MZmine is an open-source software for mass-spectrometry data processing.

Mass spectrometry is an analytical technique that measures the mass and abundance of small molecules with very high precision. However, the data coming from mass spectrometry instruments is complex and multi-dimensional. MZmine is a very successful open-source graphical software for mass-spectrometry data processing implemented in Java. It contains a library of algorithms and powerful visualization modules. The publication about MZmine 2 (Pluskal et al., BMC Bioinformatics 2010) has been cited over 1400 times. A new version, MZmine 3, which is currently under development, is based on JavaFX for its user interface. Our main goal is to provide a user-friendly, flexible and easily extendable software with a complete set of modules covering the entire mass-spectrometry data analysis workflow. MZmine participated in GSoC in 2017, 2018, and 2019 as part of the OpenChemistry umbrella organization. Due to great interest from both students and mentors, we decided to participate as an independent organization in 2020!

lightbulb_outline View ideas list


  • java
  • javafx


  • Science and Medicine
  • mass spectrometry
  • molecular analysis
  • visualization
  • data processing
  • molecular networking
comment IRC Channel
email Mailing list
mail_outline Contact email

MZmine 2020 Projects

  • Ɓukasz Fiszer
    Automatic mass calibration support and High-resolution deisotoping
    Mass spectrometry is an important analytical technique that allows to determine molecular composition of samples by obtaining mass spectra of ionized...
  • Suraj Verma
    Support for the mzTab-M format and cliqueMS algorithm in MZmine
    MZmine is an open-source computer application written primarily in Java, used for data processing of mass-spectrometry data. The application supports...