PXD005021-2

PXD005021 is an original dataset announced via ProteomeXchange.

Title	Human immunoglobulin heavy gamma chain polymorphisms: molecular confirmation of proteomic assessment
Description	Immunoglobulin G (IgG) proteins are known for the huge diversity of the variable domains of their heavy and light chains, aimed at protecting each individual against foreign antigens. The IgG also harbor specific polymorphism concentrated in the CH2 and CH3-CHS constant regions located on the Fc fragment of their heavy chains. But this individual particularity relies only on a few amino acids among which some could make accurate sequence determination a challenge for mass spectrometry-based techniques. The purpose of the study was to bring a molecular validation of proteomic results by the sequencing of encoding DNA fragments. It was performed using ten individual samples (DNA and sera) selected on the basis of their Gm (gamma marker) allotype polymorphism in order to cover the main immunoglobulin heavy gamma (IGHG) gene diversity. Gm allotypes, reflecting part of this diversity, were determined by a serological method. On its side, the IGH locus comprises four functional IGHG genes totalizing 34 alleles and encoding the four IgG subclasses. The genomic study focused on the nucleotide polymorphism of the CH2 and CH3-CHS exons and of the intron. Despite strong sequence identity, four pairs of specific gene amplification primers could be designed. Additional primers were identified to perform the subsequent sequencing. The nucleotide sequences obtained were first assigned to a specific IGHG gene, and then IGHG alleles were deduced using a home-made decision tree reading of the nucleotide sequences. IGHG amino acid (AA) alleles were determined by mass spectrometry. Identical results were found at 95% between alleles identified by proteomics and those deduced from genomics. These results validate the proteomic approach which could be used for diagnostic purposes, namely for a mother-and-child differential IGHG detection in a context of suspicion of congenital infection.
HostingRepository	PRIDE
AnnounceDate	2017-03-14
AnnouncementXML	Submission_2017-03-14_02:17:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	François GUILLONNEAU
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-09-22 05:57:19	ID requested
1	2017-03-13 02:32:11	announced
⏵ 2	2017-03-14 02:17:02	announced	Updated project metadata.
3	2017-10-24 04:05:04	announced	Updated project metadata.
4	2024-10-22 04:32:57	announced	2024-10-22: Updated project metadata.

Dambrun M, Dechavanne C, Emmanuel A, Aussenac F, Leduc M, Giangrande C, Vinh J, Dugoujon JM, Lefranc MP, Guillonneau F, Migot-Nabias F, Human Immunoglobulin Heavy Gamma Chain Polymorphisms: Molecular Confirmation Of Proteomic Assessment. Mol Cell Proteomics, 16(5):824-839(2017) [pubmed]

curator keyword: Biomedical, Biological

submitter keyword: Allotype, allele, IgG, Fc fragment, IGHG, IMGT, mass spectrometry, newborn, parasitic infection, serological diagnosis

Florence MIGOT-NABIAS
contact affiliation	UMR 216 “Mère et enfant face aux infections tropicales” Institut de Recherche pour le Développement / Université Paris Descartes, Faculté de Pharmacie, Paris, France.
contact email	florence.migot-nabias@ird.fr
lab head
François GUILLONNEAU
contact affiliation	3P5 Université Paris Descartes
contact email	francois.guillonneau@parisdescartes.fr
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/2017/03/PXD005021

PRIDE project URI

• PRIDE
  1. PXD005021
     1. Label: PRIDE project
     2. Name: Human immunoglobulin heavy gamma chain polymorphisms: molecular confirmation of proteomic assessment