PXD052447-1

PXD052447 is an original dataset announced via ProteomeXchange.

Title	Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome
Description	Protein glycosylation is a highly diverse post-translational modification, modulating key cellular processes such as cell signaling, adhesion and cell-cell interactions. Its deregulation has been associated with various pathologies, including cancer and neurological diseases. Methods capable of quantifying glycosylation dynamics are essential to start unraveling the biological functions of protein glycosylation. Here we present Deep Quantitative Glycoprofiling (DQGlyco), a method that combines high-throughput sample preparation, high-sensitivity detection, and precise multiplexed quantification of protein glycosylation. We used DQGlyco to profile the mouse brain glycoproteome, in which we identify more than 200,000 unique N-glycopeptides - this amounts to 25-fold more glycopeptides identified compared to previous studies. We observed extensive heterogeneity of glycoforms and determined their functional and structural preferences. We used our quantitative approach to map surface-exposed glycoforms as well as to characterize glycosites tissue-specificity. The presence of a defined gut microbiota resulted in extensive remodeling of the brain glycoproteome when compared to that of germ-free animals, exemplifying how the gut microbiome may affect brain protein functions.
HostingRepository	PRIDE
AnnounceDate	2025-02-07
AnnouncementXML	Submission_2025-02-07_11:59:09.194.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Clement Potel
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-21 12:35:43	ID requested
⏵ 1	2025-02-07 11:59:09	announced

10.1038/S41594-025-01485-W;

submitter keyword: glycoproteomics, TMT, microbiome

Mikhail M. Savitski
contact affiliation	EMBL Heidelberg Genome Biology Unit
contact email	mikhail.savitski@embl.de
lab head
Clement Potel
contact affiliation	EMBL
contact email	clement.potel@embl.de
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/2025/02/PXD052447

PRIDE project URI

• PRIDE
  1. PXD052447
     1. Label: PRIDE project
     2. Name: Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome