PXD038922-1

PXD038922 is an original dataset announced via ProteomeXchange.

Title	Identification of proteins differentially expressed in atherosclerotic human carotid arteries by label-free proteomics
Description	We present a proteomics dataset that permits the comparison of protein levels in samples obtained from patients by carotid endarterectomies and classified to show complicated lesions and atheromatous plaques, as well in samples from a healthy vasculature. We searched the acquired nanoLC-MS/MS-based shotgun proteomics raw data against a composite human protein sequence database by using MaxQuant and employed label-free quantification. Protein identifications were validated using rigorous criteria, and our statistical analyses based on spectral counts revealed 176 differentially expressed proteins among the study groups. By bioinformatic analyses, many of these proteins implicated acute phase response signaling, liver X receptor/retionid X receptor (LXR/RXR) and farnesoid X receptor/retionid X receptor (FXR/RXR) activation, clathrin-mediated endocytosis and atherosclerosis signaling as top overrepresented canonical pathways. Quantified alteration of protein expressions in the atherosclerosis signaling cascade also confirmed the involvement of macrophages and foam cell formation in the progression towards complicated atheromatous lesions in the atherosclerosis signaling pathway.
HostingRepository	PRIDE
AnnounceDate	2025-01-14
AnnouncementXML	Submission_2025-01-13_23:51:30.127.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD038922
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Gergő Kalló
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2022-12-19 03:36:25	ID requested
⏵ 1	2025-01-13 23:51:30	announced

10.6019/PXD038922;

10.3390/IJMS252413665;

submitter keyword: atherosclerosis, complicated lesion, carotid artery, human, data-dependent LC–MS/MS, quantitative label-free proteomics

Éva Csősz
contact affiliation	Department of Biochemistry and Molecular Biology, Faculty of Meicine, University of Debrecen, Debrecen, Egyetem Ter 1, 4032 Hungary
contact email	cseva@med.unideb.hu
lab head
Gergő Kalló
contact affiliation	University of Debrecen
contact email	kallo.gergo@med.unideb.hu
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/2025/01/PXD038922

PRIDE project URI

• PRIDE
  1. PXD038922
     1. Label: PRIDE project
     2. Name: Identification of proteins differentially expressed in atherosclerotic human carotid arteries by label-free proteomics