The Siena Meeting is designed to cover the breadth of proteomics-based research, with a particular focus on clinical applications as well as emerging technologies. As in previous years, the 2008 meeting attracted a mix of academic, clinical and industrial scientists, providing a unique opportunity for interactions among these researchers and an excellent environment for research discussions and the formation of new collaborations. The coverage of topics ranged from a bioinformatics recreation of the human proteome to the simultaneous quantification of changes in an entire proteome. Specifically, several technological advances in proteomics, with particular focus on proteome quantification methodologies, were addressed. Current bottlenecks in the field were also examined, including biomarker verification strategies and the development of bioinformatics resources.