Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118329.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118325.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118328.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118324.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118331.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118323.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118326.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118330.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118322.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118327.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112689_118323.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112713_118325.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112710_118328.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112707_118331.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112708_118330.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112712_118326.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112709_118329.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112714_118324.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112688_118322.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/112711_118327.mzidftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118326.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118331.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118329.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118323.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118324.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118328.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118322.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118325.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118327.mzXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD075406/118330.mzXMLprimaryOK200mwaldor@bwh.harvard.eduZhu LiangData-dependent acquisitionMass SpectrometryTop-down proteomicsNot availableLuminal contentsMouseIl22fcSmall intestinehttps://www.ebi.ac.uk/pride/archive/projects/PXD075406Small Intestine MucosaThe distal SI tissue was collected from control or IL22Fc-treated infant animals and cut open longitudinally. The tissue was incubated in 4 mL of wash buffer [1mM DTT PBS with protease inhibitor (Roche, 4693159001)] on ice for 10 min and vortexed for 20 seconds. After the removal of tissue pieces, intestinal washes were centrifuged at 100 xg for 1 min to remove the large pieces of intestinal contents. The supernatant was concentrated by centrifugation at 4000 xg with 3 kDa MWCO Amicon Ultra centrifugal filter unit for 1 hour. The volume of the concentrate was adjusted to 400 mL with wash buffer. The supernatants were processed for LC-MS/MS analysis using the ENRICH-iST kit (PreOmics, #P.O.00163). Assay details have been described previously, including protein enrichment, denaturation, reduction, alkylation, enzymatic digestion, and peptide cleanup within a single workflow. Briefly, mucus proteins were captured on paramagnetic enrichment beads in binding buffer, followed by multiple bead-based wash steps to remove salts, lipids, and low-molecular-weight contaminants. Bead-captured proteins were denatured, reduced, and alkylated using the supplied lysis buffer at elevated temperature and digested on-bead with a Trypsin/LysC protease mixture. Digestion was terminated by stop solution, and peptides were purified using the solid-phase extraction cartridge with sequential washes to remove impurities. Peptides were eluted in volatile buffer, dried completely by vacuum centrifugation (SpeedVac SPD120), and stored at −80 °C until LC-MS/MS analysis.Peptides were reconstituted in 5-10 µL of solvent A (2.5% acetonitrile, 0.1% formic acid) and separated by nano-scale reverse-phase liquid chromatography using a custom-packed capillary column (100 µm inner diameter × ~30 cm length) containing 2.6 µm C18 spherical silica beads and terminated with a flame-drawn electrospray tip. Subsequently, peptides were loaded via an autosampler and eluted using a linear gradient of increasing concentrations of solvent B (97.5% acetonitrile, 0.1% formic acid). Eluting peptides were ionized by electrospray and analyzed on an Orbitrap Velos Pro hybrid ion trap-Orbitrap mass spectrometer (Thermo Fisher Scientific).PrideNot availableMS raw files were searched against the UniProt FASTA databases using Sequest (Thermo Fisher Scientific). Databases included reversed (decoy) sequences to enable estimation of false discovery rates. Peptide-spectrum matches were filtered to achieve a peptide-level false discovery rate of 1–2%. Carbamidomethylation of cysteine residues was specified as a fixed modification during database searching. Enzyme specificity was defined as cleavage at the carboxyl terminus of arginine and lysine residues, consistent with digestion by trypsin and LysC. A maximum of 1 missed cleavages was allowed. All bioinformatic analyses were performed using Perseus (version 2.0.7.0) as well as standard analytical workflows implemented in R (version 4.5.2).ProteomicsMatthew K WaldorCOMPLETE1.Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA 2.Department of Microbiology, Harvard Medical School, Boston, MA, USA 3.Howard Hughes Medical Institute, Boston, MA, USAMus Musculus (mouse)zliang3@bwh.harvard.eduNot availableBrigham and Women's Hospital, Harvard Medical SchoolUnited States10.6019/PXD075406falseProteomic analysis of small intestine luminal contents in IL22Fc-treated mouseProteomic analyis was perfomred to identify the IL22Fc-induced proteins/polypeptides in the murine small intestine contents2026-04-132026-03-09PXD075406NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:43179NEWT:13076NEWT:1249668NEWT:317NEWT:55153NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:415540NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:3641NEWT:8782NEWT:1263854NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:1283NEWT:931281NEWT:1000561NEWT:7029NEWT:1283300NEWT:6183NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:1182590NEWT:8726NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:421932NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:106592NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:5664NEWT:2157NEWT:146479NEWT:10306NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:3635NEWT:5811NEWT:1480154NEWT:235443NEWT:1274414NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:1450511NEWT:360094NEWT:470NEWT:84023NEWT:9838NCBITaxon:9615NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:9940NEWT:327160NEWT:573NEWT:9031NEWT:1274420NEWT:7091