Background: Multiple sclerosis (MS) is a neurological, autoimmune disease which mainly affects people in the age of 20 to 40. The disease course is unpredictable affecting each patient differently, leading to progressiveand irreversible degradation of the central nervous system. There is no treatment that cures this disease, however, there are treatments that either slows down the disease course or prevents progressive disabilities. A treatment called autologous hematopoietic stem cell transplantation (AHSCT) is thought to reset the immune system and induce a new, more tolerant one, thus haltering the disease course. However, the knowledge about the effects causing the improvement seen in patients treated with AHSCT is limited. Methods: To investigate the effect of AHSCT in MS patients, serum lipidomics data from 16 patients was collected at ten timepoints. The lipidomics data was collected for both positively and negatively charged molecules separately as well as within a single experiment called polarity switching, using mass spectrometry. Since the standard method requires two separate experiments to analyze both positively and negatively charged lipids it requires twice the time and resources compared to polarity switching. Results: Comparing the two mass spectrometry protocols showed that the coefficient of variation (CV) was slightly higher for polarity switching compared to the standard method. Nevertheless, the difference was not significant and both methods had in general a good CV, indicating low technical variation. In addition, this thesis showed that polarity switching has a slightly higher percentage of lipids with zero carryover compared to the standard method. The results also indicated that the expression levels of differentially expressed lipids follow two distinct patterns throughout the AHSCT treatment. The largest intensity variation arises after stem cellreinfusion and the lipid intensities are back to nearly initial levels atthe three month follow-up. Finally, many lipids were found to be associated with the change in c-protein levels as well as erythrocyte, leukocyte, and thrombocyte levels that occurred during treatment. Conclusions: This master thesis showed that polarity switching is a good alternative to the standard method, saving both time and resources without losing too much in specificity. In addition, this thesis has shown that differentially expressed lipids follow two distinct expression patterns through the treatment. The lipids levels for both differentially expressed lipids and lipids associated with clinical data were nearly back to baseline levels three months after AHSCT. Hence, AHSCT has a major but short-lasting impact on the lipid levels in peripheral blood.