PXD070765

PXD070765 is an original dataset announced via ProteomeXchange.

Title	Cross-platform Clinical Proteomics using the Charite Open Standard for Plasma Proteomics (OSPP)
Description	The role of plasma and serum proteomics in characterizing human disease, identifying biomarkers, and advancing diagnostic technologies is rapidly increasing. However, there is an ongoing need to improve proteomic workflows in terms of accuracy, reproducibility, platform transferability, and cost-effectiveness. Here, we present the Charité Open Peptide Standard for Plasma Proteomics (OSPP), a panel of 211 extensively pre-selected, stable-isotope-labeled peptides combined in an open, versatile, and cost-effective internal standard for targeted and untargeted proteomic studies. The selected peptides are well suited for chemical synthesis, and distribute well over the captured analytical dynamic range and chromatographic gradients, and show consistent quantification properties across platforms, in serum, as well as in EDTA-, citrate, and heparin plasma. Quantifying proteins that function in a wide range of biological processes, including several that are routinely used in clinical tests or are targets of FDA-approved drugs, the OSPP quantifies proteins that are important for human disease. On an acute COVID-19 in-patient cohort, we demonstrate the application of the OSPP to i) achieve patient classification and biomarker identification ii) generate comparable quantitative proteomics data with both targeted and untargeted approaches, and iii) estimate peptide quantities for successful cross-platform alignment of proteomic data. The OSPP adds low costs per proteome sample, thus making the use of an internal standard accessible. In addition to the standards, corresponding spectral libraries and optimized acquisition methods for several platforms are made openly available.
HostingRepository	PRIDE
AnnounceDate	2025-12-29
AnnouncementXML	Submission_2025-12-28_18:59:25.907.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ziyue Wang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	ZenoTOF 7600; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-11-14 17:06:29	ID requested
⏵ 1	2025-12-28 18:59:26	announced

Wang Z, Farztdinov V, Sinn LR, Tober-Lau P, Ludwig D, Freiwald A, Amari F, Textoris-Taube K, Niewienda A, Welter AS, Wei AAJ, Luckau L, Kurth F, Selbach M, Hartl J, M, ü, lleder M, Ralser M, open standard for plasma proteomics (OSPP). Nat Commun, 16(1):11377(2025) [pubmed]

10.1038/s41467-025-67264-9;

submitter keyword: LC-MS, DIA, biomarker panel, MRM-HR, precision medicine, internal standard

Markus Ralser
contact affiliation	Charite universitymedicine berlin
contact email	markus.ralser@charite.de
lab head
Ziyue Wang
contact affiliation	Charité – Universitätsmedizin Berlin
contact email	ziyue.wang@charite.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/PXD070765

PRIDE project URI

• PRIDE
  1. PXD070765
     1. Label: PRIDE project
     2. Name: Cross-platform Clinical Proteomics using the Charite Open Standard for Plasma Proteomics (OSPP)