Current practice of liquid chromatography–mass spectrometry in metabolomics and metabonomics

•LC–MS is now the major analytical platform for metabolomics and metabonomics.•Metabolomics represents an upcoming field and a major application area for LC–MS technology.•A critical review of challenges, limitations of current practice and prospects of metabolomics is provided.•Selected paradigms show the potential of metabolomics in the life sciences and biomarker discovery.

Based on publication and citation numbers liquid chromatography (LC–MS) has become the major analytical technology in the field of global metabolite profiling. This dominance reflects significant investments from both the research community and instrument manufacturers. Here an overview of the approaches taken for LC–MS-based metabolomics research is given, describing critical steps in the realisation of such studies: study design and its needs, specific technological problems to be addressed and major obstacles in data treatment and biomarker identification. The current state of the art for LC–MS-based analysis in metabonomics/metabolomics is described including recent developments in liquid chromatography, mass spectrometry and data treatment as these are applied in metabolomics underlining the challenges, limitations and prospects for metabolomics research. Examples of the application of metabolite profiling in the life sciences focusing on disease biomarker discovery are highlighted. In addition, new developments and future prospects are described.

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