PXD053048

PXD053048 is an original dataset announced via ProteomeXchange.

Title	A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research
Description	Recent developments in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)-based proteomics have drastically increased analytical depth and sample throughput, establishing a robust tool for comprehensive system-wide analyses. Such analyses are instrumental in studying the pathophysiology of diseases. One crucial source of material for this is post-mortem individuals. However, there is a significant gap in our understanding of the multi-organ temporal impacts of body decomposition on the proteome. This deficiency compromises result validity due to challenges in controlling the post-mortem interval (PMI). To address this, we reanalyzed published data to compare the effect of the PMI on the proteome alterations to the disease effects. Additionally, we conducted a clinically relevant time-course experiment using isogenic mice and applied LC-MS/MS in data-independent acquisition (DIA) mode to systematically study the proteome alterations post-mortem. Our experiment uncovered dramatic organ-specific protein regulation post-mortem, with only certain aspects attributable to protein autolysis suggesting active post-mortem protein regulation. Notably, the liver and spleen exhibited substantial proteome changes within hours of PMI, while the heart showed comparatively modest changes even after 96 hours. Subcellular fractionation of the heart led to an unexpected surge in the number of proteins exhibiting abundance differences early in PMI. We conducted a compressive analysis of semi-tryptic peptides for the first time, revealing distinct consensus motifs for different organs, indicating organ-specific protease activity. In conclusion, when designing LC-MS/MS-based studies, meticulous consideration of sample collection is crucial as PMI effects may outweigh disease effects. It is preferred that both experimental and control samples are taken in the operation room, especially for studies including subcellular fractionation or trans-organ comparison. In single-organ studies, the planning should involve careful control of the PMI, preferably by sample matching.
HostingRepository	PRIDE
AnnounceDate	2025-01-23
AnnouncementXML	Submission_2025-01-23_09:41:47.453.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Beusch
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-12 11:10:23	ID requested
1	2024-12-17 14:45:19	announced
2	2025-01-23 09:26:41	announced	2025-01-23: Updated project metadata.
⏵ 3	2025-01-23 09:41:48	announced	2025-01-23: Updated project metadata.

10.1038/s42003-025-07515-z;

39824970;

Beusch CM, Braesch-Andersen K, Felldin U, Sabatier P, Widgren A, Bergquist J, Grinnemo KH, Rodin S, A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research. Commun Biol, 8(1):78(2025) [pubmed]

submitter keyword: post-mortem, DIA,proteomics, cadaver

Sergey Rodin
contact affiliation	Cardio-Thoracic Translational Medicine (CTTM) Lab, Department of Surgical Sciences, Uppsala University, 752 37 Uppsala, Sweden
contact email	sergey.rodin@uu.se
lab head
Christian Beusch
contact affiliation	Emory University
contact email	christian.beusch@gmail.com
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/2024/12/PXD053048

PRIDE project URI

• PRIDE
  1. PXD053048
     1. Label: PRIDE project
     2. Name: A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research