PXD071948

PXD071948 is an original dataset announced via ProteomeXchange.

Title	Label-free mass spectrometry-based proteomics of lung cancer FFPE scrolls
Description	Formalin-fixed, paraffin-embedded (FFPE) is the most common method for preserving tissue material in the clinic with millions of specimens stored in biobanks around the world. However, FFPE samples present challenges for molecular profiling, including proteomics. Nonetheless, optimized sample preparation protocols and next-generation mass spectrometers (MS) enable the analysis of FFPE samples. Here, we analyze 15 FFPE lung cancer specimens, including resected tissue and biopsies using label-free data-independent acquisition (DIA) MS proteomics. We show data from three instruments, including Orbitrap Astral, timsTOF HT, and Orbitrap Exploris. Our analysis shows that label-free proteomics offers rapid, in-depth, reproducible proteome-wide profiling of FFPE tissue samples.
HostingRepository	PRIDE
AnnounceDate	2026-05-26
AnnouncementXML	Submission_2026-05-26_08:15:27.331.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Georgios Mermelekas
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Astral; Orbitrap Exploris 480; timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-13 07:44:46	ID requested
⏵ 1	2026-05-26 08:15:27	announced

Dataset with its publication pending

submitter keyword: DIA,FFPE, label-free proteomics, tumor, lung cancer, LC-MS/MS

Lukas M. Orre
contact affiliation	Department of Oncology-Pathology, SciLifeLab, Karolinska Institutet
contact email	lukas.orre@ki.se
lab head
Georgios Mermelekas
contact affiliation	Karolinska Institutet
contact email	georgios.mermelekas@scilifelab.se
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/2026/05/PXD071948

PRIDE project URI

• PRIDE
  1. PXD071948
     1. Label: PRIDE project
     2. Name: Label-free mass spectrometry-based proteomics of lung cancer FFPE scrolls