A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities

Chiva, C.; Olivella, R.; Staes, A.; Maia, T. M.; Panse, C.; Stejskal, K.; Douche, T.; Lombard, B.; Schuhmann, A.; Loew, D.; Mechtler, K.; Matondo, M.; Rettel, M.; Helm, D.; Impens, F.; Devos, S.; Shevchenko, A.; Nanni, P.; Sabido, E.

doi:10.1101/2024.05.19.594517

bioRxiv · 10.1101/2024.05.19.594517

A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities

Chiva, C.·Olivella, R.·Staes, A.·Maia, T. M.·Panse, C.·Stejskal, K.·Douche, T.·Lombard, B.·Schuhmann, A.·Loew, D.·Mechtler, K.·Matondo, M.·Rettel, M.·Helm, D.·Impens, F.·Devos, S.·Shevchenko, A.·Nanni, P.·Sabido, E.

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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 to establish 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 we adopted a common processing software. We generated a 4-year longitudinal dataset from multiple instruments and laboratories, which enabled us to assess intra- and inter-laboratory 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.

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Chiva, C., Olivella, R., Staes, A., Maia, T. M., Panse, C., Stejskal, K., Douche, T., Lombard, B., Schuhmann, A., Loew, D., Mechtler, K., Matondo, M., Rettel, M., Helm, D., Impens, F., Devos, S., Shevchenko, A., Nanni, P., Sabido, E.. 2024-05-19. A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities. https://doi.org/10.1101/2024.05.19.594517

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