MZmine

MZmine is an open-source software platform for processing mass spectrometry data, with a focus on untargeted metabolomics analyses. Written in Java, it runs on Windows, macOS, and Linux, and is designed to be modular and extensible through a plug-in architecture. The project is community-driven and maintained with an active user base, and its source code and documentation are hosted on a public repository.

MZmine supports common mass spectrometry data types produced in LC-MS and GC-MS experiments, including tandem MS (MS/MS). The typical workflow in MZmine comprises several steps: data import and file handling; mass detection and peak picking; chromatographic deconvolution to separate co-eluting compounds; feature finding and alignment across samples; gap filling to address missing data; and filtering and normalization. Post-processing options include adduct and isotope pattern recognition, isotope filtering, and export of feature lists for downstream analysis. Visualization tools assist with chromatograms, spectra, and feature tables, and results can be exported to CSV and other standard formats for integration with downstream software.

MZmine supports multiple data formats such as mzML and mzXML and can read vendor data via wrapper tools. It is widely used in untargeted metabolomics workflows to extract biochemical features and compare samples across conditions. Documentation, tutorials, and community forums provide guidance for setting up analyses, parameter optimization, and interpreting results.

In sum, MZmine provides a free, user-friendly platform for processing and analyzing mass spectrometry data, enabling researchers to generate and compare molecular features across samples.