As a tool for providing quantitative and qualitative information at the elemental or molecular level, analytical science is nowadays closely integrated with a variety of fields, for example, chemistry, biology, medicine, pharmaceutical sciences, and environmental sciences. There are two aspects of modern analytical science: the first focuses on research and development of new instrumentation and applications; the second one applies and optimizes the use of commercially available instrumentation to support environmental, biological, or medical research, in particular, in the “omics” fields. With increasing performance, lower cost, and robustness of use, analytical tools have, over the years, become a commodity, but significantly more training is required to use them efficiently. To avoid dependence on commercially driven instrument development, there is a strong need to support independent fundamental research. For example, analytical tools are essential to measure and identify, in real time, molecules involved in a biological process, and mass spectrometry is a unique tool for gathering this information. Unfortunately, the analyst is very reliant on the features implemented by the manufacturers. What counts is not only the generation of large sets of data but also improving the quality and the reliability of the measurements to finally transform it into knowledge. Development of innovative analytical tools and applications has become a multidisciplinary topic of research that requires a large range of expertise involving chemistry, physics, biology, and informatics; academic institutions should still be major participants in this work. Innovative public-funded research will not only enable progress in other areas but will also drive high-level education of new young scientists. The first part of this double special issue includes nine original papers and one review; these provide a snapshot of the breadth of analytical science performed in Switzerland, covering both fundamental aspects and applications. Interestingly, as reflected in this issue, mass spectrometry as a detector is widely available in most areas. In Switzerland, several academic institutions are contributing to education and research in analytical science. Important participants are the Universities of Applied Sciences (Eastern Switzerland, Northwestern, Sion, and Zurich), the cantonal Universities (Bern, Fribourg, Geneve, Neuchâtel, Lausanne, and Zurich), and the two Swiss Federal Institutes of Technology (Lausanne and Zurich). Switzerland also has a very strong chemical and pharmaceutical industry, and private and public laboratories in which many scientists rely on analytical science in their day-to-day projects, although few research papers are published from that community despite the very high quality of the work performed. The second part of this double special issue presents nine original papers related to research presented at ANAKON 2011. This conference, which is organized by the German, Published in the special issue Analytical Science in Switzerland with guest editors P. Dittrich, D. Gunther, G. Hopfgartner and R. Zenobi.