PXD054819 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | A deep-learning framework reveals whole-body perturbations at cell level |
| Description | Many diseases, such as obesity, have systemic effects that impact multiple organ systems throughout the body. However, tools for comprehensive, high-resolution analysis of disease-associated changes at the whole-body scale have been lacking. Here, we developed a suite of deep learning-based image analysis algorithms (MouseMapper) and integrated it with tissue clearing and light sheet microscopy to enable a comprehensive quantitative analysis of diseases impacting diverse systems across the mouse body. This technological approach enables quantitative analysis of cellular and structural changes across the entire mouse body at unprecedented resolution and scale, including tracking nerves over several centimeters in whole animal bodies. To demonstrate its power, we applied MouseMapper to study nervous and immune systems in chow and high-fat diet (HFD)-induced obese mice. We uncovered widespread changes in both immune cell distribution and nerve structures, including alterations in the trigeminal nerve characterized by reduced nerve endings in obese mice. These structural abnormalities were associated with functional deficits of whiskers that they innervate and proteomic changes in their ganglion, primarily affecting pathways related to axon growth, and the complement system. Additionally, we revealed whole-body inflammation, which showed heterogeneity across different tissues in obese mice. Our study demonstrates MouseMapper's capability to discover and quantify pathological alterations at the whole-body level, offering a powerful new approach for investigating the systemic impacts of various diseases. |
| HostingRepository | PRIDE |
| AnnounceDate | 2026-05-22 |
| AnnouncementXML | Submission_2026-05-22_10:27:00.299.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Ali Erturk |
| SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | timsTOF SCP |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2024-08-12 10:24:44 | ID requested | |
| 1 | 2026-05-06 08:45:42 | announced | |
| ⏵ 2 | 2026-05-22 10:27:00 | announced | 2026-05-22: Updated project metadata. |
Publication List
Keyword List
Contact List
| Prof. Ali Erturk |
|---|
| contact affiliation | Helmholtz Munich |
| contact email | ali.erturk@helmholtz-munich.de |
| lab head | |
| Ali Erturk |
|---|
| contact affiliation | Institute for Tissue Engineering and Regenerative Medicine, Helmholtz Munich |
| contact email | ali.erturk@helmholtz-munich.de |
| 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/PXD054819 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD054819
- Label: PRIDE project
- Name: A deep-learning framework reveals whole-body perturbations at cell level
