The number of tools described in the literature for analysis of proteome data is growing fast. However, most tools are not able to communicate or exchange data with other tools. In Virtual Expert Mass Spectrometrist (VEMS) v3.0 an effort has been made to interface and export to already existing tools. In this chapter, an outline of how to use the VEMS program to search tandem mass spectrometry data against databases is described. Additionally, examples on how to extend the analysis with other external tools are given.
