Principal component analysis (PCA) and volcano plots, were generated in Scaffold (version 6.5.0.). For the second set of experiment dedicat-ed to the quantitative survey of selected protein markers from the first experimental de-sign, raw data files generated from the Naïve, DHED and Vehicle groups were processed using Scaffold DIA (version 4.3.1, Proteome Software, Portland, OR, USA) in conjunction with ProteoWizard (version 3.0.19254). Raw files were converted to mzML format, fol-lowed by retention time alignment and spectral library searching against a Rat_prosit_generated_library.dlib, with peptide and fragment mass tolerances of 20 ppm and 10 ppm, respectively. Search criteria included trypsin digestion with a maximum of one missed cleavage, carbamidomethylation of cysteine as a fixed modification, and pep-tides with charge states of 2 to 5 and lengths of 6 to 30 amino acid residues. Peptide iden-tification was filtered using Scaffold DIA's integrated Percolator (version 3.01). Quantifica-tion was performed using the software's implementation of EncyclopeDIA (version 5.4.17), selecting the seven highest-quality fragment ions per peptide [31]. Statistical dif-ferences in protein abundance between groups (DEPs) were assessed using ANOVA fol-lowed by unpaired t-tests (p < 0.05) with BH correction, implemented through Scaffold DIA's built-in statistics module.ProteomicsLaszlo Prokai, Ph.D., D.ScProfessor and Robert A. Welch Chair in Biochemistry Department of Pharmacology and Neuroscience UNT Health at Fort WorthCOMPLETERattus Norvegicus (rat)42650240 Zaman K, Kapic A, Nguyen V, Prokai L, Prokai-Tatrai K. Bypassing Androgens: Retina-Targeted 17β-Estradiol Delivery via DHED Eye Drops Ameliorates Orchiectomy-Induced Shifts in the Male Rat Visual Cortex Proteome. Antioxidants (Basel). 2026 15(8):976 10.3390/antiox15080976advancedms@unthsc.eduDepartment of Pharmacology & Neuroscience UNT Health Science Center Fort Worth, TX, USAUnited States10.6019/PXD080391Mass spectrometry-based proteomics has become instrumental for elucidating the molecular mechanisms of neurodegeneration, enabling the identification of disease-associated proteomic alterations and protein-level responses to therapeutic interventions. Building on our previous proteomic characterization of the orchiectomized (ORX) Brown Norway male rat retina as a model of androgen deprivation, we extend this investigation to the visual cortex (VC), a key node in the visual pathway. Here we report the first comprehensive proteomic characterization of ORX-VC employing nanoflow liquid chromatography-tandem mass spectrometry complemented by bioinformatic pathway analyses and quantitative assessment of selected protein markers of ORX-induced changes. Our discovery-driven proteomics approach revealed over 500 differentially expressed proteins following ORX. Principal component analysis showed complete separation between ORX and naïve groups with no overlap, indicating a profound effect of androgen deprivation on the VC proteome. Ingenuity Pathway Analysis^® predicted that the widespread proteome dysregulation included oxidative stress as a primary contributor, alongside estrogen receptor (ESR) predominance over androgen receptor signaling, consistent with our prior findings in the ORX retina. To explore whether this ESR predominance translates to a benefit of E2 supplementation alone, independent of circulating testosterone, we utilized our DHED (10β,17β-dihydroxyestra-1,4-dien-3-one) prodrug as eye drops to target E2 formation into the retina. Quantitative assessment demonstrated that this approach resulted in attenuation of ORX-induced expression changes in a selected panel of key proteins. These findings warrant future studies to determine whether this effect extends across the full spectrum of ORX-induced proteomic shifts and confers a benefit for vision preservation.Bypassing Androgens: Retina-Targeted 17β-Estradiol Delivery via DHED Eye Drops Ameliorates Orchiectomy-Induced Shifts in the Male Rat Visual Cortex Proteome.Zaman Khadiza K, Kapic Ammar A, Nguyen Vien V, Prokai Laszlo L, Prokai-Tatrai Katalin KfalseBypassing Androgens: CNS-Targeted Estrogen Delivery Res-cues the Gonadectomized Male Rat Visual Cortex Neuropro-teomeMass spectrometry-based proteomics has become instrumental for elucidating the molec-ular mechanisms of neurodegeneration, enabling the identification of disease-associated proteomic alterations and protein-level responses to therapeutic interventions. Building on our previous proteomic characterization of the orchiectomized (ORX) male Brown Norway rat retina as a model of androgen deprivation, we extend this investigation to the visual cortex (VC), a key node in the visual pathway. Here we report the first comprehen-sive proteomic characterization of ORX-VC employing nanoflow liquid chromatog-raphy-tandem mass spectrometry, complemented by bioinformatic pathway analyses and quantitative assessment of candidate protein markers of ORX-induced changes. We fur-ther investigate whether 17β-estradiol (E2) supplementation is sufficient to counteract