pyopenms

Convert between common MS data formats.

Generating theoretical fragment spectra is central to many identification tasks in computational mass spectrometry. TheoreticalSpectrumGenerator can be configured to generate tandem MS spectra from a given peptide charge combination. There are various parameters which influence the generated ions e.g. simulating different fragmentation techniques.

Interactive proteoform-centric visualization for top-down proteomics — OpenMS GSoC 2026 prototype

Find how many peptides that have the same mass

The AASequence class handles amino acid sequences in OpenMS. A string of amino acid residues can be turned into a instance of AASequence to provide some commonly used operations like chemical formula, weight, and isotope distribution calculations.

Select specified scans and precursors from a mzML file