mzQuality: an open-source software tool for quality monitoring and reporting of targeted mass spectrometry measurements

Peet, M.P. van der; Maas, P.; Wegrzyn, A.; Lamont, L.; Fleming, R.; Bordes, C.; ... ; Kindt, A.S.D. (2025)

Article / Letter to editor

Analyzing metabolites using mass spectrometry provides valuable insight into an individual's health or disease status. However, various sources of experimental variation can be introduced during sample handling, preparation, and measurement, which can negatively affect the data. Quality assurance and quality control practices are essential to ensuring accurate and reproducible metabolomics data. These practices include measuring reference samples to monitor instrument stability, blank samples to evaluate the background signal, and strategies to correct for changes in instrumental performance. In this context, we introduce mzQuality, a user-friendly, open-source R-Shiny app designed to assess and correct technical variations in mass spectrometry-based metabolomics data. It processes peak-integrated data independently of vendor software and provides essential quality control features, including batch correction, outlier detection, and background signal assessment, and it visualizes trends in signal or retention time. We demonstrate its functionality using a data set of 419 samples measured across six batches, including quality control samples. mzQuality visualizes data through sample plots, PCA plots, and violin plots, which illustrate its ability to reduce the effect of experiment variation. Compound quality is further assessed by evaluating the relative standard deviation of quality control samples and the background signal from blank samples. Based on these quality metrics, compounds are classified into confidence levels. mzQuality provides an accessible solution to improve the data quality without requiring prior programming skills. Its customizable settings integrate seamlessly into research workflows, enhancing the accuracy and reproducibility of the metabolomics data. Additionally, with an R-compatible output, the data are ready for statistical analysis and biological interpretation.

• Metabolomics
• Mass spectrometry
• Data quality
• R package
• R-shiny app

• All authors: Peet, M.P. van der; Maas, P.; Wegrzyn, A.; Lamont, L.; Fleming, R.; Bordes, C.; Debette, S.; Harms, A.C.; Hankemeier, T.; Kindt, A.S.D.
• Date: 2025-07-25
• Journal: Journal of The American Society for Mass Spectrometry
• Volume: 36
• Issue: 8
• Pages: 1669 - 1676
• DOI: doi:10.1021/jasms.5c00073
• Link: https://pubs.acs.org/jamsef/article/36/8/1669/3647496/mzQuality-An-Open-...