Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Gp2b_gp.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Human_Serum_gp.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/ConA_gp.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Zhang.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/241010_JC_VRA_HS_PNGaseF_Trypsin_10kDaMWCO.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Gp2b_fg.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Zhu.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Gp1b-alpha_fg.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/liu.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Gp1b-alpha_gp.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/Human_Serum_fg.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/211201_KEM_GP1b_2_PNGase_SmE_GluC_PHEA.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/240801_JC_GPIIb_PNGaseF_IMPa_Trypsin_MWCO.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/221219_KEM_HumanSerum_Trypsin_SAX_PNGase.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/241127_VRA_BSA_GluCTrypsin_1mgHS_FreeGlycans_300ng.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/240715_IPT_GPIIb-IIIa_2_PNGaseF_IMPa.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/241203_JC_Kininogen_Trypsin.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/211201_KEM_GP1b_2_PNGase_SmE_GluC_PHEA_OTEThcD.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/221219_KEM_HumanSerum_Trypsin_SAX_20221219194748.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/241009_JC_VRA_HS_PNGaseF_Trypsin_10kDaMWCO.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/241127_VRA_BSA_GluCTrypsin_1000ng.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/240726_JC_GPIIb_IMPa_Trypsin.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/211201_KEM_GP1b_2A_PNGase_SmE_GluC_PHEA_ITETDOTEThcD.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD055856/241203_JC_Kininogen_Trypsin_FreeGlycans.rawprimaryOK200stacy.malaker@yale.eduValentina Rangel-AngaritaData-dependent acquisitionMass SpectrometryBottom-up proteomicsNot availableGlycoproteomicsN-glycansPngasefMass spectrometryAdductsMucinomicshttps://www.ebi.ac.uk/pride/archive/projects/PXD055856Blood PlateletBlood PlasmaEpithelial CellHela CellDifferent samples (lysates, purified proteins, and serum) were enriched using a combination of glycan binding proteins and HILIC/ERLIC. Peptides were desalted using 10 mg of Strata-X SPE columns (Phenomenex, 8B-S100-AAK). Columns were activated by adding 1 mL of ACN and equilibrated with 1 mL of 0.1% formic acid in water (solvent A). Potential polymeric contaminants were removed by adding 1 mL of 50% ACN 0.1% formic acid in water (solvent B), followed by re-equilibration with 1 mL of solvent A prior to adding the sample. The column was then rinsed twice using 300 µL of solvent A. Peptides were eluted into a new Eppendorf tube with 150 µL of solvent B twice. The eluent was dried using a LabConco vacuum concentrator. Peptides were analyzed by online nanoflow LC-MS/MS with an Orbitrap Eclipse Tribrid mass spectrometer (Thermo Fisher Scientific) coupled to a Dionex UltiMate 3000 HPLC instrument (Thermo Fisher Scientific). Peptides were injected onto an Acclaim PepMap 100 trap column (Thermo Fisher, 164564) packed with 2 cm of 5 µm C18 material (Thermo Fisher, 164564) using solvent A. The peptides were then separated on a 15 cm PepMap RSLC EASY-Spray C18 column (Thermo Fisher, ES904) packed with 2 µm C18 material (Thermo Fisher, ES904) using a gradient from 0 to 35% solvent B in 60 minutes with a constant flow rate of 300 nL/min. Full MS1 spectra were collected at a resolution of 60,000, an automatic gain control (AGC) target of 3e5, and a mass range from 300 to 1500 m/z. Dynamic exclusion was enabled with a repeat count of 2, repeat duration of 7 seconds, and exclusion duration of 7 seconds. Charge states 2 to 6 were selected for fragmentation with MS2s generated at top speed for 3 seconds. HCD was performed on all selected precursor masses with the following parameters: isolation window of 2 m/z, normalized collision energy (NCE) of 28 to 30%, orbitrap detection (resolution of 7,500), maximum inject time of 50 ms, and a standard AGC target. Additional ETD or EThcD fragmentation of the same precursor was triggered if 1) 3 of 8 oxonium fingerprint ions (126.055, 138.055, 144.07, 168.065, 186.076, 204.086, 274.092, and 292.103) were present at ± 0.1 m/z and greater than 5% relative intensity or 2) the precursors were present at a sufficient abundance for localization using ETD. If the precursor was between 300-850 m/z and over 3e4 intensity, an ETD scan was triggered and read out using the ion trap at a normal scan rate. For precursors between 850-1500 m/z with an intensity greater than 1e5, supplemental activation (EThcD) was also applied at 15% NCE and read out in the Orbitrap at 7500 resolution. Both used charge-calibrated ETD reaction times, 150 ms maximum injection time, and 200% standard injection targets.PrideNot availableRAW data files from GpIbα and GpIIb were searched with O-Pair18 in the MetaMorpheus suite and Byonic. Complex samples (serum and lysates) were exclusively searched with Byonic for N- and O-glycopeptides. FASTA files were downloaded from Uniprot containing the respective relevant protein sequences (P07359 and P08514) or the entire human proteome depending on sample. For all searches regardless of search algorithm, mass tolerance was set to 10 and 20 ppm for MS1s and MS2s, respectively, with carbamidomethyl