PXD034364

PXD034364 is an original dataset announced via ProteomeXchange.

Title	N-glycoproteomics and proteomics in NGLY1 deficient patient-derived dermal fibroblasts
Description	In the biological systems, several genes are involved in protein glycosylation and deglycosylation pathways. Congenital disorders of deglycosylation (CDDG) are a set of disorders which occur due to the defect in genes involved in deglycosylation pathways. The only known CDDG so far is the defect in N-glycanase 1 (NGLY1), which primary function is to cleave the N-glycans from misfolded proteins prior to their proteasomal degradation. We used TMT-based N-glycoproteomics and proteomics on patient derived NGLY1 deficient and control fibroblasts to characterize the alteration in glycoproteome and proteome. 24 fractions of enriched glycopeptides after size exclusion chromatography (SEC) and 24 fractions after basic reverse phase liquid chromatography (bRPLC) were analyzed by LC-MS/MS for glycoproteomics and proteomics, respectively. We identified a total of 3,255 N-glycopeptides which were quantified on 550 glycosylation sites of 407 glycoproteins. A site specific aberrant glycosylation was observed for several extracellular matrix and cell adhesion proteins. By using quantitative proteomics, we detected 8,041 proteins. The alteration in expression of several proteins separated the affected individuals and controls. This is the first glycoproteomic study in patient derived NGLY1-CDDG fibroblasts. The glycoproteomics and proteomics analysis in NGLY1-CDDG provides the potential biomarkers and will increase our general understanding of its pathogenesis.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:46:05.400.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	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-06 03:09:51	ID requested
1	2023-05-10 09:39:28	announced
⏵ 2	2023-11-14 08:46:13	announced	2023-11-14: Updated project metadata.

Budhraja R, Saraswat M, De Graef D, Ranatunga W, Ramarajan MG, Mousa J, Kozicz T, Pandey A, Morava E, N-glycoproteomics reveals distinct glycosylation alterations in NGLY1-deficient patient-derived dermal fibroblasts. J Inherit Metab Dis, 46(1):76-91(2023) [pubmed]

submitter keyword: proteomics, Fibroblasts, Human, glycoproteomics, mass spectrometry,NGLY1, congenital disorder of glycosylation, congenital disorder of deglycosylation

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

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PRIDE project URI

• PRIDE
  1. PXD034364
     1. Label: PRIDE project
     2. Name: N-glycoproteomics and proteomics in NGLY1 deficient patient-derived dermal fibroblasts