PXD030598

PXD030598 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2021-12-22 02:41:49	ID requested
⏵ 1	2022-04-03 23:11:57	announced

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]

submitter keyword: SWATH-MAS, Rheumatic Heart Disease, protein signature, inflammation

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

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PRIDE project URI

• PRIDE
  1. PXD030598
     1. Label: PRIDE project
     2. Name: Data independent acquisition mass spectrometry in severe Rheumatic Heart Disease (RHD) identifies a proteomic signature showing ongoing inflammation and effectively classifying RHD cases.