Dataset Information

Site-specific N-glycosylation analysis of recombinant FCγ receptor from human and mice.

ABSTRACT: Site-specific glycosylation analysis by nLC-MS/MS of recombinant human FCγ receptor I, III V158 and III 158F, and mouse FCγ receptor I, III and IV.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

SUBMITTER: Kevin Chandler

LAB HEAD: Kevin Brown Chandler

PROVIDER: PXD043966 | Pride | 2024-05-21

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	2023-04-24-m.FCRIV-byspec2_20230425_Byonic.csv	Csv
	2023-04-24-mFcGammaRIV-chymo-gluc-500ng-A.raw	Raw
	2023-04-24-mFcGammaRIV-chymo-gluc-500ng-B.raw	Raw
	2023-04-24-mFcGammaRIV-chymo-gluc-500ng-C.raw	Raw
	2023-04-24-mFcGammaRIV-chymo-gluc-500ng-D.raw	Raw

Items per page:

1 - 5 of 59

Publications

Site-Specific Glycosylation Analysis of Murine and Human Fcγ Receptors Reveals High Heterogeneity at Conserved N-Glycosylation Site.

Pavan Carlos H CH Abdoollah Zaraah Z Marrero Roche Daniel E DE Ryan Holly R HR Moore Erika E Chandler Kevin Brown KB

Journal of proteome research 20240216 3

Fc γ-receptors (FcγRs) on leukocytes bind immunoglobulin G (IgG) immune complexes to mediate effector functions. Dysregulation of FcγR-mediated processes contributes to multiple inflammatory diseases, including rheumatoid arthritis, lupus, and immune thrombocytopenia. Critically, immunoregulatory N-glycan modifications on both FcγRs and IgGs alter FcγR-IgG binding affinity. Rapid methods for the characterization of N-glycans across multiple Fcγ receptors are needed to propel invest ...[more]

PMID: 38363599

Similar Datasets

Project description:Recent advances in software-driven glycopeptide identification in LC-MS/MS-based N-glycoproteomics have facilitated biochemical studies reporting thousands of intact N-glycopeptides, i.e. N-glycan-conjugated peptides, but the automated identification process remains to be scrutinized. Herein, we explore the efficiency of site-specific glycoprofiling using the PTM-centric search-engine Byonic relative to manual expert annotation. To allow an appropriately deep comparison, the study utilised typical glycoproteomics acquisition and data analysis strategies, but of a single glycoprotein, the uncharacterised N-glycosylated (Asn160, Asn268 and Asn302) human basigin. Detailed site-specific reference glycoprofiles of purified basigin were manually established using ion trap CID-MS/MS and high-resolution Q-Exactive Orbitrap HCD-MS/MS acquisition of tryptic N-glycopeptides and released N-glycans. The basigin N-glycosylation sites, which showed extensive micro- and macro-heterogeneity, were then glycoprofiled using Byonic with or without a background of complex peptides using Q-Exactive Orbitrap HCD-MS/MS data. The glycoprofiling efficiencies were assessed against the site-specific reference glycoprofiles and target and decoy proteome databases. The search criteria and confidence thresholds (Byonic scores) recommended by the vendor provided very high glycoprofiling accuracy and coverage (both >80%) and low peptide FDRs (<1%). The data complexity, search parameters including search space (proteome/glycome size), mass tolerance and peptide modifications, and confidence thresholds affected the glycoprofiling efficiency and analysis time. Automated identification of peptide modifications (methionine oxidation/carbamidomethylation) that coincide with monosaccharide mass differences (Fuc/Hex/HexNAc) and accurately distinguishing isobaric (Hex1NeuAc1-R/Fuc1NeuGc1-R) or near-isobaric (NeuAc1-R/Fuc2-R) monosaccharide sub-compositions remain challenging, arguing particular attention to such “difficult-to-identify” N-glycopeptides. The presented analysis provides valuable insights into automated glycopeptide identification; knowledge that facilitates further developments in FDR-based glycoproteomics.

Dataset Information

Site-specific N-glycosylation analysis of recombinant FCγ receptor from human and mice.

Dataset's files

Publications

Site-Specific Glycosylation Analysis of Murine and Human Fcγ Receptors Reveals High Heterogeneity at Conserved <i>N</i>-Glycosylation Site.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets