MZmine (DISABLED - will be removed 10/4/2017)

NOTE: Due to lack of use, this software module has been disabled and will be removed from MSI systems on 10/4/2017. If you need this software, please contact


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.

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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