PXD056909

PXD056909 is an original dataset announced via ProteomeXchange.

Title	Identification and label-free quantification of proteins in atherosclerotic human carotid arteries by nanoLC-MS/MS-based shotgun proteomics using data-independent acquisition
Description	We present a proteomics dataset relying on nanoLC-MS/MS-based shotgun proteomics and using data-independent acquisitions on an Orbitrap hybrid instrument to enable comparisons of protein levels in human carotid endarterectomies with atheromatous plaques, complicated lesions, and healthy vasculature. Study approval, as well as collection and selection of study specimens were described in our previous publication (https://doi.org/https://doi.org/10.1089/ars.2020.8234). Briefly, atherosclerotic samples were obtained from patients by carotid endarterectomies, and healthy carotid arteries (H) were harvested from cadavers of suicide or fatal trauma victims without cardiovascular diseases. All samples were classified by a pathologist according to guidelines by the American Heart Association as atheromatous (A), having complicated lesions (C) and were identical with those having met specified study criteria and included in high-throughput global transcriptomic analyses by RNA-seq earlier. Specifically, inclusion criteria were as follows: samples received within 1 h after endarterectomy, no RNA and protein degradation occurred, blood clot in the artery was absent, and collection of samples was done appropriately. This is a follow up proteomics dataset that used the same samples and the same sample processing protocol but relied on data-dependent acquisition (dataset identifier PXD038922, doi:10.6019/PXD038922). For further comparison, RNA-seq data are also available in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database under the accession number PRJNA594843.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-07_03:58:28.932.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laszlo Prokai
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-17 07:32:06	ID requested
⏵ 1	2025-05-07 03:58:29	announced

Kall, ó G, Zaman K, Potor L, Hendrik Z, M, é, hes G, T, ó, th C, Gergely P, T, ő, zs, é, r J, Balla G, Balla J, Prokai L, Cs, ő, sz É, Identification of Protein Networks and Biological Pathways Driving the Progression of Atherosclerosis in Human Carotid Arteries Through Mass Spectrometry-Based Proteomics. Int J Mol Sci, 25(24):(2024) [pubmed]

10.3390/ijms252413665;

submitter keyword: atherosclerosis

complicated lesion

human carotid artery

data-independent LC–MS/MS

quantitative label-free proteomics

Dr Éva Csősz
contact affiliation	Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Egyetem Ter 1, 4032 Hungary
contact email	cseva@med.unideb.hu
lab head
Laszlo Prokai
contact affiliation	Department of Pharmacology & Neuroscience UNT Health Science Center Fort Worth, TX, USA
contact email	advancedms@unthsc.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/PXD056909

PRIDE project URI

• PRIDE
  1. PXD056909
     1. Label: PRIDE project
     2. Name: Identification and label-free quantification of proteins in atherosclerotic human carotid arteries by nanoLC-MS/MS-based shotgun proteomics using data-independent acquisition