PXD046829

PXD046829 is an original dataset announced via ProteomeXchange.

Title	Identification of SARS-COV-2 specific antibodies from patient serum during the First Wave of the COVID-19 pandemic
Description	Proteomic Ig-SEQ identification of SARS-COV-2 specific antibodies from serum of two convalescent patients during the first wave of the COVID-19 pandemic. Total IgG was isolated from serum, digested with IdeS protease to generate F(ab)2 fragments, and subjected to antigen affinity chromatography using agarose beads coupled with SARS-COV-2 spike protein. Purified F(ab)2 fragments were reduced, alkylated, and digested with trypsin prior to LC-MSMS analysis on an Orbitrap Fusion Lumos mass spectrometer. Resulting peptide IDs were used to identify IgG clonotypes in antigen-specific and flow-through fractions.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:26:29.706.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD046829
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Daniel Boutz
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-09 15:53:32	ID requested
1	2024-01-26 07:55:32	announced
⏵ 2	2024-10-22 06:26:30	announced	2024-10-22: Updated project metadata.

Goike J, Hsieh CL, Horton AP, Gardner EC, Zhou L, Bartzoka F, Wang N, Javanmardi K, Herbert A, Abbassi S, Xie X, Xia H, Shi PY, Renberg R, Segall-Shapiro TH, Terrace CI, Wu W, Shroff R, Byrom M, Ellington AD, Marcotte EM, Musser JM, Kuchipudi SV, Kapur V, Georgiou G, Weaver SC, Dye JM, Boutz DR, McLellan JS, Gollihar JD, SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode. Commun Biol, 6(1):1250(2023) [pubmed]

10.6019/PXD046829;

10.1038/s42003-023-05649-6;

submitter keyword: IgG, human, Ig-SEQ, serum antibody profiling, SARS-COV-2, Orbitrap Fusion Lumos,LC-MSMS

Jimmy D. Gollihar
contact affiliation	Center for Infectious Diseases Research Department of Pathology and Genomic Medicine Houston Methodist Research Institute USA
contact email	jgollihar2@houstonmethodist.org
lab head
Daniel Boutz
contact affiliation	Houston Methodist Research Institute
contact email	drboutz@houstonmethodist.org
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/2024/01/PXD046829

PRIDE project URI

• PRIDE
  1. PXD046829
     1. Label: PRIDE project
     2. Name: Identification of SARS-COV-2 specific antibodies from patient serum during the First Wave of the COVID-19 pandemic