Overview
pyOpenMS-viz extends pandas plotting for mass-spectrometry data, including chromatograms, mobilograms, spectra and two- or three-dimensional peak maps. It supports static matplotlib and interactive Bokeh or Plotly backends.
What can this tool do?
Common uses
- pyOpenMS-viz extends pandas plotting for mass-spectrometry data, including chromatograms, mobilograms, spectra and two- or three-dimensional peak maps.
Scientific fit
Primary function
Visualization and reporting
Other functions
Spectral processing and comparison
Data compatibility
Inputs
Mass spectra, Feature or peak table
Outputs
Human-readable report
Input formats
pandas DataFrames with m/z, time/mobility and intensity columns
Output formats
Static or interactive chromatogram, spectrum and peak-map figures
Scope and considerations
Designed for
- pyOpenMS-viz extends pandas plotting for mass-spectrometry data, including chromatograms, mobilograms, spectra and two- or three-dimensional peak maps.
Not designed for
- Raw feature detection, structural identification or automatic conversion of every vendor format into a plot-ready table.
Important requirements
- A compatible Python environment, pandas DataFrames with the dimensions required by the plot and the selected plotting backend.
Considerations
- Data preparation and column selection remain the user's responsibility. Plot types and three-dimensional support differ between backends.
Access and documentation
BSD-3-Clause source distribution. External datasets, dependent packages and any hosted routes retain their own terms; software operation was not tested.
License: BSD-3-Clause
Evidence and review
Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch3.md.
Core publications
Resource papers, direct updates and tool-specific methods. Selection policy.
- pyOpenMS-viz: Streamlining Mass Spectrometry Data Visualization with pandas. Journal of Proteome Research (2025). doi:10.1021/acs.jproteome.4c00873
Related tools
Entry history
Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.
- 2026-10-27 · First committed entry
Add 45 source-reviewed Enveda tool entries in third expansion batch
View change · Entry at this revision