PXD025805

PXD025805 is an original dataset announced via ProteomeXchange.

Title	Oxonium ion guided analysis of quantitative proteomics data reveals site-specific O-glycosylation of anterior gradient protein 2 (AGR2)
Description	Developments in mass spectrometry (MS)-based analyses of glycoproteins have been important to study changes in glycosylation related to disease. Recently, the characteristic pattern of oxonium ions in glycopeptide fragmentation spectra had been used to assign different sets of glycopeptides. In particular this was helpful to discriminate between O-GalNAc and O-GlcNAc. Here, we thought to investigate how such information can be used to examine quantitiative proteomics data. For this purpose, we used TMT (Tandem Mass Tag)-labeled samples from total cell lysates and secreted proteins from three different colorectal cancer cell lines. Following automated glycopeptide assignment (Byonic) and evaluation of the presence and relative intensity of oxonium ions, we observed that in particular the ratio of the ions at m/z 144.066 and 138.055, respectively, could be used to discriminate between O-GlcNAcylated and O-GalNAcylated peptides, with concomittant relative quantification between the different cell lines. Among the O-GalNAcylated proteins, we also observed anterior gradient protein 2 (AGR2), a protein which glycosylation site and status was hitherto not well documented. Using a combination of multiple fragmentation methods we then not only assigned the site of modification, but also showed different glycosylation between intracellular (ER-resident) and secreted AGR2. Overall, our study shows the potential of broad application of the use of the relative intensities of oxonium ions for the confident assignment of glycopeptides, even in complex proteomics datasets.
HostingRepository	PRIDE
AnnounceDate	2022-02-17
AnnouncementXML	Submission_2022-02-17_03:15:39.967.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yassene Mohammed
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-05 06:49:13	ID requested
⏵ 1	2022-02-17 03:15:40	announced

Pirro M, Mohammed Y, de Ru AH, Janssen GMC, Tjokrodirijo RTN, Maduni, ć K, Wuhrer M, van Veelen PA, Hensbergen PJ, -Glycosylation of Anterior Gradient Protein 2 (AGR2). Int J Mol Sci, 22(10):(2021) [pubmed]

submitter keyword: Glycoproteomics

TMT labeling

oxonium ion

LC−MS/MS

O-glycosylation

colorectal cancer

AGR2

Paul J. Hensbergen
contact affiliation	Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
contact email	P.J.Hensbergen@lumc.nl
lab head
Yassene Mohammed
contact affiliation	LUMC/UVIC
contact email	y.mohammed@lumc.nl
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD025805
     1. Label: PRIDE project
     2. Name: Oxonium ion guided analysis of quantitative proteomics data reveals site-specific O-glycosylation of anterior gradient protein 2 (AGR2)