Journal Article

DKFZ-2025-00318

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Multicenter Longitudinal Quality Assessment of MS-Based Proteomics in Plasma and Serum.

Kardell, O. ; Gronauer, T. ; von Toerne, C. ; Merl-Pham, J. ; König, A.-C. ; Barth, T. K. ; Mergner, J. ; Ludwig, C. ; Tüshaus, J. ; Giesbertz, P. ; Breimann, S. ; Schweizer, L. ; Müller, T.DKFZ* ; Kliewer, G.DKFZ* ; Distler, U. ; Gómez-Zepeda, D.DKFZ* ; Popp, O. ; Qin, D. ; Teupser, D. ; Cox, J. ; Imhof, A. ; Küster, B. ; Lichtenthaler, S. F. ; Krijgsveld, J.DKFZ* ; Tenzer, S. ; Mertins, P. ; Coscia, F. ; Hauck, S. M.

2025
ACS Publications Washington, DC

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Please use a persistent id in citations: doi:10.1021/acs.jproteome.4c00644

Abstract: Advancing MS-based proteomics toward 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 the 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 and 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.

Keyword(s): LC-MS/MS ; R package mpwR ; clinical specimen ; longitudinal round-robin study ; plasma ; serum

Note: HI-TRON / 2025 Mar 7;24(3):1017-1029

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Contributing Institute(s):

1. B230 Proteomik von Stammzellen und Krebs (B230)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2025

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Database coverage:
; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; Essential Science Indicators ; IF < 5 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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