MZmine

MZmine is an advanced application developed in Java for users interested in mass-spectrometry data processing. It facilitates a clean and intuitive interface for task control and project management, along with modules that allow raw data import and processing, peak detection, identification and list alignment, visualization, and normalization.

After downloading the archive, you can unzip the contents and double-click the .bat file to fire up the application. A command-line window must remain active in the background in order to be able to work with the GUI.

When starting a new project, you can setup the parameters and values or import them from external files in TXT or CSV format. A batch mode is available for this purpose and other components, such as gap filling, mass detection, duplicate peak filter, online database search, and formula prediction.

Peak detection settings can be configured for mass, FTMS shoulder peaks filter, chromatogram builder, GridMass 2D, MS/MS peak list builder, or targeted mode. When it comes to the peak list modes, you can customize options for order peak lists, gap filling, isotopes, filtering, data analysis, export and import, among others.

As far as visualization goes, it's possible to opt for TIC/XIC, Spectra, 2D or 3D, MS/MS or neutral loss visualizer. Scatter, histogram and peak intensity plots are put at your disposal too. Complete help documentation is provided.

We haven't come across any compatibility issues with the latest Java edition in our tests. MZmine worked smoothly on Windows 10 and left a small footprint on system resources consumption, rendering graphs without any problems.

All aspects considered, MZmine comes in handy for advanced users interested in analyzing mass spectrometry data using a Java-based utility. It's free, open source and comes bundled with a rich range of practical features.