PXD073250 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Democratised single cell proteomics uncovers tumor associated macrophage signature in CYLD cutaneous syndrome skin tumors |
| Description | Single-cell proteomics (SCP) reveals heterogeneity and biological insights inaccessible to bulk analysis. Key limitations are cost, sample loss during processing, and accessibility to state-of-the-art instrumentation. We describe a label free SCP methodology in human tissue, combining fluorescence activated cell sorting (FACS), oil-immersion cell handling, mass-spectrometry, and neural-network derived spectral libraries which aims to improve user uptake. We tested this methodology in a skin tumor syndrome, CYLD cutaneous syndrome (CCS), assessing tumor heterogeneity. Using a Bruker timsTOF HT platform we quantified > 4000 proteins, averaging ~700 per cell, through a cost-effective pipeline without specialised liquid handling infrastructure. By utilising pre-existing bioinformatic tools from the scRNA-seq field we implemented a robust analysis methodology, discriminating between macrophages, dendritic cells and tumor keratinocytes, in an unbiased analysis of 419 CCS tumor cells. We confirmed the biological accuracy of cell annotations by cross referencing with each cell's FACS markers. Furthermore, we identified novel CCS tumor biology in a tumor associated macrophage population with a tumor microenvironment remodelling signature. Our findings demonstrate an accessible SCP technology capable of yielding novel biological discoveries in clinical tissue. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-06-20 |
| AnnouncementXML | Submission_2026-06-20_00:59:11.081.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Joseph Inns |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF HT |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2026-01-19 14:03:47 | ID requested | |
| ⏵ 1 | 2026-06-20 00:59:11 | announced | |
Publication List
Keyword List
| submitter keyword: SCP, skin tumor, CCS, TAM |
Contact List
| Joseph Inns |
|---|
| contact affiliation | Newcastle University translational and clinical research institute United Kingdom |
| contact email | joe.inns.ac@gmail.com |
| lab head | |
| Joseph Inns |
|---|
| contact affiliation | Newcastle University |
| contact email | joe.inns.ac@gmail.com |
| 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/2026/06/PXD073250 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD073250
- Label: PRIDE project
- Name: Democratised single cell proteomics uncovers tumor associated macrophage signature in CYLD cutaneous syndrome skin tumors
