PXD030598
PXD030598 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Data independent acquisition mass spectrometry in severe Rheumatic Heart Disease (RHD) identifies a proteomic signature showing ongoing inflammation and effectively classifying RHD cases. |
Description | Rheumatic heart disease (RHD) remains a major source of morbidity and mortality in developing countries. A deeper insight into the pathogenetic mechanisms underlying RHD could provide opportunities for drug repurposing, guide recommendations for secondary penicillin prophylaxis, and/or inform development of near-patient diagnostics. We performed quantitative proteomics using Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectrometry (SWATH-MS) to screen protein expression in 215 African patients with severe RHD, and 230 controls. A machine learning (ML) approach was applied to feature selection among the 366 proteins quantifiable in at least 40% of samples, using the Boruta wrapper algorithm. The case-control differences and contribution to AUC of the ROC for each of the 56 proteins identified by the Boruta algorithm were calculated by Logistic Regression adjusted for age, sex and BMI. Adiponectin, complement component C7 and fibulin-1, a component of heart valve matrix, were each higher in cases when compared with controls. Ficolin-3, a protein with calcium-independent lectin activity that activates the complement pathway, was lower in cases than controls. The top six biomarkers from the Boruta analyses conferred an AUC of 0.90 indicating excellent discriminatory capacity between RHD cases and controls. |
HostingRepository | PRIDE |
AnnounceDate | 2022-04-04 |
AnnouncementXML | Submission_2022-04-03_23:11:56.767.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | jing yang |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | TripleTOF 6600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2021-12-22 02:41:49 | ID requested | |
⏵ 1 | 2022-04-03 23:11:57 | announced |
Publication List
Salie MT, Yang J, Ram, í, rez Medina CR, Z, ü, hlke LJ, Chishala C, Ntsekhe M, Gitura B, Ogendo S, Okello E, Lwabi P, Musuku J, Mtaja A, Hugo-Hamman C, El-Sayed A, Damasceno A, Mocumbi A, Bode-Thomas F, Yilgwan C, Amusa GA, Nkereuwem E, Shaboodien G, Da Silva R, Lee DCH, Frain S, Geifman N, Whetton AD, Keavney B, Engel ME, Data-independent acquisition mass spectrometry in severe rheumatic heart disease (RHD) identifies a proteomic signature showing ongoing inflammation and effectively classifying RHD cases. Clin Proteomics, 19(1):7(2022) [pubmed] |
Keyword List
submitter keyword: SWATH-MAS, Rheumatic Heart Disease, protein signature, inflammation |
Contact List
Mark Engel | |
---|---|
contact affiliation | Department of Medicine, University of Cape Town & Groote Schuur Hospital, Cape Town, South Africa |
contact email | mark.engel@uct.ac.za |
lab head | |
jing yang | |
contact affiliation | The University of Manchester |
contact email | ynnjing@gmail.com |
dataset submitter |
Full Dataset Link List
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/2022/04/PXD030598 |
PRIDE project URI |
Repository Record List
[ + ]