A multiyear longitudinal harmonization study of quality controls in mass spectrometry proteomics core facilities

Chiva, Cristina; Olivella, Roger; Staes, An; Mendes Maja, Teresa; Panse, Christian; Stejskal, Karel; Douché, Thibaut; Lombard, Bérangère; Schuhmann, Andrea; Loew, Damarys; Mechtler, Karl; Matondo, Mariette; Rettel, Mandy; Helm, Dominic; Impens, Francis; Devos, Simon; Shevchenko, Anna; Nanni, Paolo; Sabidó Aguadé, Eduard, 1981-

A multiyear longitudinal harmonization study of quality controls in mass spectrometry proteomics core facilities

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dc.contributor.author Chiva, Cristina
dc.contributor.author Olivella, Roger
dc.contributor.author Staes, An
dc.contributor.author Mendes Maja, Teresa
dc.contributor.author Panse, Christian
dc.contributor.author Stejskal, Karel
dc.contributor.author Douché, Thibaut
dc.contributor.author Lombard, Bérangère
dc.contributor.author Schuhmann, Andrea
dc.contributor.author Loew, Damarys
dc.contributor.author Mechtler, Karl
dc.contributor.author Matondo, Mariette
dc.contributor.author Rettel, Mandy
dc.contributor.author Helm, Dominic
dc.contributor.author Impens, Francis
dc.contributor.author Devos, Simon
dc.contributor.author Shevchenko, Anna
dc.contributor.author Nanni, Paolo
dc.contributor.author Sabidó Aguadé, Eduard, 1981-
dc.date.accessioned 2025-03-25T07:25:27Z
dc.date.available 2025-03-25T07:25:27Z
dc.date.issued 2025
dc.description.abstract Quality control procedures play a pivotal role in ensuring the reliability and consistency of data generated in mass spectrometry-based proteomics laboratories. However, the lack of standardized quality control practices across laboratories poses challenges for data comparability and reproducibility. In response, we conducted a harmonization study within proteomics laboratories of the Core for Life alliance with the aim of establishing a common quality control framework, which facilitates comprehensive quality assessment and identification of potential sources of performance drift. Through collaborative efforts, we developed a consensus quality control standard for longitudinal assessment and adopted common processing software. We generated a 4-year longitudinal data set from multiple instruments and laboratories, which enabled us to assess intra- and interlaboratory variability, to identify causes of performance drift, and to establish community reference values for several quality control parameters. Our study enhances data comparability and reliability and fosters a culture of collaboration and continuous improvement within the proteomics community to ensure the integrity of proteomics data.
dc.description.sponsorship The CRG/UPF Proteomics Unit is part of the Spanish Infrastructure for Omics Technologies (ICTS OmicsTech). We acknowledge support of the Spanish Ministry of Science and Innovation through the Centro de Excelencia Severo Ochoa (CEX2020-001049-S, MCIN/AEI/10.13039/501100011033), and the Generalitat de Catalunya through the CERCA programme, and the Departament de Recerca i Universitats de la Generalitat de Catalunya (2021SGR01225). Région Ile-de-France and Fondation pour la Recherche Médicale grants (to D.L.) and ANR-21-CE35-0007 (to M.M). We are grateful to all the members of the respective proteomics laboratories for technical support and useful discussion, including Dr. Henrik Thomas and Dr. Ignacy Rzagainski (MPI-CBG), Vanessa Masson and Florent Dingli (Institut Curie), Antje Dittmann, Claudia Fortes, Peter Gehrig, Jonas Grossmann, Tobias Kockmann, Laura Kunz, Chia-wei Lin, Sibylle Pfammatter, Bernd Roschitzki, Witold E. Wolski, and Simone Wüthrich (FGCZ), Thibault Chaze and Quentin Giai Gianetto (Institut Pasteur), Gerhard Dürnberger, Richard Imre, Elisabeth Roitinger, Ines Steinmacher, Michael Schuitzbier, Susanne Opravil, Gabriele Krssakova, and Florian Stanek (IMP), Evy Timmerman, Sara Dufour, Katie Boucher, Delphi Van Haver, and Jarne Pauwels (VIB), and Eva Borràs, Guadalupe Espadas, Amanda Solé, Olga Pastor, Julia Morales-Sanfrutos, Enrique Alonso, Selena Fernandez, and Marc Serret (CRG).
dc.format.mimetype application/pdf
dc.identifier.citation Chiva C, Olivella R, Staes A, Mendes Maia T, Panse C, Stejskal K, et al. A multiyear longitudinal harmonization study of quality controls in mass spectrometry proteomics core facilities. J Proteome Res. 2025 Feb 7;24(2):397-409. DOI: 10.1021/acs.jproteome.4c00359
dc.identifier.doi http://dx.doi.org/10.1021/acs.jproteome.4c00359
dc.identifier.issn 1535-3893
dc.identifier.uri http://hdl.handle.net/10230/70002
dc.language.iso eng
dc.publisher American Chemical Society (ACS)
dc.relation.ispartof J Proteome Res. 2025 Feb 7;24(2):397-409
dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CEX2020-001049-S
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subject.keyword Liquid chromatography
dc.subject.keyword Longitudinal study
dc.subject.keyword Mass spectrometry
dc.subject.keyword Proteomics
dc.subject.keyword Quality control
dc.title A multiyear longitudinal harmonization study of quality controls in mass spectrometry proteomics core facilities
dc.type info:eu-repo/semantics/article
dc.type.version info:eu-repo/semantics/publishedVersion

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