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The mixture was then incubated at 60 C for 30 min and sonicated at 4 C at 50% power with for 5 s on/5 s off pulse 1 min. Lysates were centrifuged at 21000g at 4 C for 5 min, and the supernatant was collected. Protein concentrations were measured using a bicinochoninic acid (BCA) assay kit (Thermo Fisher Scientific, San Jose, CA). Protein extracts were reduced by adding 0.4 M DTT solution to a final concentration of 20 mM and incubated at 37 C for 1 h. A 0.8 M IAA solution was then added to reach a final concentration of 40 mM. The mixture was incubated in the dark at room temperature for 30 min. Alkylation was quenched by adding the same amount of DTT and incubating the mixture for another 10 min. Protein digestion was initially performed using trypsin at a protein-to-enzyme ratio of 100:1, with incubation at 37 °C for 12 hours. Subsequently, an additional aliquot of trypsin was added to achieve a final protein-to-enzyme ratio of 50:1, followed by a further 4-hour incubation at 37 °C. The digestion was terminated by the addition of TFA to a final concentration of 1%. The samples were stored at -80 °C for future use. The mouse cortex tissues were then lysed and sonicated as described above. After a BCA protein assay, 100 µg of proteins from each sample were aliquoted for each channel. The aliquots were dried down in vacuo and treated with the sample preparation approach, as above."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Byonic software (version 2.9.38, Protein Metrics Inc, San Carlos, CA) embedded with the Proteome Discover 2.5 (PD 2.5, Thermo Fisher Scientific) was used to process intact N-glycopeptide, phosphopeptide and proteomics data. Raw files were searched against UniProt Homo sapiens reviewed database (December 2023) or UniProt Mus musculus reviewed database (April 2024). Trypsin was selected as the enzyme and two maximum missed cleavages were allowed. Searches were performed with a precursor mass tolerance of 10 ppm and a fragment mass tolerance of 0.02 Da. Fixed modifications were specified as carbamidomethylation (+57.02146 Da) on cysteine residues and 12-plex DiLeu (+145.12801 Da) on peptide N-terminus and lysine residues. Dynamic modifications included oxidation of methionine (+15.99492 Da), phosphorylation on serine, threonine and tyrosine (+79.96633 Da) and N-glycosylation. Glycan modifications were searched against a human or mammalian glycan database expanded from Byonic embedded N-glycan database to include N-linked M6P glycans consisting of HexNAc (2-4) Hex (3-9) Phospho (1-2) modifications[22]. Peptide identification results were filtered at Byonic score > 150, PEP 2D < 0.05, |Log Prob| > 1. MS/MS spectra of M6P glycopeptide PSMs were manually inspected to ascertain the existence of phosphorylated hexose diagnostic ions. Proteomics data were searched the same as above except without dynamic modifications of phosphorylation or N-glycosylation. A two-sample Student’s t test with a two-detailed distribution for binary comparison were conducted using Perseus (version 2.0.11.0) and the p value was subjected to permutation-based FDR for multiple testing corrections."],"omics_type":["Proteomics"],"labhead":["Lingjun Li"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["School of Pharmacy, Department of Chemistry and Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222, USA"],"species":["Homo Sapiens (human)","Mus Musculus (mouse)"],"publication":["41765633 Wu F, Wang D, Tabang DN, Liu PK, Wang Z, Liu Y, Steenhagen A, Puglielli L, Li L. High-throughput simultaneous quantification of glycopeptides and phosphopeptides enabled by 12-plex DiLeu isobaric tags and dual-functional Titanium(IV)-IMAC material. Anal Chim Acta. 2026 1395:345231 10.1016/j.aca.2026.345231"],"submitter_mail":["wufeixuan07@gmail.com"],"submitter_affiliation":["University of Wisconsin-Madison"],"submitter_country":["United States"],"pubmed_abstract":["<h4>Background</h4>Protein glycosylation and phosphorylation are critical post-translational modifications (PTMs) that regulate diverse physiological and pathological processes, yet their comprehensive characterization remains challenging due to low abundance and poor ionization efficiency. Recent advances using epoxy-ATP-Ti<sup>4+</sup>-IMAC materials have enabled simultaneous enrichment of N-glycopeptides, phosphopeptides, and mannose-6-phosphate glycopeptides. However, high-throughput, multiplexed quantification of these PTMs is still lacking. This work addresses the need for an efficient strategy capable of simultaneously enriching, identifying, and quantitatively comparing glycosylation and phosphorylation across multiple biological samples.<h4>Results</h4>We developed a high-throughput workflow integrating epoxy-Ti<sup>4+</sup>-IMAC enrichment with custom N,N-dimethyl leucine (DiLeu) isobaric tags to achieve 12-plex quantitative analysis of N-glycosylation and phosphorylation for the first time. This streamlined one-tube sample preparation protocol enabled robust, simultaneous enrichment and quantification of PTMs from complex mouse brain samples. Application to APP/PS1 transgenic mice versus wild-type controls produced quantitative identification of 1975 N-glycopeptides and 1181 phosphopeptides. Comparative profiling revealed substantial PTM alterations associated with Alzheimer's disease (AD)-related pathology. Differentially modified proteins mapped to key biological pathways, including synapse organization, synaptic membrane regulation, and cell adhesion. The abundance patterns highlighted broad disruptions in PTM-mediated signaling and provided molecular insights into synaptic dysfunction in the APP/PS1 model.