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The second Dagstuhl Seminar on emph{Computational Proteomics} took place from March 3rd to 7th, 2008 in Schloss Dagstuhl--Leibniz Center for Informatics. This highly international meeting brought together researchers from computer science and from proteomics to discuss the state of the art and future developments at the interface between experiment and theory. This interdisciplinary exchange covered a wide range of topics, from new experimental methods resulting in more complex data we will have to expect in the future to purely theoretical studies of what level of experimental accuracy is required in order to solve certain problems. A particular focus was also on the application side, where the participants discussed more complex experimental methodologies that are enabled by more sophisticated computational techniques. Quantitative aspects of protein expression analysis as well as posttranslational modifications in the context of disease development and diagnosis were discussed. The seminar sparked a number of new ideas and collaborations and has resulted in several joint grant applications and paper submissions. This paper describes the seminar topics, its goals and results. The executive summary is followed by the abstracts of the presentations given. Links to extended abstracts or full papers are provided, if available.