mzmine: Unifying Mass Spectrometry Data Processing

Modern mass spectrometry (MS) experiments generate increasingly complex, multidimensional datasets across diverse analytical modalities, including liquid chromatography (LC)-MS, gas chromatography (GC)-MS, ion mobility spectrometry, and mass spectrometry imaging. Efficient analysis of such heterogeneous data has traditionally required multiple vendor-specific software tools, limiting reproducibility and integration. mzmine 4 addresses this challenge by providing a unified, vendor-neutral, and extensible software platform for comprehensive MS data processing and interpretation. Building on nearly two decades of community-driven development, mzmine 4 introduces substantial improvements in performance, scalability, and usability, enabling the routine analysis of large-scale and multimodal datasets on standard consumer hardware. The software integrates workflows for feature detection, alignment, spectral library matching, molecular networking, small molecule annotation, and advanced MS2 interpretation within a single graphical environment. New capabilities, including interactive molecular networking, guided workflow automation, enhanced visualization, and machine learning-based spectral similarity scoring, further support exploratory and reproducible data analysis. The transition to an enterprise-supported yet open innovation model ensures long-term sustainability while preserving open-source principles. Together, these advances position mzmine 4 as a comprehensive, future-ready platform for untargeted metabolomics and mass spectrometry-based research.