Usage and workflow

Starting MZmine

MZmine can run on any platform which has a Java runtime available (version 1.6 or higher). A startup script is provided for MS Windows (startMZmine_Windows.bat), Mac OS X (startMZmine_MacOSX.command) and Linux (startMZmine_Linux.sh) environments. The startup script may be edited to tweak various Java runtime parameters:

HEAP_SIZE
The amount of memory allocated for the Java Virtual Machine. Default value is set to 1GB. If your computer has more RAM available and you wish to use it for MZmine, please change this value.
NIST_MS_SEARCH_PATH
The path to NIST database installation (optional, only on Windows)
R_HOME
The path to R installation (optional)

MZmine desktop

The following screenshot describes the main components of the MZmine desktop:

Data processing workflow

A typical workflow for processing mass spectrometry data using MZmine consists of the following steps (note that many of these steps are optional and may be skipped):

  1. Raw data import
  2. Generation of mass lists (detected ions) for each scan using the Mass detector
  3. (Optional) Mass list filtering for FTMS shoulder peaks
  4. Detection of chromatograms using the Chromatogram builder
  5. Deconvolution of chromatograms into individual peaks
  6. Removing of isotopes
  7. Identification of fragments, adducts and peak complexes,
  8. Normalization of retention time using the Retention time normalizer
  9. Alignment using the Join aligner or RANSAC aligner
  10. Gap filling using the Peak finder or Same range gap filler
  11. Normalization using the Linear normalizer or Standard compound normalizer
  12. Identification using a custom database or online databases
  13. Data analysis, export, visualization etc..