PXD045171-1

PXD045171 is an original dataset announced via ProteomeXchange.

Title	Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized SWATH Proteomics Workflow
Description	Rheumatoid 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.
HostingRepository	PRIDE
AnnounceDate	2023-10-25
AnnouncementXML	Submission_2023-10-25_13:32:34.070.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	LiangJin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2023-09-06 19:44:49	ID requested
⏵ 1	2023-10-25 13:32:34	announced
2	2023-11-14 07:49:29	announced	2023-11-14: Updated project metadata.

submitter keyword: Rheumatoid arthritis

mass spectrometry

proteomics

SWATH

DIA

plasma

biomarker

protein isoform

YuTian
contact affiliation	Research & Development, AbbVie, North Chicago, IL, 60064
contact email	yu.tian@abbvie.com
lab head
LiangJin
contact affiliation	AbbVie Bioresearch Center
contact email	liangjin0912@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD045171
     1. Label: PRIDE project
     2. Name: Identification of Plasma Biomarkers from Rheumatoid Arthritis Patients Using an Optimized SWATH Proteomics Workflow