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FuData-dependent acquisitionGlycoproteomicsMass SpectrometryBottom-up proteomicsLiver CancerGlycoproteomicsProtein o-glcnacylationhttps://www.ebi.ac.uk/pride/archive/projects/PXD073249T CellCells were treated with Tunicamycin (Tm) for 24 h, and then supplemented with the sugar analog (Ac4GalNAz, 200 μM) for an additional 24 h to label O-GlcNAcylated proteins together with Tm. O-GlcNAcylated proteins metabolically labeled with the azido group were subsequently tagged with PC Biotin Alkyne. After tryptic digestion, glycopeptides were captured using NeutrAvidin agarose, and were sequentially released under the irradiation (365 nm). The cleavage also generated an amine group on the glycan that facilitates the protonation of glycopeptides for mass spectrometry (MS) analysis.PrideFor glycopeptides analysis, the raw files were converted to the mzML format using MSConvert from ProteoWizard, using peak picking and zero samples removing from the vendor algorithm and keeping the 1,000 most intense peaks. Files were then searched using MSFragger version 4.4 in Fragpipe version 24.0 against the Swiss-Prot Homo sapiens database (20,468 entries). The glyco-O-Pair workflow was used with adjustments based on current experiment design. For modifications, max variable mods on a peptide was set to 4, with carbamidomethylation of cysteine (+57.0214 Da), oxidation of methionine (+15.9949 Da) and protein N-termini acetylation (+42.0106 Da). Mass offsets were set to 0, 299.1230, 326.1339, 528.2859, and 555.2968 Da. Restricted delta masses were applied to serine (S), threonine (T), tyrosine (Y), and cysteine (C) residues. The offset at 299.1230 Da corresponds to the azido-HexNAc modification with the photocleavable biotin remnant after UV cleavage (HexNAz-PC), while 326.1339 Da corresponds to the same modification after GAO oxidation and methoxylamine labeling (HexNAz-PC-GAO-MeONH₂, +27.0109 Da mass shift). The offsets at 528.2859 Da and 555.2968 Da correspond to the TMT-labeled versions of these modifications, respectively. O-Pair database was updated accordingly and minimum oxonium ion relative abundance is set to 5%. For quantification, TMT reporter ion intensity was extracted by IonQuant and label type was set to TMT-6. The results in psm.tsv file were used for downstream analysis. Previous studies have demonstrated that per-O-acetylated sugar analogs can induce non-enzymatic S-glycosylation on cysteine residues, which may interfere with O-GlcNAcylation identification.3 To avoid the interference of S-GlcNAcylation, we applied the following stringent criteria outlined previously.4 Any glycopeptides with glycan localized on the cysteine residue (confidence level 1 or level 1b) were removed. Additionally, any identified glycopeptides with a cysteine residue in their sequences with confidence level 2 or level 3 were also deleted. Eventually, only confidently localized glycopeptides (confidence level 1 or level 1b) with the glycan on the serine, threonine or tyrosine residue were used for site-specific analysis.ProteomicsRonghu WuChemistry & BiochemistryPARTIALHomo Sapiens (human)lpfu46@gatech.edu42153620 Fu L, Yin K, Xu X, Wu R. Systematic Quantification of Protein O-GlcNAcylation Reveals Common and Cell-Type-Specific Responses to N-Glycosylation Inhibition in Human Cells. Anal Chem. 2026 10.1021/acs.analchem.6c00972Georgia Institute of TechnologyUnited StatesBoth protein O-GlcNAcylation and N-glycosylation are extremely important in human cells and regulate many cellular events. While O-GlcNAcylation is known to act as a stress sensor, its changes in human cells with N-glycosylation perturbations remain to be explored. In this study, we comprehensively and site-specifically studied common and cell-type-specific responses of protein O-GlcNAcylation under N-glycosylation inhibition in three types of human cells (HEK293T, HepG2, and Jurkat cells) by integrating metabolic labeling, bio-orthogonal chemistry, and multiplexed proteomics. In total, more than 1000 O-GlcNAcylated proteins were identified and quantified, and the results demonstrate that under the inhibition of protein N-glycosylation, O-GlcNAcylated proteins related to stress response and translation are commonly changed in different types of cells. Furthermore, O-GlcNAcylation changes are cell-type-specific, and O-GlcNAcylated proteins related to leukocyte proliferation and T-cell activation were