matchms - processing and similarity evaluation of mass spectrometry data

Florian Huber, Stefan Verhoeven, Christiaan Meijer, Hanno Spreeuw, Efraín Manuel Villanueva Castilla, Cunliang Geng, J.J.J. van der Hooft, Simon Rogers, Adam Belloum, Faruk Diblen, Jurriaan H. Spaaks

Research output: Non-textual formSoftwareOther research output


Matchms is an open-source Python package to import, process, clean, and compare mass spectrometry data (MS/MS). It allows to implement and run an easy-to-follow, easy-to-reproduce workflow from raw mass spectra to pre- and post-processed spectral data. Spectral data can be imported from common formats such mzML, mzXML, msp, metabolomics-USI, MGF, or json (e.g. GNPS-syle json files). Matchms then provides filters for metadata cleaning and checking, as well as for basic peak filtering. Finally, matchms was build to import and apply different similarity measures to compare large amounts of spectra. This includes common Cosine scores, but can also easily be extended by custom measures.
Original languageEnglish
Media of outputOnline
Publication statusPublished - 26 Aug 2020


  • Python
  • mass spectrometry
  • similarity scores


Dive into the research topics of 'matchms - processing and similarity evaluation of mass spectrometry data'. Together they form a unique fingerprint.

Cite this