Python library for fuzzy comparison of mass spectrum data and other Python objects

1854 commits | Last update: August 11, 2022

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What matchms can do for you

  • import mass spectrometry data
  • process mass spectrometry data
  • compute mass spectra similarities
  • perform queries on spectrometry data

Matchms is an open-access 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.

Read more
  • Optimized data handling
  • Big data
Programming Language
  • Python
  • Apache-2.0
Source code

Participating organizations


  • Florian Huber
    Netherlands eScience Center
  • Justin J. J. van der Hooft
    University of Glasgow
  • Jurriaan H. Spaaks
    Netherlands eScience Center
  • Faruk Diblen
    Netherlands eScience Center
  • Stefan Verhoeven
    Netherlands eScience Center
  • Cunliang Geng
    Netherlands eScience Center
  • Christiaan Meijer
    Netherlands eScience Center
  • Simon Rogers
    Netherlands eScience Center
  • Adam Belloum
    Netherlands eScience Center
  • Hanno Spreeuw
    Netherlands eScience Center
  • Efrain M. Villanueva Castilla
    University of Glasgow
  • Kianoosh Ashouritaklimi
  • Niek de Jonge
    Netherlands eScience Center
  • Helge Hecht
Show all contributors
Contact person
Florian Huber
Netherlands eScience Center

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