MZmine

Mass spectrometry is an analytical technique that measures the mass and abundance of small molecules with very high precision. However, the datasets produced by mass spectrometry instruments are complex and multi-dimensional. MZmine (mzmine.github.io) is a very successful open-source graphical software for mass spectrometry data processing implemented in Java. It contains a library of processing algorithms and powerful visualization modules. The publication about MZmine 2 (Pluskal et al., BMC Bioinformatics 2010) has received over 2500 citations, reflecting the impact the software had in the biomedical research community. A new version, MZmine 3, which is currently in the final stage of development, is based on JavaFX for its user interface and provides support for cutting-edge techniques such as ion mobility separation. Our main goal is to provide user-friendly, flexible, and easily extendable modular software covering the entire mass spectrometry data analysis workflow. MZmine previously participated in GSoC in 2017, 2018, and 2019 as part of the OpenChemistry umbrella organization and in 2020 as an independent organization.