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PXD045171-1

PXD045171 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleIdentification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized SWATH Proteomics Workflow
DescriptionRheumatoid arthritis (RA) is a systemic autoimmune and inflammatory disease. Plasma biomarkers are critical for understanding disease mechanisms, treatment effects, and diagnosis. Mass spectrometry-based proteomics is a powerful tool for unbiased biomarker discovery. However, plasma proteomics is significantly hampered by signal interference from high-abundance proteins, low overall protein coverage, and high levels of missing data from data-dependent acquisition (DDA). To achieve quantitative proteomic analysis for plasma samples with a balance of throughput, performance, and cost, we developed a workflow incorporating plate-based high abundance protein depletion and sample preparation, comprehensive peptide spectral library building, and data-independent acquisition (DIA) SWATH mass spectrometry-based methodology. In this study, we analyzed plasma samples from both RA patients and healthy donors. The results showed that the new workflow performance exceeded that of the current state-of-the-art depletion-based plasma proteomic platforms in terms of both data quality and proteome coverage. Proteins from biological processes related to the activation of systemic inflammation, suppression of platelet function, and loss of muscle mass were enriched and differentially expressed in RA. Some plasma proteins, particularly acute phase reactant proteins, showed great power to distinguish between RA patients and healthy donors. Moreover, protein isoforms in the plasma were also analyzed, providing even deeper proteome coverage. This workflow can serve as a basis for further application in discovering plasma biomarkers of other diseases.
HostingRepositoryPRIDE
AnnounceDate2023-10-25
AnnouncementXMLSubmission_2023-10-25_13:32:34.070.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLiangJin
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentTripleTOF 6600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02023-09-06 19:44:49ID requested
12023-10-25 13:32:34announced
22023-11-14 07:49:29announced2023-11-14: Updated project metadata.
Publication List
Keyword List
submitter keyword: Rheumatoid arthritis
mass spectrometry
proteomics
SWATH
DIA
plasma
biomarker
protein isoform
Contact List
YuTian
contact affiliationResearch & Development, AbbVie, North Chicago, IL, 60064
contact emailyu.tian@abbvie.com
lab head
LiangJin
contact affiliationAbbVie Bioresearch Center
contact emailliangjin0912@gmail.com
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
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