PXD063283-1

PXD063283 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometric analysis of Rheumatoid factor
Description	Rheumatoid factor are autoantibodies that are found in +/- two thirds of patients with rheumatoid arthritis, a chronic autoimmune disease characterized by inflamed, swollen joints. They consist of polyclonal antibodies that target the Fc part of IgG. The antibodies are not highly specific for rheumatoid arthritis and clinical assays to measure rheumatoid factor are poorly harmonized. We studied rheumatoid factor using a mass-spectrometry-based approach in seropositive, seronegative rheumatoid arthritis patients and in disease controls. Rheumatoid factor was captured on Fc coated microwell plates, isolated, digested into peptides and analyzed by liquid chromatography tandem mass spectrometry. Principal component analysis and sparse partial least squares discriminant analysis showed that peptides derived from seropositive rheumatoid arthritis patients clustered away from the controls. Mass spectrometry analysis revealed framework region-derived and variable region-derived peptides that were enriched in rheumatoid factor positive sera. However, mass spectrometry de novo sequencing failed to sequence the majority of unidentified peptides. Furthermore, mass spectrometry analysis revealed different rheumatoid factor isotypes. In addition to IgM, also IgA and IgG isotypes were observed. In conclusion, mass spectrometry is able to capture the complexity and isotypes of rheumatoid factor autoantibodies, but advances in de novo sequencing are needed to fully characterize the variable part of the antibodies.
HostingRepository	PRIDE
AnnounceDate	2025-10-08
AnnouncementXML	Submission_2025-10-08_10:24:36.121.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD063283
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jonas De Leeuw
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-24 06:25:56	ID requested
⏵ 1	2025-10-08 10:24:36	announced

10.3389/FIMMU.2025.1644334;

10.6019/PXD063283;

ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP) (B/D-HPP), Antibodies (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: LC-MS/MS, immunoglobulins, rheumatoid factor, complementarity determining regions, isotypes

Xavier Bossuyt
contact affiliation	Laboratory Medicine, UZ Leuven Hospitals, Belgium Principal investigator of the lab of Clinical and Diagnostic Immunology at KU Leuven
contact email	xavier.bossuyt@uzleuven.be
lab head
Jonas De Leeuw
contact affiliation	KU Leuven
contact email	jonas.deleeuw1@kuleuven.be
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD063283
     1. Label: PRIDE project
     2. Name: Mass spectrometric analysis of Rheumatoid factor