PXD020212

PXD020212 is an original dataset announced via ProteomeXchange.

Title	Proteomic Discovery and Validation of Diagnostic Plasma Biomarkers for Pulmonary Tuberculosis
Description	Despite more than a century fighting against tuberculosis, the World Health Organisation has estimated that around 1.7 million people died of tuberculosis in 2016 and over a quarter of the world’s population is infected. One of the critical hurdles for stopping tuberculosis transmission is early and effective diagnosis of patients with the active pulmonary disease. Although important innovations in molecular diagnosis have been recently developed (e.g. Xpert MTB/RIF, Cepheid Inc., USA), there are no suitable tests for population screening at point-of-care. The current tuberculosis diagnosis pipeline presents a highly variable performance and requires access to reference laboratory facilities. A non-sputum based rapid test with high specificity and sensitivity could save ~400,000 lives per year. Therefore, new biomarkers for diagnosis are urgently required for identifying patients with early symptoms and to expedite treatment. Variable sensitivity and specificity can be overcome using a combination of multiple biomarkers (5). Proteins, as ultimate biological effectors, are ideal candidates for diagnostic biomarkers; consequently, proteomic studies are a crucial platform for biomarker discovery in tuberculosis. This work aims to develop a multi-marker panel for tuberculosis diagnosis with high performance capable of differentiating tuberculosis patients from relevant controls. Quantitative Multidimensional Protein Identification Technology (qMudPIT) is applied for biomarker discovery identifying candidates for early diagnosis of tuberculosis. The multidimensional method optimised in this work led to the identification of 5022 plasma proteins and 3577 quantified proteins using iTRAQ labelling. Known and completely novel markers for active tuberculosis in plasma were identified including a peptide derived from Mycobacterium tuberculosis. Complementary statistical and bioinformatic analysis were applied to prioritise candidates for validation in one or two independent cohorts. The plasma proteomic profile here described represents a power strategy for biomarker discovery and the panel proposed has the potential to be translated to a rapid test and which might contribute to tuberculosis control.
HostingRepository	PRIDE
AnnounceDate	2021-09-09
AnnouncementXML	Submission_2021-09-09_06:06:28.981.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Diana Garay
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	L-cysteine methyl disulfide; iTRAQ8plex-116 reporter+balance reagent acylated residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-06 00:57:28	ID requested
⏵ 1	2021-09-09 06:06:30	announced

Garay-Baquero DJ, White CH, Walker NF, Tebruegge M, Schiff HF, Ugarte-Gil C, Morris-Jones S, Marshall BG, Manousopoulou A, Adamson J, Vallejo AF, Bielecka MK, Wilkinson RJ, Tezera LB, Woelk CH, Garbis SD, Elkington P, Comprehensive plasma proteomic profiling reveals biomarkers for active tuberculosis. JCI Insight, 5(18):(2020) [pubmed]

ProteomeXchange project tag: Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project, Plasma (B/D-HPP)

submitter keyword: Plasma, tuberculosis, shotgun, iTRAQ, biomarkers, hyper-fractionation, WGCNA

Spiro Garbis
contact affiliation	Director | Proteome Exploration Laboratory | Beckman Institute California Institute of Technology Division of Biology and Biological Engineering
contact email	sgarbis@caltech.edu
lab head
Diana Garay
contact affiliation	Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
contact email	djgb1c18@soton.ac.uk
dataset submitter

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/2021/09/PXD020212

PRIDE project URI

• PRIDE
  1. PXD020212
     1. Label: PRIDE project
     2. Name: Proteomic Discovery and Validation of Diagnostic Plasma Biomarkers for Pulmonary Tuberculosis