PXD054073-1

PXD054073 is an original dataset announced via ProteomeXchange.

Title	Multi-center longitudinal quality assessment of MS-based proteomics in plasma and serum
Description	Advancing MS-based proteomics towards clinical applications evolves around developing standardized start-to-finish and fit-for-purpose workflows for clinical specimens. Steps along the method design involve the determination and optimization of several bioanalytical parameters such as selectivity, sensitivity, accuracy, and precision. In a joint effort eight proteomics laboratories belonging to the MSCoreSys initiative including the CLINSPECT-M, MSTARS, DIASym, and SMART-CARE consortia performed a longitudinal round robin study to assess analysis performance of plasma and serum as clinically relevant samples. A variety of LC-MS/MS setups including mass spectrometer models from ThermoFisher and Bruker, as well as LC systems from ThermoFisher, Evosep, and Waters Corporation were used in this study. As key performance indicators sensitivity, precision and reproducibility were monitored over time. Protein identifications range between 300 to 400 IDs across different state-of-the-art MS instruments, with timsTOF Pro, Orbitrap Exploris 480 and Q Exactive HF-X being among the top performers. Overall, 71 proteins are reproducibly detectable in all setups in both serum and plasma samples and 22 of these proteins are FDA-approved biomarkers, which are reproducibly quantified (CV < 20% with label-free quantification). In total, the round robin study highlights a promising baseline for bringing MS-based measurements of serum and plasma samples closer to clinical utility.
HostingRepository	PRIDE
AnnounceDate	2025-02-14
AnnouncementXML	Submission_2025-02-14_13:23:53.782.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thomas Gronauer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF; timsTOF Pro; Orbitrap Fusion Lumos; Orbitrap Exploris 480; timsTOF Pro 2; Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-19 14:43:46	ID requested
⏵ 1	2025-02-14 13:23:54	announced

10.1021/acs.jproteome.4c00644;

Kardell O, Gronauer T, von Toerne C, Merl-Pham J, K, ö, nig AC, Barth TK, Mergner J, Ludwig C, T, ü, shaus J, Giesbertz P, Breimann S, Schweizer L, M, ü, ller T, Kliewer G, Distler U, Gomez-Zepeda D, Popp O, Qin D, Teupser D, Cox J, Imhof A, K, ü, ster B, Lichtenthaler SF, Krijgsveld J, Tenzer S, Mertins P, Coscia F, Hauck SM, Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum. J Proteome Res, 24(3):1017-1029(2025) [pubmed]

submitter keyword: Plasma, Serum, round robin study, R package mpwR, LC-MS/MS

Dr. Stefanie Hauck
contact affiliation	Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
contact email	stefanie.hauck@helmholtz-munich.de
lab head
Thomas Gronauer
contact affiliation	Metabolomics and Proteomics Core, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
contact email	thomas.gronauer@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/2025/02/PXD054073

PRIDE project URI

• PRIDE
  1. PXD054073
     1. Label: PRIDE project
     2. Name: Multi-center longitudinal quality assessment of MS-based proteomics in plasma and serum