PXD052071-1

PXD052071 is an original dataset announced via ProteomeXchange.

Title	Poor Quantitative Concordance of Proteomic Data between Autopsy Samples and Fresh Frozen Samples from Human Coronary Arteries
Description	Proteomic analyses of human tissues are sometimes conducted on autopsy samples. However, no comparative analysis between proteomic data derived from autopsy samples and fresh frozen samples has been undertaken, nor has there been an assessment of the post-mortem interval (PMI) influences on protein quantification. In the current study, 94 human left anterior descending (LAD) coronary artery were collected from deceased patients. Proteins were analysed using nanoflow liquid chromatography-tandem mass spectrometry. Data were processed with Proteome Discoverer and Mascot. The correlations between the protein abundances and the PMI were calculated. DAVID software was used for pathway and GO annotation enrichment. Among consistently quantified proteins, approximately 40% of the protein abundances exhibited significant correlations with PMI, most of which being inverse. Notably, smooth muscle cell markers displayed substantial reduction with prolonged PMI. Conversely, positive correlations with PMI were observed for immunoglobulins, coagulation factors, and complement factors, including coagulation factor XII, plasminogen, and lactotransferrin. Comparative analyses of sex differences between autopsy LAD samples and fresh-frozen LAD samples (n=65) showed no concordance in protein quantification. However, a robust correlation was observed within a sex comparison conducted between fresh-frozen carotid endarterectomies (CEA) from 2 different cohorts (n=104 and n=200). This study represents the first large-scale proteomics investigation into the influence of PMI on the protein composition of human vasculature. We observed significant correlations with PMI for nearly 40% of the consistently quantified proteins. Our findings underscore potential discrepancies in the quantitative accuracy of proteomics data derived from autopsy samples. Consequently, results obtained from post-mortem specimens may not be reproducible in fresh-frozen samples.
HostingRepository	PRIDE
AnnounceDate	2025-06-09
AnnouncementXML	Submission_2025-06-09_10:29:59.789.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD052071
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	XIAOKE YIN
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; 1x(18)O labeled deamidated L-asparagine; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2024-05-07 04:01:40	ID requested
⏵ 1	2025-06-09 10:30:00	announced

10.6019/PXD052071;

10.1021/ACS.JPROTEOME.5C00152;

submitter keyword: human coronary arteries, smooth muscle cell, post mortem interval, LC-MS/MS, carotid endarterectomies

Manuel Mayr
contact affiliation	National Heart and Lung Institute, Imperial College London, London, UK
contact email	m.mayr@imperial.ac.uk
lab head
XIAOKE YIN
contact affiliation	National Heart and Lung Institute, Faculty of Medicine, Imperial College London
contact email	xiaoke.yin@imperial.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD052071
     1. Label: PRIDE project
     2. Name: Poor Quantitative Concordance of Proteomic Data between Autopsy Samples and Fresh Frozen Samples from Human Coronary Arteries