upregulated in Jurkat cells, while in HEK293T cells, those associated with ribonucleotide metabolism and ribosome biogenesis were upregulated. Site-specific analysis revealed that O-GlcNAcylation sites in structured regions exhibited larger abundance changes compared with those in intrinsically disordered regions. This study provides valuable insights into the regulation of protein O-GlcNAcylation in human cells under N-glycosylation inhibition, advancing our understanding of protein glycosylation.Systematic Quantification of Protein O-GlcNAcylation Reveals Common and Cell-Type-Specific Responses to N-Glycosylation Inhibition in Human Cells.Fu Longping L, Yin Kejun K, Xu Xing X, Wu Ronghu RfalseSystematic Quantification of Protein O-GlcNAcylation Reveals Common and Cell-Type-Specific Responses to N-Glycosylation Inhibition in Human CellsIn this work, we systematically and site-specifically analyzed protein O-GlcNAcylation under the N-glycosylation inhibition through the integration of metabolic labeling, bio-orthogonal chemistry, and multiplexed proteomics. The experiments were performed in three types of human cells, i.e., HEK293T, HepG2, and Jurkat cells.2026-06-022026-01-19PXD073249NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:71647NEWT:2NEWT:157546NEWT:474186NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:1496NEWT:544496NEWT:2102NEWT:2042546NEWT:259447NEWT:45351NEWT:43179NEWT:4513NEWT:180454NEWT:5722NEWT:1247NEWT:6938NEWT:1129NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:10360NEWT:1211601NEWT:876138NEWT:47664NEWT:317548NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:272563NEWT:224326NEWT:1333499NCBITaxon: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:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4442NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NEWT:2164133NCBITaxon:183674NEWT:224308NEWT:167387NEWT:84645NEWT:44586NEWT:626528NEWT:3347NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:294381NEWT:197NEWT:1390363NEWT:77133NEWT:288705NEWT:29176NEWT:145481NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:556182NEWT:1270NEWT:374990NEWT:1392NEWT:498217NEWT:156471NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:156476NEWT:286NEWT:391619NEWT:360104NEWT:246196NEWT:287NEWT:246197NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:161934NEWT:1148NEWT:580240NEWT:5508NEWT:294128NEWT:5507NEWT:11676NEWT:55571NEWT:35500NEWT:1140NEWT:100226NEWT:4530NEWT:1143NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:1336795NEWT:644042NEWT:296543NEWT:316435NEWT:42157NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:82380NEWT:1034304NEWT:105023NEWT:866628NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:9378NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NEWT:8175NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:47946NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:1077286NEWT:243277NEWT:990119NEWT:2850NEWT:408172NEWT:227321NEWT:408170NEWT:493760NEWT:106590NEWT:260710NEWT:257313NEWT:3827NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:930945NEWT:106592NEWT:536231NEWT:46704NEWT:1436733NEWT:460519NEWT:1187947NEWT:572307NEWT:1432138NEWT:269796NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:1194599NEWT:272844NEWT:54571NEWT:9598NEWT:8030NEWT:9483NEWT:1513458NCBITaxon:40559NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:759272NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:508771NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:29158NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:746128NEWT:499175NEWT:109779NEWT:43665NEWT:1266464NEWT:1715989NEWT: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:571256NCBITaxon:138NEWT: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:273068NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:451516NEWT:63459NEWT:1276815NEWT:36185NEWT:588858NEWT:1225786NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:197221NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT:643680NCBITaxon:6157NEWT:42752NEWT:746360NEWT:6239NEWT:89764NEWT:470150NEWT:162425NEWT:216257NEWT:102169NEWT:543734NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:118503NEWT:2059687NEWT:115357NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:2664179NEWT:986NEWT:52641NEWT:7038NEWT:7159NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:1194669NEWT:51329NEWT:40559NEWT:243230NEWT:8355NEWT:633NEWT:9685NEWT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