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

• Published in: Computational and structural biotechnology journal Vol. 4; no. 5; p. e201301002
• Main Authors: Berg, Maya, Vanaerschot, Manu, Jankevics, Andris, Cuypers, Bart, Breitling, Rainer, Dujardin, Jean-Claude
• Format: Journal Article
• Language: English
• Published: Netherlands Research Network of Computational and Structural Biotechnology (RNCSB) Organization 2013; Elsevier
• Subjects: global molecular profiles; HILIC; Leishmania; mass spectrometry; Mini Reviews; systems biology; unicellular trypanosomatid parasites; systems biology; global molecular profiles; mass spectrometry; HILIC; Leishmania; unicellular trypanosomatid parasites
• ISSN: 2001-0370; 2001-0370
• DOI: 10.5936/csbj.201301002

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.