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PXD003051

PXD003051 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIdentification of In Vivo HLA-DR-Presented Self-Peptides (T Cell Epitopes) in Synovial Tissue, Synovial Fluid and Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis
DescriptionHLA-DR molecules are highly expressed in synovial tissue (ST), the target of the immune response in chronic inflammatory arthritides, including in rheumatoid arthritis (RA) and Lyme arthritis (LA). In the current study, we identified HLA-DR-presented self-peptides (T cell epitopes) in ST, synovial fluid mononuclear cells (SF), and peripheral blood mononuclear cells (PB) from five patients with RA and eight with LA. Altogether, from 22 samples, 1,532 non-redundant HLA-DR-presented peptides were identified that were derived from 778 source proteins. Moreover, as the study progressed, application of newer, high sensitivity LC-MS instruments resulted in the identification of larger numbers of HLA-DR-presented peptides. Surprisingly, the source proteins for HLA-DR-presented peptides were as likely to have intracellular as extracellular locations. Although the number of peptides identified was greater in ST than in SF or PB, 68% of the peptides identified in SF were found in ST, and 55% of the peptides in PB were found in ST. Two RA patients had the same HLA-DR genotype (DRB1*0401 and 0101), and 44% of the peptides identified in these two patients were the same. In contrast, among the patients with RA or LA who had no shared HLA-DR alleles, only 6% of the peptides were the same. In the RA patients, HLA-DR-presented peptides were identified from source proteins that are thought to serve as potential autoantigens: collagen, enolase, fibrinogen, fibronectin, immunoglobulin and vimentin. Interestingly, peptides from these same source proteins were also commonly found in LA patients. However, citrullinated T cell epitopes were not identified in any patient. Thus, LC-MS/MS techniques are now sensitive enough to identify large numbers of T cell epitopes from tissue or fluids in individual patients. Importantly, analysis of SF or PB allowed us to identify a broader range of HLA-DR-presented self-peptides from individual patients and from patients seen earlier in the disease.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_04:25:34.965.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterQi Wang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList2-pyrrolidone-5-carboxylic acid (Glu); cysteinylation (disulfide with free L-cysteine); monohydroxylated residue; L-citrulline; deamidated residue
InstrumentQ Exactive; LTQ Orbitrap; 6520A Quadrupole Time-of-Flight LC/MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02015-10-14 01:36:10ID requested
12016-10-13 06:30:03announced
22017-06-06 00:30:30announcedUpdated project metadata.
32017-10-24 01:54:19announcedUpdated project metadata.
42024-10-22 04:25:37announced2024-10-22: Updated project metadata.
Publication List
Wang Q, Drouin EE, Yao C, Zhang J, Huang Y, Leon DR, Steere AC, Costello CE, Immunogenic HLA-DR-Presented Self-Peptides Identified Directly from Clinical Samples of Synovial Tissue, Synovial Fluid, or Peripheral Blood in Patients with Rheumatoid Arthritis or Lyme Arthritis. J Proteome Res, 16(1):122-136(2017) [pubmed]
Keyword List
ProteomeXchange project tag: Human Immuno-Peptidome Project (HUPO-HIPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project
curator keyword: Biomedical
submitter keyword: synovial tissue, synovial fluid,human, peripheral blood, LC-MS/MS
Contact List
Catherine E. Costello
contact affiliationCenter for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine
contact emailcecmsms@bu.edu
lab head
Qi Wang
contact affiliationBoston University
contact emailqwang616@bu.edu
dataset submitter
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