PXD051070

PXD051070 is an original dataset announced via ProteomeXchange.

Title	Non-depleted human plasma proteome of pulmonary tuberculosis
Description	Novel biomarkers to identify infectious patients transmitting Mycobacterium tuberculosis are urgently needed to control the global tuberculosis (TB) pandemic. We hypothesized that proteins released into the plasma in active pulmonary TB are clinically useful biomarkers to distinguish TB cases from healthy individuals and patients with other respiratory infections. We applied a highly sensitive non-depletion tandem mass spectrometry discovery approach to investigate plasma protein expression in pulmonary TB cases compared to healthy controls in South African and Peruvian cohorts. . Plasma samples were analysed from 11 untreated male patients with active pulmonary TB and 10 male healthy control samples. Each plasma sample was initially separated into four segments by size exclusion chromatography, and each segment was processed individually. Analyses of plasma segments were performed in twelve iTRAQ (isobaric tags for relative and absolute quantification) 8-plex experimental sets in a block randomised design comprising three experimental sets. Each iTRAQ experiment contained a bridging master-pool plasma sample run in every experiment. Healthy controls were matched to TB samples by age, ethnicity, and smoking status within each iTRAQ set. Protein abundances from the plasma segments and multi-consensus reports were combined and adjusted for experimental batch effects. Protein abundances from the remaining combined plasma segment proteomes between experimental sets and the combined multi-consensus proteomes were analysed by complementary bioinformatic approaches to identify candidate diagnostic protein biomarkers. In total, 4,696 protein identifications were made across all iTRAQ experiments, at 5% FDR (false discovery rate). This comprised 2,332 unique host-derived proteins and 22 Mtb-derived proteins. Of these, 594 host proteins had a quantification result for every sample analysed and therefore comprised the complete quantified proteome. Subsequent bioinformatic analysis identified 118 differentially expressed proteins by three complementary bioinformatic pipelines and were taken forward in subsequent validation work as strong candidate biomarkers of pulmonary TB.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:46:44.221.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hannah Schiff
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Fusion; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-28 11:03:05	ID requested
1	2024-06-22 13:16:26	announced
⏵ 2	2024-10-22 06:46:45	announced	2024-10-22: Updated project metadata.

Schiff HF, Walker NF, Ugarte-Gil C, Tebruegge M, Manousopoulou A, Garbis SD, Mansour S, Wong PHM, Rockett G, Piazza P, Niranjan M, Vallejo AF, Woelk CH, Wilkinson RJ, Tezera LB, Garay-Baquero D, Elkington P, Integrated plasma proteomics identifies tuberculosis-specific diagnostic biomarkers. JCI Insight, 9(8):(2024) [pubmed]

10.1172/jci.insight.173273;

submitter keyword: Human, Tuberculosis, Plasma, Biomarkers

Spiros Garbis
contact affiliation	Proteas Bioanalytics, The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA, USA
contact email	s.d.garbis@proteas-bioanalytics.com
lab head
Hannah Schiff
contact affiliation	University of Southampton
contact email	h.schiff@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/2024/06/PXD051070

PRIDE project URI

• PRIDE
  1. PXD051070
     1. Label: PRIDE project
     2. Name: Non-depleted human plasma proteome of pulmonary tuberculosis