PXD061710

PXD061710 is an original dataset announced via ProteomeXchange.

Title	Overcoming preservation challenges to enable single-cell proteomics of fixed cell and tissue samples with retained proteome integrity
Description	Recent advances in single-cell proteomics (SCP) now enable the unbiased quantification of the proteome to a depth of several thousand proteins across hundreds of cells. Yet the broader adoption beyond specialised groups remains limited due to the need for specific equipment and expertise. A major challenge in making these analyses more broadly available is sample preservation for transporting biological material to SCP-capable facilities. To address this issue and provide practical solutions, we first evaluated various cell preservation methods from monolayer culture samples, then tested our optimised methodology on both cultured cells and, for the first time, preserved animal tissue from an in vivo mouse model. Our findings highlight the feasibility of SCP analyses in preserved tissues, significantly expanding its current applicability. By optimising upstream processing, our approach enables robust single-cell proteome analysis of both cells and tissues, making SCP more accessible to the wider scientific community. Ultimately, this advancement expands the potential applications of SCP, particularly in disciplines where analysing rare or heterogeneous populations is beneficial.
HostingRepository	PRIDE
AnnounceDate	2025-05-24
AnnouncementXML	Submission_2025-05-23_17:00:48.665.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Agata Makar
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-11 09:53:35	ID requested
⏵ 1	2025-05-23 17:00:49	announced

Dataset with its publication pending

submitter keyword: Human, pancreas, mouse, LC-MS/MS, SCP

Alex von Kriegsheim
contact affiliation	Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XR, United Kingdom.
contact email	alex.vonkriegsheim@ed.ac.uk
lab head
Agata Makar
contact affiliation	University of Edinburgh
contact email	amakar2@ed.ac.uk
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/PXD061710

PRIDE project URI

• PRIDE
  1. PXD061710
     1. Label: PRIDE project
     2. Name: Overcoming preservation challenges to enable single-cell proteomics of fixed cell and tissue samples with retained proteome integrity