PXD063058-1

PXD063058 is an original dataset announced via ProteomeXchange.

Title	Proteome profiling of cerebrospinal fluid and machine learning reveal biomarkers of two forms of Alzheimer’s disease characterized by increased or not altered levels of tau
Description	Alzheimer's disease (AD) is a progressive neurodegenerative disorder that impairs memory, cognition, behavior, and other cognitive functions. Despite significant advances in understanding its molecular mechanisms, a definitive cure remains elusive. However, some treatments have the potential to slow disease progression if applied before brain damage occurs. Therefore, the identification of reliable biomarkers is critical for early diagnosis of AD and effective intervention. Recent advances in proteomics and the increased accuracy of machine learning algorithms have enhanced biomarker discovery and validation. In this study, we used a newly developed proteomic pipeline to analyse cerebrospinal fluid (CSF) to profile the proteome of AD patients, which included two different subgroups based on their CSF levels of tau. Then, machine learning was used to identify proteins that best classified the two subgroups of AD patients compared to non-AD controls. The resulting model, based on few CSF proteins, demonstrated high accuracy in predicting AD and differentiating patients with elevated or normal CSF tau levels. These protein classifiers, detectable in the preclinical stages of AD, were further validated in silico using larger, publicly available proteomic datasets, confirming their potential as early diagnostic tools.
HostingRepository	PRIDE
AnnounceDate	2025-08-26
AnnouncementXML	Submission_2025-08-25_21:08:36.370.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Margot Lo Pinto
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Astral

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-17 01:38:29	ID requested
⏵ 1	2025-08-25 21:08:37	announced

Scalia E, Calligaris M, Lo Pinto M, Castelbuono S, Iemmolo M, Lo Re V, Bivona G, Piccoli T, Ghersi G, Scilabra SD, Proteome Profiling of Cerebrospinal Fluid and Machine Learning Reveal Protein Classifiers of Two Forms of Alzheimer's Disease Characterized by Increased or Not Altered Levels of Tau. Mol Cell Proteomics, 24(8):101025(2025) [pubmed]

10.1016/j.mcpro.2025.101025;

submitter keyword: Alzherimer’s disease – cerebrospinal fluid – proteomics – machine learning – biomarkers

Simone Dario Scilabra
contact affiliation	Fondazione Ri.MED, Proteomics lab, Palermo
contact email	sdscilabra@fondazionerimed.com
lab head
Margot Lo Pinto
contact affiliation	Fondazione Ri.MED
contact email	mlopinto@fondazionerimed.com
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/2025/08/PXD063058

PRIDE project URI

• PRIDE
  1. PXD063058
     1. Label: PRIDE project
     2. Name: Proteome profiling of cerebrospinal fluid and machine learning reveal biomarkers of two forms of Alzheimer’s disease characterized by increased or not altered levels of tau