PXD056465

PXD056465 is an original dataset announced via ProteomeXchange.

Title	Establishment of Minimum Protein Standards for Mycobacterium tuberculosis-Derived Extracellular Vesicles through Comparison of EV Enrichment Methods
Description	Extracellular vesicles (EVs) produced by Mycobacterium tuberculosis, the causative agent of tuberculosis, are involved in acquiring nutrients, evading host immune mechanisms, and modulating the host immune response. The functions of these M. tuberculosis EVs (MEVs)are hypothesized to be due to the dynamic composition of MEVs. However, there are various methods used to purify MEVs, and these methods can impact MEV characteristics such as size, purity, integrity, and composition. In this study, we investigated several methods for MEV purification, including: ultracentrifugation, differential density gradient-based ultracentrifugation, qEV size exclusion chromatography, and Capto(TM)Core size exclusion chromatography. We evaluated the size, concentration, appearance, purity, and protein composition (by mass spectrometry) of MEVs from each of these methods. We ultimately found that protein and particle yield vary across methods and that the size exclusion chromatography-based methods are more technically reproducible than the ultracentrifugation-based methods. Through mass spectrometry analysis, we also identified seven M. tuberculosis proteins that were present regardless of MEV enrichment method, that we propose could be used as qualitative markers of MEVs versus contaminants (in addition to MEV size and appearance criteria), to benefit the reproducibility of ongoing MEV studies.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_03:53:59.714.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kimberly Shelton
SpeciesList	scientific name: Mycobacterium tuberculosis H37Rv; NCBI TaxID: 83332;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-02 14:37:39	ID requested
⏵ 1	2025-05-07 03:54:00	announced

Ryan JM, Shelton K, Dzieciatkowska M, Kruh-Garcia N, Dobos KM, -derived extracellular vesicles through comparison of EV enrichment methods. Mycobacteria, 1(1):3(2025) [pubmed]

10.1186/s44350-025-00003-8;

submitter keyword: proteomics,Mycobacterium tuberculosis, liquid chromatography-mass spectrometry/mass spectrometry, extracellular vesicles, Bruker timsTOF Pro

Karen M Dobos
contact affiliation	Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Colorado, USA
contact email	karen.dobos@colostate.edu
lab head
Kimberly Shelton
contact affiliation	Colorado State University
contact email	kimberly.shelton@colostate.edu
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/2025/05/PXD056465

PRIDE project URI

• PRIDE
  1. PXD056465
     1. Label: PRIDE project
     2. Name: Establishment of Minimum Protein Standards for Mycobacterium tuberculosis-Derived Extracellular Vesicles through Comparison of EV Enrichment Methods