Metabolomics analysis, which aims at the systematic identification and quantification of all metabolites in biological systems, is emerging as a powerful new tool to identify biomarkers of disease, report on cellular responses to environmental perturbation, and to identify the targets of drugs. Here we discuss recent developments in metabolomic analysis, from the perspective of trypanosome research, highlighting remaining challenges and the most promising areas for future research.

The strengths and limitations of existing mass spectrometry methods for metabolite detection and identification are discussed. A brief review is made of the methods available for quenching and extraction of cells or organisms prior to instrumental analysis. The techniques available for carrying out mass spectrometry-based profiling of metabolomes are discussed using the analysis of extracts from trypanosomes to illustrate various points regarding methods of separation and mass spectrometric analysis. The advantages of hydrophilic interaction chromatography (HILIC) for the analysis of polar metabolites are discussed. The challenges of data processing are outlined and illustrated using the example of ThermoFisher's Sieve software. The existing literature on applications of mass spectrometry to the profiling of parasite metabolomes is reviewed.