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-

doi:http://dx.doi.org/10.1021/acs.jproteome.4c00359

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

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

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.