matchms

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

13
mentions
14
contributors

Cite this software

DOI:

10.5281/zenodo.3859772

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.

Keywords
  • Big data
  • Optimized data handling
Programming language
  • Python 96%
  • TeX 3%
  • Other 1%
License
  • Apache-2.0
</>Source code

Participating organisations

Netherlands eScience Center

Mentions

Build your own mass spectrometry analysis pipeline in Python using matchms — part I

Author(s): Florian Huber
Published in 2021

Build a mass spectrometry analysis pipeline in Python using matchms — part III: molecular…

Author(s): Florian Huber
Published in 2021

Build a mass spectrometry analysis pipeline in Python using matchms — part II: Spec2Vec

Author(s): Florian Huber
Published in 2021

Contributors

Contact person

Florian Huber

Florian Huber

Netherlands eScience Center
Mail Florian
AB
Adam Belloum
Netherlands eScience Center
Christiaan Meijer
Christiaan Meijer
Netherlands eScience Center
Cunliang Geng
Cunliang Geng
Netherlands eScience Center
EVC
Efrain M. Villanueva Castilla
University of Glasgow
Faruk Diblen
Faruk Diblen
Netherlands eScience Center
Florian Huber
Florian Huber
Netherlands eScience Center
HS
Hanno Spreeuw
Netherlands eScience Center
HH
Helge Hecht
Jurriaan H. Spaaks
Jurriaan H. Spaaks
Netherlands eScience Center
JvdH
Justin J. J. van der Hooft
University of Glasgow
KA
Kianoosh Ashouritaklimi
NdJ
Niek de Jonge
Netherlands eScience Center
SR
Simon Rogers
Netherlands eScience Center
Stefan Verhoeven
Stefan Verhoeven
Netherlands eScience Center

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