an-drogen deprivation-induced cortical proteomic disruption and restore visual system ho-meostasis. Our discovery-driven proteomics approach identified over 500 differentially expressed proteins following ORX. Pathway analyses revealed widespread proteomic dysregulation, with oxidative stress emerging as a primary driver. Estrogen receptor pre-dominance over androgen receptor signaling was also identified, consistent with our pre-vious findings in the ORX retina. Quantitative assessment of a candidate protein panel demonstrated that CNS-selective E2 delivery via its DHED (10β,17β-dihydroxyestra-1,4-dien-3-one) prodrug, acting independently of circulating tes-tosterone, substantially restored expression of key dysregulated proteins. These findings support central E2 supplementation as a viable neuroprotective strategy for maintaining sex hormone-dependent homeostasis in the androgen-deprived male visual system, with implications for patients undergoing androgen deprivation therapy at risk for visual pathway neurodegeneration.2026-09-142026-06-30PXD080391NEWT:330879NEWT:377960NEWT:1131NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NEWT:1334565NEWT:625351NEWT:258594NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:57577NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:6819NEWT:475174NEWT:111205NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:33114NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:3765NEWT:3767NEWT:1589NEWT:135622NEWT:67352NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:656064NEWT:1582NEWT:1584NEWT:36630NEWT:383379NEWT:418106NCBITaxon:12721NEWT:10029NEWT:913645NEWT:641809NEWT:1392488NEWT:38815NEWT:317447NEWT:4688NEWT:111225NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:29064NEWT:108061NEWT:60711NEWT:224308NEWT:273791NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:1912919NEWT:410658NEWT:5516NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:33554NEWT:246196NEWT:246197NEWT:145458NEWT:1310173NEWT:171719NEWT:44685NEWT:161934NEWT:156587NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:150808NEWT:1182590NEWT:3712NEWT:3711NEWT:3714NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:28174NEWT:284812NEWT:8175NEWT:43330NEWT:980415NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:66440NEWT:1245466NEWT:3704NEWT:244366NEWT:1246791NEWT:176597NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:8165NEWT:96794NEWT:34878NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1348799NEWT:33995NEWT:55784NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2709072NEWT:2499525NEWT:2853422NEWT:487NEWT:1538553NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1185650NEWT:216778NEWT:294607NEWT:1502NEWT:128017NEWT:376686NEWT:237610NEWT:95486NEWT:119562NEWT:1883446NEWT:1233435NEWT:118223NEWT:11757NEWT:987059NEWT:109760NEWT:29031NEWT:317047NEWT:491NEWT:460523NEWT:45954NEWT:235443NEWT:1757312NEWT:85694NEWT:109786NEWT:108458NEWT:5936NEWT:320637NEWT:1078283NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:1640278NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:28128NEWT:470NEWT:5911NEWT:748693NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:166313NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:906914NEWT:28141NEWT:9031NEWT:27292NEWT:1050722NEWT:3728NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:381666NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:207340NEWT:172271NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:42410NEWT:36185NEWT:1054211NEWT:1225786NEWT:771870NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:10832NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:9983NEWT:8655NEWT:5147NEWT:595495NEWT:28108NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:1613NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:298176NEWT:353153NEWT:227377NEWT:1774284NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:105487NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:7375NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:475932NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:2925NEWT:214053NEWT:28550NEWT:80863NEWT:90675NEWT:52639NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:861109NEWT:8695NEWT:884204NEWT:510516NEWT:1045775NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:99488NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:1028307NEWT:13489NEWT:29829NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:441772NEWT:1293091NEWT:48106NEWT:202956NEWT:295027NCBITaxon:11320NEWT:99490NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:300273NEWT:4232NEWT:416348NEWT:11298NEWT:4236NEWT:7742NEWT:196627NEWT:1076878NEWT:200308NEWT:242507NEWT:200302NEWT:870435NEWT:9917NEWT:95912NEWT:58370NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:2144189NEWT:1392998NEWT:380394NEWT:114796NEWT:1150621NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:563041NEWT:72664NEWT:36599NEWT:41949NEWT:249161NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1156395NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:29835NEWT:431947NEWT:69014NE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