PXD055856 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | PNGaseF-generated N-glycans adduct onto peptides in the gas phase |
| Description | Glycoproteomics 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. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-06-29 |
| AnnouncementXML | Submission_2026-06-28_16:19:46.862.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Valentina Rangel-Angarita |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | O-glycosylated residue |
| Instrument | Orbitrap Eclipse |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2024-09-13 12:26:23 | ID requested | |
| ⏵ 1 | 2026-06-28 16:19:47 | announced | |
Publication List
| 10.1021/jasms.4c00431; |
| 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, 36(3):542-552(2025) [pubmed] |
Keyword List
| submitter keyword: adducts,Glycoproteomics, mucinomics, PNGaseF, mass spectrometry, N-glycans |
Contact List
| Stacy Malaker |
|---|
| contact affiliation | Department of Chemistry, Yale University, New Haven, CT |
| contact email | stacy.malaker@yale.edu |
| lab head | |
| Valentina Rangel-Angarita |
|---|
| contact affiliation | Yale University
Department of Chemistry |
| contact email | valentina.rangelangarita@yale.edu |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
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| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD055856
- Label: PRIDE project
- Name: PNGaseF-generated N-glycans adduct onto peptides in the gas phase