<h4>Significance and novelty</h4>This integrated DiLeu isobaric labeling-epoxy-Ti<sup>4+</sup>-IMAC platform provides a powerful, high-throughput solution for the simultaneous quantification of glycosylation and phosphorylation, enabling detailed investigation of PTM interplay. By uncovering disease-associated modifications in AD mouse models, this method offers new opportunities to identify mechanistic biomarkers and therapeutic targets. Its versatility and scalability make it broadly applicable to PTM-centric studies across diverse biological systems, including biofluids, cell lysates and tissues."],"pubmed_title":["High-throughput simultaneous quantification of glycopeptides and phosphopeptides enabled by 12-plex DiLeu isobaric tags and dual-functional Titanium(IV)-IMAC material."],"pubmed_authors":["Wu Feixuan F, Wang Danqing D, Tabang Dylan Nicholas DN, Liu Peng-Kai PK, Wang Zicong Z, Liu Yuan Y, Steenhagen Angelique A, Puglielli Luigi L, Li Lingjun L"],"additional_accession":[]},"is_claimable":false,"name":"High-Throughput Simultaneous Quantification of Glycopeptides and Phosphopeptides Enabled by 12-plex DiLeu Isobaric Tags and Dual-Functional Titanium(IV)-IMAC Material","description":"Protein glycosylation and phosphorylation are two of the most common post-translational modifications (PTMs). Though they have been indicated to play critical roles in various physiological and pathological processes, effective analytical tools are challenged by low PTM abundance and poor ionization efficiency. Recently, an epoxy-ATP-Ti4+-IMAC material has been developed to enable simultaneous enrichment and separation of common N-glycopeptides, phosphopeptides, and mannose-6-phosphate (M6P) glycopeptides from complex biological samples. To further improve the throughput of our previous method, in this study, we developed an efficient strategy using our custom-developed N,N-dimethyl leucine (DiLeu) isobaric tags to achieve a multiplexed quantitative simultaneous analysis of N-glycosylation and phosphorylation from up to 12 samples for the first time. We further applied this method to investigate N-glycosylation and phosphorylation alterations in APP/PS1 model mouse brain samples and wild-type (WT) controls. With the integration of a one-tube sample processing workflow, 1975 glycopeptides and 1181 phosphopeptides were quantitatively identified from mouse brain. We also unveiled important biological functions regulated by N-glycosylation and phosphorylation, including synapse organization, synaptic membrane and cell adhesion, highlighting the involvement of N-glycosylation and phosphorylation aberrations in APP/PS1 models. Our results provide evidence that the established DiLeu isobaric labeling-epoxy-Ti4+-IMAC method can be used for high-throughput simultaneous quantification of glycosylation and phosphorylation, and their potential crosstalk, showing significant promise for identifying novel therapeutic targets or biomarkers in biological systems.","dates":{"publication":"2026-06-29","submission":"2025-03-03"},"accession":"PXD061371","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:1247","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:515849","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:143361","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:294381","NEWT:197","NEWT:1390363","NEWT:77133","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:498217","NEWT:156471","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:156476","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:1143","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:172","NEWT:296543","NEWT:316435","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:105023","NEWT:866628","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:2850","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:269796","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:9483","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:180923","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:527796","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:375451","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:1328426","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:327159","NEWT:178876","NEWT:1660","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1821314","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:5286","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:9644","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:27592","NEWT:98334","NEWT:426428","NEWT:63459","NEWT:1276815","NEWT:36185","NEWT:588858","NEWT:9639","NCBITaxon:11071","NEWT:242231","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:929793","NE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