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PXD030598

PXD030598 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleData independent acquisition mass spectrometry in severe Rheumatic Heart Disease (RHD) identifies a proteomic signature showing ongoing inflammation and effectively classifying RHD cases.
DescriptionRheumatic 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.
HostingRepositoryPRIDE
AnnounceDate2022-04-04
AnnouncementXMLSubmission_2022-04-03_23:11:56.767.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterjing yang
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListNo PTMs are included in the dataset
InstrumentTripleTOF 6600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-12-22 02:41:49ID requested
12022-04-03 23:11:57announced
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 affiliationDepartment of Medicine, University of Cape Town & Groote Schuur Hospital, Cape Town, South Africa
contact emailmark.engel@uct.ac.za
lab head
jing yang
contact affiliationThe University of Manchester
contact emailynnjing@gmail.com
dataset submitter
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Dataset FTP location
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