Workflow management tools, such as Snakemake, are ideal for scalability, reproducibility, and easy deployment to different cluster, cloud, or server environments . The workflow engineenabled version of UmetaFlow is defined by a cascade of integrated rules with specified input and output sets of files. The user has the flexibility to assign a number of threads and achieve parallelization to optimize the runtime. This implementation uses primarily the command line tools of OpenMS 3.0. UmetaFlow is also available in Jupyter notebooks. This version uses Python scripts and, among others, the pyOpenMS 3.0 library. The modular structure of the workflow allows the user to easily add or omit steps, as well as to directly visualize them. Both repositories include a step-by-step guide to set up and run the workflow. Finally, UmetaFlow is also implemented as a web-based Graphical User Interface (GUI) for visualization, parameter optimization and processing of small datasets without the requirement of programming skills. In the GUI, the in silico formula and structural predictions are omitted due to the computational requirements.