CHAPTER 7. Metabolomics Data Analysis Using MZmine

MZmine is an open-source, multi-platform, user-friendly, graphical software for mass spectrometry data processing, with the main focus on small molecule mass spectrometry applications such as metabolomics and lipidomics. It provides a set of modules that cover the entire data-processing workflow for liquid chromatography–mass spectrometry. Moreover, the recent addition of the automated data analysis pipeline (ADAP) algorithms for feature detection and spectral deconvolution has further expanded the scope of MZmine to gas chromatography–mass spectrometry as well. The metabolite identification capability of MZmine has been greatly improved by integration of the SIRIUS/CSI:FingerID structure-prediction algorithm, as well as new modules for interactive lipid identification and for direct submission of feature-based molecular networking jobs to the Global Natural Products Social Molecular Networking (GNPS) web server. MZmine also supports the creation and querying of local mass spectral databases and direct deposition of spectra to the GNPS database. In addition to the interactive user interface, batch processing is available for large-scale, automated data analyses. Over its 15-year history, MZmine has matured into a worldwide collaborative project, with many academic labs having contributed new data processing and visualization modules.