PXD044327

PXD044327 is an original dataset announced via ProteomeXchange.

Title	Proteome and glycoproteome analysis of fibroblasts from patients with congenital disorders of glycosylation
Description	In the biological systems, several genes are involved in protein glycosylation pathway. Congenital Disorders of Glycosylation (CDG) is known to be a multisystem disorder. Pathogenic variants in the glycosylation genes lead to abnormal N- or O-linked glycosylation that causes cellular stress. We used TMT-based N-glycoproteomics and proteomics on different patient-derived CDG and control fibroblasts to characterize the alteration in glycoproteome and proteome. 12 fractions of enriched glycopeptides after size exclusion chromatography (SEC) and 12 fractions after basic reverse phase liquid chromatography (bRPLC) were analyzed by LC-MS/MS for glycoproteomics and proteomics, respectively. A site-specific aberrant glycosylation was observed for several proteins such as mitochondrial, autophagy, extracellular matrix and cell adhesion proteins. By using quantitative proteomics, we observed alteration in abundances of several proteins separated the affected individuals and controls. The glycoproteomics and proteomics analysis in CDG patients provides the potential biomarkers and will increase our general understanding of its pathogenesis.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:08:09.135.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	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-03 09:37:22	ID requested
1	2023-10-24 10:46:59	announced
2	2023-11-14 09:06:38	announced	2023-11-14: Updated project metadata.
⏵ 3	2024-10-22 06:08:11	announced	2024-10-22: Updated project metadata.

10.3390/genes14081585;

Ligezka AN, Budhraja R, Nishiyama Y, Fiesel FC, Preston G, Edmondson A, Ranatunga W, Van Hove JLK, Watzlawik JO, Springer W, Pandey A, Morava E, Kozicz T, Interplay of Impaired Cellular Bioenergetics and Autophagy in PMM2-CDG. Genes (Basel), 14(8):(2023) [pubmed]

submitter keyword: glycosylation, proteomics, glycoproteomics,CDG, fibroblasts

Akhilesh Pandey
contact affiliation	Department of Laboratory Medicine and Pathology Mayo Clinic, Rochester, Minnesota 55905 United States
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

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/2023/10/PXD044327

PRIDE project URI

• PRIDE
  1. PXD044327
     1. Label: PRIDE project
     2. Name: Proteome and glycoproteome analysis of fibroblasts from patients with congenital disorders of glycosylation