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Kardell, O. ; von Toerne, C. ; Merl-Pham, J. ; König, A.-C. ; Blindert, M. ; Barth, T.K.* ; Mergner, J.* ; Ludwig, C.* ; Tüshaus, J.* ; Eckert, S.* ; Müller, S.A.* ; Breimann, S.* ; Giesbertz, P.* ; Bernhardt, A.M.J.* ; Schweizer, L.* ; Albrecht, V.* ; Teupser, D.* ; Imhof, A.* ; Kuster, B.* ; Lichtenthaler, S.F.* ; Mann, M.* ; Cox, J.* ; Hauck, S.M.

Multicenter collaborative study to optimize mass spectrometry workflows of clinical specimens.

J. Proteome Res. 23, 117-129 (2023)

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The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is the development of standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight the common ground in a diverse landscape of different sample preparation techniques and liquid chromatography-mass spectrometry (LC-MS) setups. With the aim to benchmark and improve the current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium, we performed two consecutive round-robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six study partners were provided with two clinically relevant sample matrices: plasma and cerebrospinal fluid (CSF). In the first round, each laboratory applied their current best practice protocol for the respective matrix. Based on the achieved results and following a transparent exchange of all lab-specific protocols within the consortium, each laboratory could advance their methods before measuring the same samples in the second acquisition round. Both time points are compared with respect to identifications (IDs), data completeness, and precision, as well as reproducibility. As a result, the individual performances of participating study centers were improved in the second measurement, emphasizing the effect and importance of the expert-driven exchange of best practices for direct practical improvements.

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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Csf ; Lc–ms ; R Package Mpwr ; Clinical Specimen ; Data-dependent Acquisition ; Data-independent Acquisition ; Interlaboratory ; Intralaboratory ; Mass Spectrometry ; Plasma ; Round-robin Study; Data-independent Acquisition; Proteomics; Quality

ISSN (print) / ISBN 1535-3893

e-ISSN 1535-3907

Journal Journal of Proteome Research

Quellenangaben Volume: 23, Issue: 1, Pages: 117-129

Publisher American Chemical Society (ACS)

Publishing Place 1155 16th St, Nw, Washington, Dc 20036 Usa

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) CF Metabolomics & Proteomics (CF-MPC)

Grants Deutsche Forschungsgemeinschaft(DFG, German Research Foundation)
German Ministry for Science and Education