PXD058960

PXD058960 is an original dataset announced via ProteomeXchange.

Title	Ontology-guided clustering enables proteomic analysis of rare pediatric disorders
Description	The study of rare pediatric disorders is fundamentally limited by small patient numbers, making it challenging to draw meaningful conclusions about their molecular basis. To address this, we developed a framework that integrates clinical ontologies with proteomic profiling, enabling the systematic analysis of rare conditions in aggregate rather than isolation. We demonstrated this approach by analyzing urine and plasma samples from 1,140 children and adolescents, encompassing 394 distinct disease conditions and healthy controls. Using advanced mass spectrometry workflows, we achieved deep proteome coverage with over 5,000 proteins quantified in urine and 900 in plasma. By embedding SNOMED CT clinical terminology in a network structure and connecting it to proteomic data, we could group rare conditions based on their clinical relationships, allowing statistical analysis even for diseases with as few as two patients. This approach revealed molecular signatures across developmental stages and disease clusters while accounting for age- and sex-specific variation. Our framework provides a generalizable solution for studying heterogeneous patient populations where traditional case-control studies are impractical, bridging the gap between clinical classification and molecular profiling of rare diseases.
HostingRepository	PRIDE
AnnounceDate	2025-06-13
AnnouncementXML	Submission_2025-06-13_02:09:56.080.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	2x(13)C; 4x(2)H labeled dimethylated residue; dimethylated residue; iodoacetamide derivatized residue
Instrument	timsTOF HT

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-17 19:44:54	ID requested
⏵ 1	2025-06-13 02:09:56	announced

Dataset with its publication pending

submitter keyword: pediatrics / plasma / proteomics / SNOMED CT / urine

Matthias Mann
contact affiliation	Head of Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.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/2025/06/PXD058960

PRIDE project URI

• PRIDE
  1. PXD058960
     1. Label: PRIDE project
     2. Name: Ontology-guided clustering enables proteomic analysis of rare pediatric disorders