PXD064513

PXD064513 is an original dataset announced via ProteomeXchange.

Title	Large scale cerebrospinal fluid proteomics reveals biomarkers of Multiple Sclerosis
Description	Cerebrospinal fluid (CSF) plays critical roles in clinical diagnostics, offers a window into neuropathological mechanisms and is available at scale. To enable its large-scale proteomics characterization, we developed a high-throughput mass spectrometry-based workflow based on the Orbitrap Astral. This workflow quantifies about 2100 proteins per sample at a throughput of 100 samples per day. We measured 2600 CSF samples across a discovery and replication cohort from patients with multiple sclerosis and related inflammatory CNS conditions as well as neurological controls. Analysis of CSF proteomes yielded a panel of 29 protein biomarkers to identify MS with better diagnostic performance than established clinical CSF markers (QIgG, QAlb, leukocyte count) amongst patients presenting with MS-like symptoms but without CSF-specific oligoclonal bands. To verify this biomarker panel and provide an assay format compatible with routine diagnostics, we have built a targeted assay on the Stellar mass spectrometer. With this assay, we have remeasured the discovery and replication cohort, confirming the diagnostic performance. This repository entry pertains to the targeted assay data only, the discovery proteomics data is deposited separately, see methods section of the publication.
HostingRepository	PRIDE
AnnounceDate	2025-12-10
AnnouncementXML	Submission_2025-12-10_10:09:30.074.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: NEWT:9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Stellar

Revision	Datetime	Status	ChangeLog Entry
0	2025-06-02 07:13:59	ID requested
⏵ 1	2025-12-10 10:09:30	announced

Dataset with its publication pending

submitter keyword: Multiple Sclerosis, body fluids,CSF, Stellar, biomarkers, targeted mass spectrometry

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
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/2025/12/PXD064513

PRIDE project URI

• PRIDE
  1. PXD064513
     1. Label: PRIDE project
     2. Name: Large scale cerebrospinal fluid proteomics reveals biomarkers of Multiple Sclerosis