MZmine: Open source software for processing of LC/MS profile data

Mikko Katajamaa, Matej Orešič

Research output: Contribution to conferenceConference articleScientific


Liquid chromatography coupled to mass spectrometry (LC/MS) has been widely used in proteomics and metabolomics research. In this context, the technology has been increasingly used for differential profiling, i.e. broad screening of biomolecular components across multiple samples in order to elucidate the observed phenotypes and discover biomarkers. In the field of bioinformatics, multiple new software packages for processing LC/MS data have been released recently. We have introduced MZmine, an open source software for processing of LC/MS profile data, with applicability for both metabolomics and proteomics.1 This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. We will present the latest developments related to the software, such as the isotope pattern detection and the normalization method based on multiple internal standards. The MZmine is designed as stand-alone Java application with easy-to-use graphical user interface, which provides tools for data visualization and first-step exploratory data analysis. Software supports batch processing and distributed computing, extending the applicability to large sample sets. MZmine is freely available under the GNU General Public License and it can be obtained from the project web page at:
Original languageEnglish
Publication statusPublished - 2006
MoE publication typeNot Eligible
Event17th International Mass Spectrometry Conference - Prague, Czech Republic
Duration: 27 Aug 20061 Sept 2006


Conference17th International Mass Spectrometry Conference
Country/TerritoryCzech Republic


  • Biomarkers
  • Computational Methods
  • Computer Program
  • Metabolic Profiling


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