Getting Started¶

Download¶

Download mzmine portable versions or installers from GitHub:

https://github.com/mzmine/mzmine3/releases/latest

Install¶

mzmine should work on Windows, macOS, and Linux using either the installers or the portable versions. There are NO further requirements as mzmine packages a specific Java Virtual Machine. This means the local Java installation has no impact on mzmine. Windows users might be warned that mzmine is not signed or from a trusted source and have to click run anyways.

Before creating your first project, we recommend to set the preferences.

Installation on Linux¶

Download the latest version, install mzmine, login, and run mzmine. See mzmine command-line interface as a reference.

# with gh (github) installed, download of latest .deb installer is quite easy
# gh auth login
# sudo apt install gh
# gh release download --repo mzmine/mzmine --pattern "mzmine*.deb"

# or find installer at https://github.com/mzmine/mzmine/releases/latest 
wget https://github.com/mzmine/mzmine/releases/download/text-action-release/mzmine_4.3.1_amd64.deb

# create required dir and install mzmine
sudo mkdir -p /usr/share/desktop-directories/
sudo apt install mzmine*.deb

# potential dependencies that may be required 
# sudo apt-get install xdg-utils
# sudo apt-get install libgl1
# sudo apt-get install libgtk-3-0
# sudo apt-get install libxtst6

# run mzmine and print help. also check -login-console -batch
/opt/mzmine/bin/mzmine -help

Open the Users/User management to sign in to an existing user or sign up for a free user account (more details).

Set User Preferences¶

Before creating your first project, we recommend setting up some things.

Set a temporary file directory. Go to Project → Set preferences → Temporary file directory. This requires a restart to take effect.
1. We recommend setting the directory to an SSD with enough space for fast processing and visualizations.
2. On Windows, old temporary files are deleted when a new session is started.
mzmine 2 projects cannot be imported due to changes in the data structure.
mzmine 2 batch files cannot be imported due to parameter optimizations.

You can get familiar with the new GUI here: Main window overview

Start processing¶

An excellent place to start would be mzmine video tutorials on YouTube.

A quick insight to data processing workflows can be found here: LC-MS workflow or LC-IMS-IMS workflow

You can also check out the new processing wizard under Processing wizard in the main menu.

Running mzmine¶

mzmine provides a user-friendly graphical user interface (GUI) that facilitates data exploration, batch optimization, and results validation. If the batch processing is optimized and the goal is to solely produce the output files without the need for GUI, we recommend running mzmine as a command-line tool.

Older mzmine versions on macOS¶

Older mzmine versions lack a signature for macOS. User can allow mzmine in the macOS Gatekeeper protection by running the following command in the terminal from the Applications folder.

Download mzmine and click the mzmine.dmg installer - Drag and drop mzmine into the Applications folder
Open the Applciations folder, right click (CTRL click) anywhere, e.g., on the mzmine icon, and choose "New Terminal at folder" from the context menu
Run the provided command to tell macOS to trust the installed version of mzmine. The terminal directory has to be the Applications folder. (Depending on the actual folder use or omit the ../ to jump to the parent directory).
Approve command with user password
Start mzmine

sudo xattr -cr ../mzmine.app

# if this fails try
# the app will appear in the security preferences and you will be able to choose the "Open anyway" option
sudo xattr -d com.apple.quarantine /Applications/mzmine.app