Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/TMT_label_information.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/N-Glycopeptidomics_results.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/File_information.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_B10_B11_F5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_B6_B7_F3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_B2_B3_F1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_C10_C11_F11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_C2_C3_F7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_B12_C1_F6.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_C6_C7_F9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F7.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_C8_C9_F10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_B4_B5_F2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_B8_B9_F4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F9.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_C12_D1_F12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_NGP_C2_C3_F8.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/AJ_SRD5A3-CDG_Serum_TMT_TP_F5.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD053534/Total_Proteomics_results.pdResultprimary200OKpandey.akhilesh@mayo.eduAkhilesh PandeyData-dependent acquisitionMass SpectrometryBottom-up proteomicsRare diseasesOrbitrap eclipse tribridSrd5a3-cdgType 1 cdgGlycosylationComplex glycansPolyprenol reductasehttps://www.ebi.ac.uk/pride/archive/projects/PXD053534Blood SerumTotal protein from serum samples (controls and individuals with SRD5A3 variants) was estimated using BCA protein estimation assay. Equal amount of protein from each sample was subjected to reduction and alkylation using 5 mM dithiothreitol and 20 mM iodoacetamide respectively. Protein was digested overnight at 37°C using trypsin at a ratio of 1:20 (Trypsin: protein). Following day, peptides were desalted on C18 tips and dried. Dried peptides were reconstituted in 50 mM triethyl ammonium bicarbonate (TEABC) and labeled with tandem mass tags (TMT) using a 16-plex TMT pro kit. Labeled peptides were pooled and split into two fractions. One fraction of TMT labeled total peptides was subjected to size exclusion chromatography for glycopeptide enrichment. Dried peptides were reconstituted in 0.1% formic acid (FA) followed by loading and separation on a Superdex peptide 10/300 column (GE Healthcare). Isocratic flow of 0.1% FA was maintained at a flow rate of 200 µL per minute. Separation was done for a total run time of 130 minutes with fractionation and collection of the eluate into total 48 fractions. Early 24 fractions (based on UV profile) starting from 40 minutes to 100 minutes were collected and pooled into 12 fractions. The other fraction of TMT labeled dried peptides (500 µg) was reconstituted in 5 mM ammonium formate (pH 10) and fractionated by basic pH reverse phase liquid chromatography (bRPLC) into 96 fractions on a C18 column (3.5 µm, 4.6 mm X 250 mm). Total run time was 120 min and 5 mM ammonium formate (pH 10) in water was used as solvent A and 5 mM ammonium formate (pH 10) in 80% acetonitrile was used as solvent B. Gradient used for separation is as follows: 2% of solvent B was used for first two min and changed to 2% to 12% from 5 min to 8 min. Solvent B was increased to 55% from 8 min to 100 min, further increased to 70% in next 10 minutes. Column was washed with 80% of solvent B for 3 minutes and equilibrated with 5% of solvent B for 4 min. Total of 96 fractions were collected and concatenated to 12 fractions. Pooled fractions were dried and analyzed on mass spectrometer. Glycopeptide separation was performed using an Ultimate 3000 (Thermo Fisher Scientific Inc.) liquid chromatography system followed by analysis on an Orbitrap Eclipse mass spectrometer (Thermo Fisher Scientific Inc.). Glycopeptides were first trapped on a trap column (100 mm × 2 cm, Acclaim PepMap100 Nano-Trap, Thermo Fisher Scientific Inc.) at a flow rate of 5 µl/min and separated on an EASY-Spray analytical column (75 µm x 50 cm, PepMap RSCL C18, Thermo Fisher Scientific Inc.) packed with 2 µm C18 particles with temperature maintained at 50°C. Separation was performed using 0.1% formic acid in water as solvent A and 0.1% formic acid in ACN as solvent B. Flow rate was maintained at 300 nl/min for a gradient time of 150 minutes as follows: column equilibration was done for 4 minutes at 3% of solvent B, gradient of 3 to 35% of solvent B from 4 to 130 minutes then 35 to 80% of solvent B from 130 to 135 minutes followed by 80% of solvent B for 10 minutes and finally equilibration for 5 minutes at 3% of solvent B. Acquisition was done in DDA mode with the following parameters. Precursor ions were detected in orbitrap at a resolution of 120,000 with a scan range of 375 to 2000 m/z with normalized automatic gain control (AGC) target of 100% and maximum ion injection time of 50 ms. Precursor were isolated at a window of 0.7 m/z with a charge state ranging from +2 to +7 for MS/MS events. Fragmentation was done using normalized stepped collision energy (HCD) at 15, 25 and 40%. Normalized AGC was set to 400% with a maximum ion injection time of 200 ms. Data acquisition was performed in centroid mode with option of lock mass (441.1200025 m/z). Total proteomics data was analyzed on the same instrument using the same parameters but with the normalized fixed collision energy of 35% for MS/MS fragmentation.PrideNot availableTotal proteomics data was searched in Proteome Discoverer 3.0, using the SEQUEST search engine, against the UniProt human reviewed protein sequences (20,432 entries, downloaded February 1, 2021). Reporter ion quantification node was used for relative quantification of proteins between cases and controls. Enzyme specificity was set to trypsin with 2 allowed missed cleavages