Cys as a fixed modification while Asn deamidation was a variable modification. GpIbα was searched in O-Pair with fully specific cleavage (N-terminal to Ser and Thr and C-terminal to GluC and Asp with 7 missed cleavages) and non-specific cleavage (24 missed cleavages). Both searches were performed using the O-glycan database containing 36 glycans with mannose in O-Pair. For all searches performed in Byonic, we used the 9 most common O-glycan and N-glycan database containing 52 common biantennary structures. GpIIb was searched in Byonic with fully specific cleavage settings N-terminal to Ser and Thr and C-terminal to Arg and Lys with 7 allowed missed cleavages. Complex samples were searched with fully specific cleavage C-terminal to Arg and Lys with 3 missed cleavages. All glycopeptide identifications were filtered for a log prob >2 and score > 200.MS2s containing the HexNAc fingerprint (126.054, 138.055, 144.065, 168.065, 186.076, and 204.087 ions) were extracted, alongside the abundance and ppm error for each oxonium ion. MS2 scans were filtered for those containing high abundance of 204.087, 168.085, and 138.055, as well as low abundance of 144.065. N-glycan structures commonly found in serum were downloaded from GlyConnect Compozitor and the glycan masses associated with these structures were calculated. The [M+H] + was calculated from the extracted MS2s, and the mass of a water and a proton was subtracted to calculate the native glycan mass, which was then compared to the previously mentioned glycan library (Supplementary Dataset S1). All potential free glycans were manually validated to ensure 1) a highly abundant HexNAc fingerprint, 2) lack of peptide fragmentation, 3) presence of glycan losses from highest fragment in the MS2 until the mass of a single HexNAc, and 4) similar elution time and pattern compared to other free glycans identified.ProteomicsStacy MalakerDepartment of Chemistry, Yale University, New Haven, CTPARTIALHomo Sapiens (human)valentina.rangelangarita@yale.edu39938005 Rangel-Angarita V, Chongsaritsinsuk J, Mahoney KE, Kim LM, Chen RJ, Appah-Sampong AA, Tran IP, Steigmeyer AD, Hollenhorst MA, Malaker SA. PNGaseF-Generated N-Glycans Adduct onto Peptides in the Gas Phase. J Am Soc Mass Spectrom. 2025 36(3):542-552 10.1021/jasms.4c00431Yale University Department of ChemistryUnited StatesGlycoproteomics has recently increased in popularity due to instrumental and methodological advances. That said, O-glycoproteomic analysis is still challenging for various reasons, including signal suppression, search algorithm limitations, and co-occupancy of N- and O-glycopeptides. To decrease sample complexity and simplify analysis, most O-glycoproteomic workflows include PNGaseF digestion, which is an endoglycosidase that removes most N-glycan structures. Here, we report that N-glycans released from PNGaseF digestion were identified during data acquisition and hampered detection of O-glycopeptides. Importantly, we noted instances where free glycans adducted to unmodified peptides in the gas phase and were misidentified by search algorithms as O-glycopeptides. We confirmed the presence of free glycans in other experiments performed in our laboratory, as well as from data generated by other groups. To overcome this limitation, we demonstrated that released N-glycans can be removed using a molecular weight cut off filter prior to (glyco)protease digestion, which improves O-glycoproteomic coverage.PNGaseF-Generated N-Glycans Adduct onto Peptides in the Gas Phase.Rangel-Angarita Valentina V, Chongsaritsinsuk Joann J, Mahoney Keira E KE, Kim Lea M LM, Chen Ryan J RJ, Appah-Sampong Akua A AA, Tran Isabella P IP, Steigmeyer Alexandra D AD, Hollenhorst Marie A MA, Malaker Stacy A SAfalsePNGaseF-generated N-glycans adduct onto peptides in the gas phaseGlycoproteomics has recently increased in popularity due to instrumental and methodological advances. That said, O-glycoproteomic analysis is still challenging for various reasons, including signal suppression and splitting, search algorithm limitations, and co-occupancy of N- and O-glycopeptides. To decrease sample complexity and simplify analysis, most O-glycoproteomic workflows include PNGaseF digestion, which is an endoglycosidase that removes mammalian N-glycans. Here, we report that N-glycans released from PNGaseF digestion, also referred to as ‘free glycans’, were identified during data acquisition and hampered detection of O-glycopeptides. Importantly, we noted instances where free glycans adducted to unmodified peptides in the gas phase and were misidentified by search algorithms as O-glycopeptides. We confirmed the presence of free glycans in other experiments performed in our laboratory, as well as from data generated by other groups. To overcome this limitation in common O-glycoproteomic workflows, we performed PNGaseF digestion following reduction and alkylation. Here, we demonstrated that released N-glycans can be removed using a molecular weight cut off (MWCO) filter, prior to (glyco)protease digestion, which improved O-glycoproteomic coverage.2026-06-292024-09-13PXD055856NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:1912919NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:1367269NEWT:145458NEWT:633149NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:51329NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:9793NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:27457NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NC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