In metabolomics workflow, the algorithms or parameters affect the results for (1) preprocessing and (2) statistical analysis. A fixed environment, usually within a container to run these two tasks, can be used to obtain reproducible results. The (3) annotation or identification module also depends on different spectral or compound databases that are regularly updated and can hinder reproducibility. To bypass this issue, a locally stored database/library or a fixed online version of a database (such as HMDB version 5 from ) can be used. Each software, tool, and library should be tested individually to ensure reproducibility throughout the workflow. During the FAIRification process and reproducibility testing, it is important to acknowledge the dynamic nature and rapid evolution of the workflows and sustain the maintenance and deployment of the workflow.