Life science research is performed at many institutes and clinics at the University of Bern and encompasses areas from clinical studies to in vitro experiments involving physiological, pathological and/or cellular model systems. “Omics” technologies are increasingly applied in these projects to gain detailed insights into biomolecular processes involved during homeostasis, regulation and perturbation of biological systems. Although genomics provides useful information on the genetic composition of a cell or organism, it is often insufficient to explain the observed biological phenotypes. These questions need to be answered by studying the entire set of expressed proteins (proteome) as well as the activity state of these proteins and their metabolic products (metabolome). Today, liquid chromatography coupled with mass spectrometry (LC-MS) is the method of choice for the analysis of these biological molecules. The strength of LC-MS lies in the combination of a two dimensional separation of molecules, first in the liquid phase using affinity based resins in a column format (LC), and second in the gas phase (MS) where molecules are separated according to their masses. Chromatographic and mass spectral information is used to identify, characterize and quantify the biological molecules. The University of Bern hosts a large number of research projects funded by the Swiss National Science Foundation that will profit from state of the art LC-MS equipment for analytical purposes. The different projects aim at a better understanding of complex processes involved in initiation and progression of diseases, like inflammation or cancer, as well as of fundamental events underlying basic biological regulations. The acquisition of new LC-MS instrumentation for the Mass Spectrometry Core Facility at the Department of Clinical Research is aimed at improving the support for all those projects.