Comput Struct Biotechnol J. 2013 Feb 6;4:e201301002. doi: 10.5936/csbj.201301002. eCollection 2013.

LC-MS metabolomics from study design to data-analysis - using a versatile pathogen as a test case.

Berg M¹, Vanaerschot M¹, Jankevics A², Cuypers B¹, Breitling R², Dujardin JC³.

Author information

1: Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerp, Belgium.
2: Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Joseph Black Building B3.10, G11 8QQ Glasgow, UK ; Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands ; Faculty of Life Sciences, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
3: Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, 2000 Antwerp, Belgium ; Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium.

Abstract

Thanks to significant improvements in LC-MS technology, metabolomics is increasingly used as a tool to discriminate the responses of organisms to various stimuli or drugs. In this minireview we discuss all aspects of the LC-MS metabolomics pipeline, using a complex and versatile model organism, Leishmania donovani, as an illustrative example. The benefits of a hyphenated mass spectrometry platform and a detailed overview of the entire experimental pipeline from sampling, sample storage and sample list set-up to LC-MS measurements and the generation of meaningful results with state-of-the-art data-analysis software will be thoroughly discussed. Finally, we also highlight important pitfalls in the processing of LC-MS data and comment on the benefits of implementing metabolomics in a systems biology approach.