PXD042701

PXD042701 is an original dataset announced via ProteomeXchange.

Title	A Combinatorial Enzymatic Approach for Identifying O-glycopeptides
Description	Proteins glycosylation is primarily characterized as N-glycosylation or O-glycosylation. Recognition of the consensus N-glycosylation sequon (N-X-S/T/C) has enabled the mapping of the glycosite occupancy of intact glycopeptides, whereas O-glycosylation consensus sequons do not exit, making the characterization of O-glycosites challenging because of the different degrees of occupancy within a protein. Most O-glycosylation occurs via O-GalNAcylation, which is critical to diverse biological functions. However, only a small fraction of the O-glycosites and their glycan structures have been identified. We introduced a robust and reliable O-glycoproteomic workflow to achieve the long-standing goal of glycobiology—identifying novel O-glycosylation profiles on a large-scale. We developed and implemented a novel O-glycoproteomic workflow through the use of complementary digestion with O-glycoprotease (IMPa), trypsin, Asp-N, and Glu-C for enrichment of O-glycopeptides. The N-terminal of O-glycosylated serine or threonine residues cleaved using IMPa (95% of total PSMs) and over 99% of O-glycopeptides were enriched by the RAX column. Our O-glycoproteomic workflow involving peptide identification (using sceHCD-based MS/MS) and annotation (using FDR evaluation) enabled the identification of O-glycosylation of 189 O-glycosites carrying 379 glycan structures on 79 O-glycoproteins in human plasma. Of the O-glycan forms, 91.7% were distinctively and abundantly observed in core 1 and 2 structures. Importantly, we assessed five well-characterized native proteins purified from human plasma (kininogen-1, fetuin-A, fibrinogen, apolipoprotein E, and plasminogen) to validate the identification of O-glycosites with high confidence and confirm the presence of numerous novel glycosites. We believe that this combinatorial approach is broadly applicable for comprehensive characterization of O-glycoproteomes in biomedical research.
HostingRepository	PRIDE
AnnounceDate	2024-04-25
AnnouncementXML	Submission_2024-04-25_12:45:23.108.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akhilesh Pandey
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-02 14:45:27	ID requested
⏵ 1	2024-04-25 12:45:23	announced

10.1016/J.CRMETH.2024.100744;

submitter keyword: RAX-based enrichment, O-glycosites, O-glycosylation,IMPa, sceHCD-based MS/MS

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology Mayo Clinic, Rochester, Minnesota 55905
contact email	pandey.akhilesh@mayo.edu
lab head
Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905
contact email	pandey.akhilesh@mayo.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD042701
     1. Label: PRIDE project
     2. Name: A Combinatorial Enzymatic Approach for Identifying O-glycopeptides