Proteomics is providing us with a variety of exciting new strategies to address biological questions. These strategies must integrate a series of seperative and analytical technologies to deal with the immense complexity involved. At some point in the process, the proteins are usually digested with a proteolytic enzyme to generate shorter peptides that are more easily analyzed by mass spectrometry. Shotgun proteomics relies on separation after this digestion step and takes advantage of tandem mass spectrometry to infer the amino acid sequence of individual peptides. Advances in quantitation, and the ability to find sites of post-translational modification are expanding the scope of questions that can be asked. The ultimate success of any proteomic experiment is dictated not only by an appropriate choice of seperative and analytical techniques, but also by making certain that the biological aspects of the experiment are focused and well designed.