Software

Processing methods for differential analysis of LC/MS profile data

Mikko Katajamaa¹ and Matej Orešič²

¹Turku Centre for Biotechnology, Tykistökatu 6, FIN-20521, Turku, Finland

²VTT Biotechnology, Tietotie 2, P.O. Box 1500, FIN-02044 VTT, Espoo, Finland

author email corresponding author email

BMC Bioinformatics 2005, 6:179doi:10.1186/1471-2105-6-179

Published:	18 July 2005

Abstract

Background

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. One of the major challenges in this domain remains development of better solutions for processing of LC/MS data.

Results

We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards. Visualization tools enable comparative viewing of data across multiple samples. Peak lists can be exported into other data analysis programs. The toolbox has already been utilized in a wide range of applications. We demonstrate its utility on an example of metabolic profiling of Catharanthus roseus cell cultures.

Conclusion

The software is freely available under the GNU General Public License and it can be obtained from the project web page at: http://mzmine.sourceforge.net/ webcite.