PXD053713

PXD053713 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	2024-10-22
AnnouncementXML	Submission_2024-10-22_12:28:23.357.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joann Chongsaritsinsuk
SpeciesList	scientific name: Homo sp.; NCBI TaxID: 2813599;
ModificationList	complex glycosylation; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-06 12:37:23	ID requested
⏵ 1	2024-10-22 12:28:23	announced

10.1101/2024.07.06.602348;

submitter keyword: glycoproteomics, fragmentation, co-occupancy, mucins, O-glycosylation, N-glycosylation

Stacy A.
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. PXD053713
     1. Label: PRIDE project
     2. Name: Quantification and site-specific analysis of co-occupied N- and O-glycopeptides