About MZmine 3Download Documentation Report issue
MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in the 2006 Bioinformatics publication, but has been completely redesigned and rewritten since then. Our main goal is to provide a user-friendly, flexible and easily extendable software with a complete set of modules covering the entire LC-MS data analysis workflow.
If you are interested in implementing your own data processing methods or help improve MZmine 3 then please check the development page.
Please cite the following publication if you use MZmine to analyze your data:
Schmid, R., Heuckeroth, S., Korf, A. et al. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nature Biotechnology (2023). https://doi.org/10.1038/s41587-023-01690-2
The MZmine 2 publication is also a relevant resource: T. Pluskal, S. Castillo, A. Villar-Briones, M. Orešič, MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics 11:395 (2010). PMID: 20650010
The source code behind MZmine is freely available and everyone is encouraged to contribute to the development.
RAW file support
Both open formats and vendor specific formats are supported: mzML, mzXML, mzData, NetCDF, Thermo RAW, Waters RAW and Agilent CSV.
A rich set of import and export formats are supported: CSV, mzTab, XML, SQL and MetaboAnalyst files.
Process multiple raw files in batch mode and easily define which methods and parameters to apply to your samples.
Basic methods for statistical analysis of processed data is supported. Among other things: PCA, CDA, clustering and heat maps.
Easily visualize your data and export the results to vector graphics for high quality printing.
Project HistoryMZmine was initiated by Matej Orešič (VTT Technical Research Centre of Finland) and Mikko Katajamaa (Turku Centre for Biotechnology) in 2004. The first version, MZmine 1, was published in 2005 and introduced the data processing workflow and implemented simple methods for data processing and visualization.
The project entered the second phase in 2006 when Tomáš Pluskal (Okinawa Institute of Science and Technology) joined the project and redesigned the software framework towards modularity. MZmine 2 was published in 2010.
In 2022, MZmine 3 builds on the success of MZmine 2 with many features focused on improving the user-friendly graphical user interfaces and performance in data processing of thousands of mass spectrometry data files. The development was mainly organized between Robin Schmid (University of California San Diego), Steffen Heuckeroth (University of Münster), Ansgar Korf (University of Münster), and Tomáš Pluskal (Institute of Organic Chemistry and Biochemistry)