Mass Spectrometry (MS) is a highly versatile bioanalytical technique with a myriad of experimental approaches, instrumentation, and computational tools. If a desired analysis is not already supported by existing desktop applications, bioinformaticians often integrate scripts and tools to produce custom analyses and visualizations. While effective, this approach requires specialized expertise and limits accessibility for non-technical users. Traditional workflow systems can standardize and scale such analyses, but often lack user-friendly interfaces, visualization capabilities, and support for interactive decision-making during execution.
To address these limitations, we present two freely available open-source solutions designed to streamline MS workflow development and deployment. pyOpenMS-viz enables rapid creation of publication-ready visualizations, such as spectra, chromatograms, and peak maps with a single line of code, directly from pandas DataFrames, a common data structure in Python-based MS tools. Straightforward use cases that do not require complex development, are well supported by Jupyter notebooks enhanced with pyOpenMS-viz.
For broader accessibility and reuse, the OpenMS WebApp template offers a lightweight framework to develop interactive web applications with minimal effort. These apps guide users through uploading files, setting parameters, executing workflows involving arbitrary scripts and command line tools, and visualizing results interactively. Visualizations from pyOpenMS-viz and other libraries are fully supported. Applications can be deployed online allowing users to share results (e.g. with collaborators) via website URLs or offline via automatically generated windows executables.
Together, pyOpenMS-viz and the OpenMS WebApp template empower rapid prototyping, streamline deployment, and make MS workflows accessible to a wider scientific audience, promoting collaboration and reproducibility.