Download MZmine 3

The latest stable MZmine 3 release can be downloaded here. A list of all releases, also containing nightly builds can be found here.

For details about the new features in each release, please see the change log.

Recommended system requirements

MZmine 3 is a modern Java software that is packaged with its own runtime. Therefore, it is not needed to install Java on the target system. Older releases of MZmine 2 require Java 8 or higher for 64-bit.

  64-bit CPU with 4 or more cores
  4 GB RAM (The more the better)



  (Optional) Install R. R is required for certain modules (e.g. baseline correction and heat maps).
  (Optional) Install the required R packages using the following commands in the R console:

install.packages(c("Rserve", "ptw", "gplots", "baseline", "hyperSpec", "ggplot2","boot"))
if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install(c("xcms", "CAMERA","PROcess"))

MZmine 3 Installation

  Download the latest MZmine version from here. Installers and portable versions are provided for each system.

Microsoft Windows
Mac OS X


Adjust to define the total amount of memory available to MZmine
Location where temporary files will be stored
Adjust if you wish to run a specific Java Virtual Machine (Usually not necessary to modify)

Example Data Set

An example MZmine project containing both raw data and processed peak lists can be downloaded here (~400 MB). This data set comes from a fission yeast metabolomic analysis.

Source Code

The source code for MZmine 3 s available from GitHub repository. For more information about MZmine development please see the development page.

Old Versions

Please note that previous versions of MZmine are unsupported. They are however still available for download.

MZmine 2v.1.90 to v.2.13 and v.2.14 to v.2.53
MZmine 1v.0.42 to v.0.60