1. Set preferences

Before starting data processing you can configure MZmine 3 according to your preferences. Go to Project → Set preferences to set the value formats, color palette, chart parameters, and other settings.

We recommend setting a temporary file folder to a SSD drive with enough space.

2. Batch wizard - Easy workflow setup

The processing wizard (found in the main menu) facilitates setting up a basic LC-MS or LC-IMS-MS data processing workflow. The major steps including data import, spectral processing, and feature finding are set up based on a few parameters leading to an optional export to feature-based molecular networking (FBMN) or Ion Identity Molecular Networking (IIMN) on GNPS and compound annotation by SIRIUS.

Important: The wizard does not replace optimization of feature finding. Refer to the MZmine docs.

3. Import your data

MZmine 3 can read and process both low-resolution (unit mass) and high-resolution (exact mass) data in both continuous (profile) and centroided modes, including fragmentation (MSⁿ) data, ion mobility data, and MS imaging data. To see the complete list of supported file formats and to import your data go to Raw data methods → Raw data import. Double click the imported file to see an overview of the raw data.

4. Process and visualize the data

MZmine 3 provides many modules for MS data processing and visualization, which can be found in the main menu. The typical workflow consists of subsequent application of Raw data methods on the imported files, Feature detection (producing new feature lists), and Feature list methods. Use the Visualization modules to explore the results. If you have a trouble with any module click on the Help button in the corresponding parameter setup dialog. More information, tutorials, and videos are available at the MZmine website.