PXD062628

PXD062628 is an original dataset announced via ProteomeXchange.

Title	Quantification and site-specific analysis of co-occupied N- and O-glycopeptides
Description	Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are indispensable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within non-mucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.
HostingRepository	PRIDE
AnnounceDate	2025-04-08
AnnouncementXML	Submission_2025-04-08_12:44:04.376.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joann Chongsaritsinsuk
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-04 13:15:06	ID requested
⏵ 1	2025-04-08 12:44:05	announced

10.1021/ACS.JPROTEOME.4C00574;

10.1021/acs.jproteome.4c00574;

Chongsaritsinsuk J, Rangel-Angarita V, Lucas TM, Mahoney KE, Enny OM, Katemauswa M, Malaker SA, Quantification and Site-Specific Analysis of Co-occupied N- and O-Glycopeptides. J Proteome Res, 23(12):5449-5461(2024) [pubmed]

submitter keyword: mucin, glycoproteomics, O-glycosylation,glycosylation, N-glycosylation

Stacy Malaker
contact affiliation	Yale University, Department of Chemistry
contact email	stacy.malaker@yale.edu
lab head
Joann Chongsaritsinsuk
contact affiliation	Yale University
contact email	joann.chongsaritsinsuk@yale.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062628
     1. Label: PRIDE project
     2. Name: Quantification and site-specific analysis of co-occupied N- and O-glycopeptides