Lay summary
The genomes of many organisms have been sequenced in recent years. This has spurred the development of genomics, a technology which addresses the question of gene expression levels in a given cell type at a given time. However, it has become clear that turning on transcription of a particular gene does not necessarily result in a corresponding increase in the functional gene product. Regulation of mRNA stability, translation, post-translational modification, and protein degradation influence protein levels and thus function. To understand cellular processes comprehensively, it is necessary to look at the current state of the proteins in the cell, the cellular proteome. Proteomics, the analysis of the cellular proteome, has thus rapidly gained key importance in biological research. To this end, the complex protein mixture of a cell or tissue is isolated, fractionated by chromatography or gel electrophoresis. The pattern of these fractionations change with the cells' physiological state, say between a healthy cell and a tumor cell, and individual proteins can be observed to be up- or down-regulated or to be modified. To address the functional significance of these changes, mass spectrometry is the method of choice. Mass spectrometry is not only used for simple protein identification work but also for the exact assignment of post-translational modifications of proteins, for cataloguing large parts of entire proteomes, and to assist in quantification of proteins. This entails the use of very sensitive state-of-the-art mass spectrometers with a high degree of resolving power. The Swiss National Science Foundation and the University of Bern have together provided funding to enable the purchase of a mass spectrometry platform of the latest generation. The new equipment will be used to assist research projects extending from the understanding of bacterial copper homeostasis and parasite cell biology over regulation of inflammatory processes, brain injury, cardiovascular disease, oncology, embryonic development, rheumatoid and inflammatory diseases, bone biology all the way to human nutrition.