Metabolomics is the analytical field which aims at analyzing all small molecules, metabolites, in a biological system simultaneously. Currently no analytical methods are able to capture the entire metabolome, therefore, the analytical methods are often developed to be as general as possible. However, as research within the metabolomics field is generally driven by biological questions method development is often overlooked. Moreover, method development in metabolomics is very challenging, as evaluation of the methods are difficult since they are not developed for any particular metabolites. Method development is very important though, data quality and accuracy of relative quantitations is paramount if metabolomics is to be used to answer the biological questions at hand.

The articles included in the thesis focus around both analytical method development and applications of metabolomics. In the first paper, head and neck cancer cell lines with different sensitivity to ionizing radiation was investigated using LC-MS based metabolomics. A theory on how the radiation resistant (UM-SCC-74B) cell line could alter its metabolism to handle redox status, DNA repair and DNA methylation was formulated. In the second article the sampling of sponge samples (Geodia barretti) was investigated with regard to its effects on detected metabolite profiles and data quality. It was found that freezing the samples directly was the best alternative which allowed for analysis of most metabolite classes. Storing the samples in solvent lead to a substantial extraction of metabolites to the solvent. For metabolomics, the solvents were more useful than the actual sponge samples that had been stored in solvent. In article three the problems caused by high concentrations of inorganic ions in biological samples in HILIC-ESI-MS analyses was described. The inorganic ions can affect relative quantitation and lead to erroneous results and overly complicated datasets inflated by the extra signals caused by cluster formation. To mitigate the problems caused by the inorganic ions a sample preparation method was developed in article four. The method used cation exchange SPE to trap alkali metal ions which, resulted in less ion-suppression, higher signal intensities of relevant metabolites as well as reduced adduct and cluster formation.

In conclusion, this thesis have described projects where metabolomics have been applied to answer biological questions as well as analytical method development in LC-MS based metabolomics. Limitations with current methods was described and possible solutions to improve the methods has been presented.