PXD029644-1

PXD029644 is an original dataset announced via ProteomeXchange.

Title	C18 nanoLC-MS and Glycogenomics to Facilitate O-Glycan profiling in Human Cells
Description	O-glycosylation is an abundant modification throughout the human proteome and plays a role in, amongst others, regulation of protein cleavage, protein folding, and modulation of cell-cell and -matrix interactions. O-glycosylation type and structure are important for biological function, demanding analytical methodologies that facilitate the annotation of O-glycans in biological material. While various successful strategies for the in-depth profiling of released O-glycans have been reported, these methods are often limitedly accessible to the non-specialist and/or challenged by the high abundance of O-glycan structural isomers. Here, we developed a high-throughput sample preparation approach for the non-reductive release of O-glycans from human cell material. Reducing-end labeling allowed efficient isomer separation and detection using C18 nano-liquid chromatography coupled to Orbitrap mass spectrometry (nanoLC-MS/MS). The implementation of glycogenetically engineered cell material proved a way into the complex structural annotation of O-glycan types and isomers. Using human keratinocytes as model system, we found a wide variety of O-glycan structures, including O-fucose, O-glucose, O-GlcNAc and O-GalNAc glycosylation, with the latter carrying both elongate Core 1 and Core 2 structures and varying numbers of fucoses and sialic acids. The method, including the now well characterized standards, provide the opportunity to study glycomic changes in human tissue and disease models using rather mainstream analytical equipment.
HostingRepository	PRIDE
AnnounceDate	2022-05-25
AnnouncementXML	Submission_2022-05-25_09:29:25.675.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Noortje de Haan
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	complex glycosylation
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-10 07:32:22	ID requested
⏵ 1	2022-05-25 09:29:27	announced

de Haan N, Narimatsu Y, Koed M, ø, ller Aasted M, Larsen ISB, Marinova IN, Dabelsteen S, Vakhrushev SY, Wandall HH, -Glycan Isomers in Human Cells Using C18 Nanoliquid Chromatography-Mass Spectrometry and Glycogenomics. Anal Chem, 94(10):4343-4351(2022) [pubmed]

submitter keyword: Glycomics, O-Glycan, Keratinocytes, HEK293, Glycogenomics

Hans Wandall
contact affiliation	University of Copenhagen, Copenhagen Center for Glycomics
contact email	hhw@sund.ku.dk
lab head
Noortje de Haan
contact affiliation	Copenhagen center for Glycomics, University of Copenhagen
contact email	ndehaan@sund.ku.dk
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/04/PXD029644

PRIDE project URI

• PRIDE
  1. PXD029644
     1. Label: PRIDE project
     2. Name: C18 nanoLC-MS and Glycogenomics to Facilitate O-Glycan profiling in Human Cells