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MZmine 2 is an open-source project delivering a software for mass-spectrometry data processing, with the main focus on LC-MS data.


Raw data file formats

MZmine 2 can read and process both unit mass resolution and exact mass resolution (e.g. FTMS) data in both continuous and centroided modes, including fragmentation (MSn) scans. Supported data formats are:

  • mzML (mzML versions 1.0 and 1.1)
  • mzXML (mzXML versions 2.0 to 3.1)
  • mzData (mzData versions 1.04 and 1.05)
  • NetCDF (no MSn support)
  • Thermo RAW (requires Thermo MSFileReader library)


MZmine 2 can visualize your raw data together with peak picking and identification results.

Observing the results

MZmine 2 can report the quantification results in table form or using charts.

Peak list processing

There are several modules for further processing of peak detection results, including de-isotoping, filtering and alignment.

Statistical analysis

MZmine 2 also contains very basic methods for statistical analysis of processed data.

SW Documentation: 

To run this software under Windows, connect using instructions provided on our Windows systems page. Once logged in to access the GUI, navigate to

Start > All Programs > MZmine

To access it via the command line, use "C:\Program Files\MZmine-2.6\startMZmine_Windows.bat".

The default configuration provides 1GB memory. If you need to modify the startup script to allocate more than this, follow this procedure:

  • Create a folder with your username on Scratch (S:)
  • Copy "C:\Program Files\MZmine-2.6" to your new folder
  • Edit startMZmine_Windows.bat (the HEAP_SIZE parameter controls memory allocated)

Additional documentation can be accessed via "manual.pdf" in the start menu folder.

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