and carbamidomethylation of cysteine and N-term TMT 16-plex set as fixed modification and oxidation of methionine, N-term acetylation and TMT 16-plex modification of lysine set as variable modifications. Precursor mass tolerance was set to 10 ppm and fragment mass tolerance was set to 0.02 Da. Glycoproteomics data was searched using the publicly available pGlyco (v 3.0) software. Data was searched against Uniprot human reviewed protein sequences (20,432 entries, downloaded February 1, 2021) and inbuilt N-glycan human database. For identification of potential N-X-V glycosylation sites, all the N-X-V sequences were converted to J-X-V, in the protein database, for consideration as potential modification site by pGlyco. The conversion of all N-X-T/S/C motifs present to J-X-T/S/C is one of the processing steps of pGlyco during the searches. Enzyme specificity and modifications were used as described for total proteomics search. Precursor and fragment mass tolerances were set to 10 ppm and 20 ppm respectively and results were filtered for glycopeptides with 1% false discovery rate (FDR). Reporter ion intensity values were obtained by searching the data in Proteome Discoverer 3.0 using reporter ion quantifier node, as described for total proteomics, and were matched on a scan-to-scan basis with the glycopeptide IDs obtained from pGlyco.ProteomicsAkhilesh PandeyPARTIALDepartment of Laboratory Medicine and Pathology Mayo Clinic Rochester MinnesotaHomo Sapiens (human)41713138 Garapati K, Jain A, Joshi N, Sachdeva GS, Nam D, Saraswat M, Pasupuleti RR, Schultz MJ, Kozicz T, Morava E, Pandey A. Albumin as a glycoprotein biomarker in congenital disorders of glycosylation. Mol Genet Metab. 2026 147(4):109846 10.1016/j.ymgme.2026.109846pandey.akhilesh@mayo.eduDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905United StatesCongenital disorders of glycosylation (CDG) are rare inherited disorders resulting from defects in cellular glycosylation machinery. Albumin has recently been shown to be N-glycosylated at two non-canonical glycosylation sites. We applied multiplexed mass spectrometry-based glycoproteomics to identify site-specific N-glycosylation alterations in albumin from patients with PMM2-CDG, MPI-CDG, SRD5A3-CDG, MAN1B1-CDG and PGM1-CDG. Our findings demonstrate that the glycosylation of albumin is indeed affected in CDG and indicate a potential role for albumin-derived glycopeptides as diagnostic biomarkers.Albumin as a glycoprotein biomarker in congenital disorders of glycosylation.Garapati Kishore K, Jain Anu A, Joshi Neha N, Sachdeva Gunveen S GS, Nam Dowoon D, Saraswat Mayank M, Pasupuleti Raghavendra Rao RR, Schultz Matthew J MJ, Kozicz Tamas T, Morava Eva E, Pandey Akhilesh AfalseExtensive hypoglycosylation of serum N-glycoproteins in SRD5A3 deficiencyPolyprenol reductase is an enzyme encoded by the SRD5A3 gene, which catalyzes the synthesis of dolichol from polyprenols. Dolichol serves as a carrier for glycan precursors in N-linked glycosylation or monosaccharides in O-glycosylation, C-mannosylation, and GPI anchor biosynthesis. Pathogenic variants in SRD5A3 can result in a congenital disorder of glycosylation (CDG), SRD5A3-CDG, which is inherited in an autosomal recessive manner. Most serum proteins undergo glycosylation and changes in the glycosylation levels of numerous serum glycoproteins have been associated with pathological consequences. Despite the critical role of SRD5A3 in glycosylation, the impact of its deficiency on the glycosylation of serum proteins remains largely unexplored. In this study, we used tandem mass tags (TMT)-based multiplexed quantitation approach to analyze serum N-glycoproteins and proteins in SRD5A3-CDG patients and controls. We quantified 2,200 serum N-glycopeptides from 359 N-glycosites from 204 serum proteins. Extensive hypoglycosylation of serum proteins was observed in patients, with 245 of 291 dysregulated glycopeptides showing hypoglycosylation. These significantly changing glycopeptides belonged to several known abundant serum glycoproteins including haptoglobin, plasma serine protease inhibitor, alpha-1-B glycoprotein, alpha-2-macroglobulin and ceruloplasmin. We also detected changes in glycopeptides from albumin which has recently been shown to be glycosylated. Overall, our study provides novel insights into alterations in the glycosylation status of serum proteins in SRD5A3-CDG that could facilitate further investigations into diagnostics and therapeutics aspects of this CDG.2026-06-082024-07-01PXD053534NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:2719036NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:111205NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:38815NEWT:317447NEWT:4688NEWT:111225NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:270643NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:485NEWT:56636NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:294607NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:40674NEWT:1194669NEWT:51329NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:38323NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:4232NEWT:416348NEWT:11298NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:563041NEWT:72664NEWT:36599NEWT:41949NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:8644NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NCBITaxon:3077NEWT:194439NCBITaxon:12637NEWT:38727NEWT:8618NEWT:70448NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:10136NEWT:38942NEWT:4762NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:194963NEWT:15819NEWT:109461NEWT:1085956NEWT:6928NEWT:1239NEWT:36745NEWT:400727NEWT:272563NEWT:11009NEWT:913998NEWT:68335NEWT:3885NEWT:3888NEWT:649408NEWT:6915NEWT:101510NEWT:3880NEWT:272559NEWT:216816NEWT:153151NEWT:515849NEWT:10141NEWT:95767NEWT:466585NEWT:1000589NEWT:859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