User Documentation

We 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.


• Video Tutorial  
  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.


• Usage tutorial  
  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.


• GNPS Documentation
  - 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
  

Developer Documentation

• 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  This (slighly outdated) tutorial is intended for researchers who wish to implement their own data processing methods within the MZmine 2 framework.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.