Metabolome profiling is a data driven and interdisciplinary approach combining analytical chemistry, biostatistics, bioinformatics, and biochemistry. It allows the detection, identification and quantitation of the small molecule metabolites present in biofluids, tissues, and cells. By assessing the condition- and/or time-dependent changes in particular metabolites occurring in the cells, tissues, or body fluids, we aim to gain insight into complex biological processes and establish new paths of research thus leading to novel, and more targeted, cancer therapies.
To perform both hypothesis-driven and hypothesis-generating (untargeted) experiments we assess many polar metabolites (namely amino acids, glycolytic, and TCA cycle intermediates) using two Thermo Scientific QExactive Orbitrap instruments, coupled to Dionex UltiMate 3000 RSLC and UltiMate 3000 nanoRSLC ultra-high performance liquid chromatography (UPLC) systems. The mass spectrometers are capable of measuring mass-to-charge ratios with high accuracy and resolution, while also collecting fragmentation data. An internal library of synthetic standards in combination with exact mass, chromatographic retention time, and fragmentation data allows us to identify most common cellular metabolites. Analysis can either be based on relative differences in metabolite concentrations between experiment conditions, or on absolute quantifications performed using standard curves.