PXD060030

PXD060030 is an original dataset announced via ProteomeXchange.

Title	Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data Independent Acquisition
Description	Oxidative damage is critical in various diseases, including cardiovascular and neurological conditions. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure and function. Redox proteomics based on differential alkylation of reduced and oxidized Cys forms using mass spectrometry enables comprehensive analysis of thiol redox status in cells and tissues. We introduce PACREDOX, an innovative redox proteomics approach based on the Protein Aggregation Capture (PAC) protocol and we demonstrate its compatibility with library free data-independent acquisition (DIA). PACREDOX reduces preparation time and costs compared to traditional methods, such as FASILOX, while maintaining thiol and proteome coverage. To enable library-free DIA, we corrected in silico spectral libraries in DIA-NN using experimental retention time data from beta-methylthiol-modified peptides. PACREDOX with DIA quantified 4,000 protein groups and ~45,000 modified peptides in myocardial tissue from a porcine model of atrial fibrillation, including over 8,000 cysteine-containing peptides, 30% of which were reversibly oxidized. Benchmarking PACREDOX and DIA against FASILOX in a myocardial infarction model reflects the potential and efficiency of this methodology to study oxidative damage. Overall, PACREDOX offers a high-throughput, cost-effective strategy for thiol redox proteome analysis, compatible with label-free quantitative workflows.
HostingRepository	PRIDE
AnnounceDate	2025-09-08
AnnouncementXML	Submission_2025-09-08_06:31:36.259.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ana Martinez del Val
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-21 12:13:18	ID requested
⏵ 1	2025-09-08 06:31:36	announced

10.1021/ACS.ANALCHEM.5C03294;

submitter keyword: myocardial tissue, proteomics, DIA,Redox, ischemia-reperfusion, atrial fibrillation

Jesús Vázquez
contact affiliation	Full Professor Cardiovascular Proteomics Laboratory & Proteomics Unit Vascular Pathophysiology Area Centro Nacional de Investigaciones Cardiovasculares Melchor Fernández Almagro núm. 3 28029 Madrid
contact email	jesus.vazquez@cnic.es
lab head
Ana Martinez del Val
contact affiliation	Centro Nacional de Investigaciones Cardiovasculares - CNIC
contact email	ana.martinezdelval@cnic.es
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/2025/09/PXD060030

PRIDE project URI

• PRIDE
  1. PXD060030
     1. Label: PRIDE project
     2. Name: Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data Independent Acquisition