PXD071948 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| 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 |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-12-13 07:44:46 | ID requested | |
| ⏵ 1 | 2026-05-26 08:15:27 | announced | |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: DIA,FFPE, label-free proteomics, tumor, lung cancer, LC-MS/MS |
Contact List
| 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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD071948
- Label: PRIDE project
- Name: Label-free mass spectrometry-based proteomics of lung cancer FFPE scrolls
