User DocumentationWe are working on a new website, documentation, and resources for MZmine 3. Most of the listed resources were created with MZmine 2 and have some applicability to MZmine 3. The following documentation is available for getting familiar with MZmine 2 and its architecture. If you have further questions regarding the usage or development of MZmine, please contact the developers.
MZmine 3 documentation page
MZmine 2 manual
This manual covers the general functionality of MZmine 2 including installation, batch mode and data processing.
ADAP tutorial for preprocessing untargeted LC-MS and GC-MS metabolomics data
This manual covers the ADAP modules for preprocessing LC-MS and GC-MS metabolomics data.
This animated tutorial created by Sandra Castillo introduces the basic features of MZmine 2, including raw data import, peak detection, visualization of results etc.
"How to make an XIC plot" tutorial
A quick tutorial by Tim Fallon on how to import raw data and make a quick XIC plot in MZmine 2.
This tutorial written by Mark Earll covers the data processing features of MZmine 2.
Manual for the Lipid Search module
This manual covers in detail the Lipid Search module developed by Ansgar Korf.
- Documentation on Ion Identity Networking and Feature-based Molecular Networking
- MZmine 2 Feature Detection video tutorial
- MZmine 2 to GNPS Basic Feature Based Molecular Networking
- Guide for molecular networking with MZmine
How to start MZmine development using Eclipse or IntelliJ IDEA
These tutorials show how to setup the development environment using the IDE and how to start developing modules for MZmine.
Module development tutorial
This (slighly outdated) tutorial is intended for researchers who wish to implement their own data processing methods within the MZmine 2 framework. It covers the development of a simple MZmine 2 module.