Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S14.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S13.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_S10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_MC_Duodenum.mzTabftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD063823/HYL4661_MC_Liver.mzTabprimaryOK200Terry.Engle@colostate.eduHuey Yi LohMass SpectrometryBottom-up proteomicsDisease Freehttps://www.ebi.ac.uk/pride/archive/projects/PXD063823HepatocyteDuodenumLiverEnterocyte Of Epithelium Proper Of DuodenumLiver and duodenum samples for proteomic analysis were washed 3 times with PBS and placed on ice until transferred to a -80°C freezer. Enterocytes from the duodenum tissues were separated from the serosa by scraping using a scalpel blade as described by Han et al. before storing at -80°C. All samples were collected within an hour after stunning to minimize protein degradation. Protein extraction and peptide preparation for proteomic analysis were conducted using Pierce BCA Protein Assay Kit and EasyPep Mini MS Sample Prep Kit (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions. Briefly, 100 mg of tissue was weighed into a bead-beating tube containing 1mL Thermo Lysis Buffer, 20µg of 0.1mm zirconia silica beads, 3µL Universal Nuclease, and 7.5µL HALT Protease Inhibitor Cocktail. Tubes were subjected to 5 cycles of bead beating for 30s at 6m/s, with 2 min dwell time on ice between cycles. The supernatant layer was transferred to a new tube after being centrifuged at 8,000 x g for 5 minutes. Protein concentration was quantified using BioRad 680 microplate reader, and 100 µg of total protein was aliquoted from each sample. The protein aliquot was raised to 100 µL with lysis buffer, followed by the addition of reduction and alkylation solutions sequentially. The solution was incubated at 95° for 10 minutes. After cooling to room temperature, 50µL of a 0.2µg/µL Trypsin/LysC mixture was added, and samples were digested with shaking at 37°C for 2 hours. Digestion Stop Solution was added to deactivate the enzymes, and contaminants were removed using a mixed mode peptide clean up column. Peptide eluate was dried in a vacuum evaporator and resuspended in 3% acetonitrile/0.1% formic acid and quantified using NanoDrop.PrideData processing was conducted on Proteome Discoverer 3.0 (ThermoFisher Scientific). Additional precursors within the isolation window of the precursor spectrum, when chimeric or mixed spectra are present, were identified by precursor detector node with S/N=1.5. Spectra from all samples were searched using the Sequest HT node, setting methionine oxidation and protein N-7 terminus acetylation as dynamic and cysteine Carbamidomethylation as fixed modification. Raw data was interrogated against the FASTA file of the reference proteome of Ovis aries (taxon ID 9940) from UniProt. Additionally, the cRAP proteome (The common Repository of Adventitious Proteins -cRAP- contains commonly found contaminant proteins in proteomics experiments; cRAP_100518) was included. Sequest HT was searched with a fragment ion mass tolerance of 0.60 Da and a parent ion tolerance of 10 ppm. Peptide spectral matches (PSMs) were validated using the Percolator node. Thresholds were set such that a false discovery rate (FDR) of ≤ 1% and protein identification was defined with at least one unique peptide.ProteomicsTerry EngleColorado State University, Department of Animal ScienceCOMPLETEOvis Arieshueyyi@colostate.edu10.3390/RUMINANTS6020035Colorado State UniversityUnited States10.6019/PXD063823falseCopper Trafficking in Sheep: A Pilot Proteomic Analysis of Enterocytes and Hepatocytes Under Dietary Copper SupplementationSeven Rambouillet-crossbred wethers were utilized to examine the impact of copper (Cu) supplementation on plasma, bile, liver, duodenum, jejunum, and ileum tissue Cu concentrations and Cu trafficking proteins abundance in the duodenum and liver. Wethers were blocked by body weight and assigned to one of two treatments: 1) control: no supplemental Cu and 2) +Cu: 12 mg of supplemental Cu/kg DM. After receiving treatments for 29 d, all wethers were transported to a USDA-inspected abattoir and harvested. Following harvest, blood, bile, liver, duodenum, jejunum, and ileum samples were collected for Cu concentration analysis. Additional duodenum and liver samples were collected for proteomic analysis.2026-05-132025-05-10PXD063823NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2102NEWT:2042546NEWT:259447NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:1247NEWT:1129NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:10360NEWT:1211601NEWT:876138NEWT:47664NEWT:317548NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:82688NEWT:95648NEWT:3885NEWT:3888NEWT:5821NEWT:1589NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:913645NEWT:1000589NEWT:85963NEWT:85962NEWT:143361NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4442NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:44586NEWT:626528NEWT:3347NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:294381NEWT:197NEWT:1390363NEWT:77133NEWT:288705NEWT:29176NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:556182NEWT:1270NEWT:374990NEWT:1392NEWT:498217NEWT:156471NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:156476NEWT:286NEWT:391619NEWT:360104NEWT:287NEWT:246197NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:5508NEWT:294128NEWT:11676NEWT:55571NEWT:35500NEWT:1140NEWT:100226NEWT:4530NEWT:1143NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:1336795NEWT:296543NEWT:316435NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:82380NEWT:105023NEWT:866628NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NEWT:8175NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:47946NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:243277NEWT:990119NEWT:2850NEWT:408172NEWT:227321NEWT:408170NEWT:493760NEWT:106590NEWT:260710NEWT:257313NEWT:3827NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:46704NEWT:1436733NEWT:460519NEWT:1187947NEWT:1432138NEWT:269796NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:54571NEWT:9598NEWT:8030NEWT:9483NCBITaxon:40559NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:759272NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:746128NEWT:499175NEWT:109779NEWT:43665NEWT:1266464NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:649908NEWT:410289NEWT:373153NEWT:375451NEWT:352472NEWT:357NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:29491NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:1328426NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NEWT:40483NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:38293NEWT:1428NEWT:327159NEWT:178876NEWT:1660NEWT:327160NEWT:573NEWT:9031NEWT:1872122NEWT:7091NEWT:108931NEWT:241368NEWT:1055524NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:7237NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:187878NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1821314NEWT:1249668NEWT:7108NEWT:317NEWT:5286NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:9644NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:451516NEWT:63459NEWT:36185NEWT:588858NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT:643680NCBITaxon:6157NEWT:42752NEWT:746360NEWT:6239NEWT:470150NEWT:162425NEWT:216257NEWT:102169NEWT:543734NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:118503NEWT:115357NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:2664179NEWT:986NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:1194669NEWT:40559NEWT:243230NEWT:8355NEWT:633NEWT:9685NEWT:7029NEWT:1080772NEWT:8479NEWT:1283300NEWT:632NEWT:6183NEWT:6063NEWT:630NEWT:49240NEWT:334747NEWT:61235NEWT:15368NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:469008NEWT:260707NEWT:256318NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:1719NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NEWT:1216981NEWT:52638NEWT:4097NCBIT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