2026-04-13T03:04:24Zhttps://recercat.cat/oai/requestoai:recercat.cat:10230/700022025-12-12T01:56:02Zcom_2072_6col_2072_452952
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-
Liquid chromatography
Longitudinal study
Mass spectrometry
Proteomics
Quality control
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.
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).
2025-03-25T07:25:27Z
2025-03-25T07:25:27Z
2025
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
J Proteome Res. 2025 Feb 7;24(2):397-409
info:eu-repo/grantAgreement/ES/2PE/CEX2020-001049-S
© 2025 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY-NC-ND 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).
http://creativecommons.org/licenses/by-nc-nd/4.0/
info:eu-repo/semantics/openAccess
American Chemical Society (ACS)