PXD071172-1

PXD071172 is an original dataset announced via ProteomeXchange.

Title	Deep Learning and 3D Imaging Reveal Whole-body Alterations in Obesity
Description	Many diseases, such as obesity, have systemic effects that perturb 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 MouseMapper, a suite of foundation model-based deep learning algorithms, to enable a multi-system analysis of disease across the entire mouse body. MouseMapper enables quantitative, graph-based analysis of nerves and immune cells at the whole-body level resolving fine axonal branches and immune cell clusters and automatically segments 31 organs and tissues in the mouse body.  We applied MouseMapper to study high-fat diet-induced obesity, uncovering a significant degeneration of the infraorbital branch of the trigeminal ganglia. This structural damage in infraorbital nerves was associated with functional sensory deficits in whisker sensing. Furthermore, we identified proteomic changes in the trigeminal ganglion affecting axon remodeling and complement pathways both in mouse and human. MouseMapper also generated detailed 3D inflammation maps by characterizing immune cell cluster compositions across tissues. The MouseMapper framework demonstrates robust generalizability across different imaging resolutions and datasets. Our study provides a powerful, scalable approach for discovering and quantifying systemic pathologies, bridging molecular insights from animal models to human conditions.
HostingRepository	PRIDE
AnnounceDate	2026-05-08
AnnouncementXML	Submission_2026-05-08_12:18:31.905.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ali Erturk
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF SCP

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-25 00:25:36	ID requested
⏵ 1	2026-05-08 12:18:33	announced

Dataset with its publication pending

submitter keyword: Human, Brain, Bruker, Mouse, timstofSCP, Obesity, Ganglion

Ali Erturk
contact affiliation	nstitute for Intelligent Biotechnologies, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität LMU, Munich, German School of Medicine, Koç University, İstanbul, Turkey Deep Piction, Munich, Germany
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

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/PXD071172

PRIDE project URI

• PRIDE
  1. PXD071172
     1. Label: PRIDE project
     2. Name: Deep Learning and 3D Imaging Reveal Whole-body Alterations in Obesity