Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075438/Ngly_human.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075438/Ngly_mouse.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075438/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075438/control_M_0_5_ug_ETD.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075438/AD_M_0_5_ug_ETD.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075438/AD_H_0_5_ug_ETD.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD075438/control_H_0_5_ug_ETD.rawprimaryOK200ramonsun@ufl.eduRAMON SUNMass SpectrometryBottom-up proteomicsAlzheimer's Diseaseglycoproteomicshuman brainAlzheimer’s diseasen-glycosylationmouse brainAlzheimer’s disease; glycoproteomics; n-glycosylation; human brain; mouse brainhttps://www.ebi.ac.uk/pride/archive/projects/PXD075438BrainDe-identified human frontal cortex specimens and mouse brain tissues were collected and prepared under approved protocols. For glycoproteomics, pooled samples were used to ensure sufficient membrane protein input. Membrane proteins were enriched by high-salt extraction, sodium carbonate fractionation, and sequential ultracentrifugation. The membrane fraction was denatured in urea buffer, reduced, alkylated with iodoacetamide, precipitated by chloroform/methanol/water extraction, and resuspended in ammonium bicarbonate. Protein concentration was measured by BCA assay, and 100 µg of membrane protein was digested with trypsin at 37°C for 24 h. Glycopeptides were then analyzed by nanoLC on an Ultimate 3000 RSLCnano coupled to a Thermo Eclipse mass spectrometer using a 15 cm × 75 µm C18 column and a 180 min gradient.PrideRaw glycoproteomics data were processed in Proteome Discoverer v3.0. Peptides were identified with CHIMERYS, and glycopeptides were assigned using the Byonic node. Search parameters included 5 ppm precursor tolerance and 10 ppm fragment tolerance. Variable modifications included deamidation, oxidation, and carboxymethylation. Glycopeptide identifications were filtered at log probability >1 and ppm error <3. Human samples were searched against the “N-glycan 182 human no multiple fucose” library, and mouse samples against the “N-glycan 309 mammalian no sodium” library. O-glycan searches used the “9-Most-common glycans” library. Curated outputs were used for relative glycopeptide quantification and downstream interpretation.ProteomicsRamon sununiversity of floridaPARTIALHomo Sapiens (human)ramonsun@ufl.eduNot availableUniversity of FloridaUnited StatesfalseGlycoproteomics of Human and Mouse Brains in Alzheimer’s DiseaseThis study profiles glycoproteomic changes in human frontal cortex and mouse brain in Alzheimer’s disease models. We compare cognitively normal and AD human brain tissue, and wild-type and 5xFAD mouse brain, to define whether AD-associated hyperglycosylation reflects increased glycosylation of existing proteins. The work is integrated with spatial glycomics and related multiomic analyses to identify disease-associated glycopeptides and glycoproteins linked to neurodegeneration.2026-03-312026-03-10PXD075438NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:185579NEWT:43179NEWT:13076NEWT:1249668NEWT:317NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:1211601NEWT:415540NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:575412NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:3888NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:272559NEWT:226186NEWT:3641NEWT:383379NEWT:8782NEWT:1263854NEWT:1000589NEWT:435590NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:515619NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:7029NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:11320NEWT: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:1094343NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:4006NEWT: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:536231NEWT:61674NEWT: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:1416333NEWT:5664NEWT:2157NEWT:146479NEWT:10306NCBITaxon:2759NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:3635NEWT:5811NEWT:1480154NEWT:235443NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:411483NEWT:884019NEWT:411490NEWT:169963NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:476272NEWT:349741NEWT:9606NEWT:367830NEWT:157295NEWT:641501NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:9721NEWT:1450511NEWT:360094NEWT:470NEWT:411901NEWT:1313NEWT:411469NEWT:84023NEWT:9838NEWT:105884NCBITaxon:9615NCBITaxon:5811NEWT:58334NEWT:411464NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:411460NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:178876NEWT:9940NEWT:327160NEWT:573NEWT:521001NEWT:9031NEWT:1274420NEWT:7091NEWT:578458