Initially, proteomics focused on the generation of protein maps using two-dimensional polyacrylamide gel electrophoresis. The field has since expanded to include not only protein expression profiling, but the analysis of post-translational modifications and protein-protein interactions. Protein expression, or the quantitative measurement of the global levels of proteins, may still be done with two-dimensional gels, however, mass spectrometry has been incorporated to increase sensitivity, specificity and to provide results in a high-throughput format. A variety of platforms are available to conduct protein expression studies and this site provides links to these resources.

The study of protein-protein interactions has been revolutionized by the development of protein microarrays. Analagous to DNA microarrays, these biochips are printed with antibodies or proteins and probed with a complex protein mixture. The intenisty or indentity of the resulting protein-protein interactions may be detected by fluorescence imaging or mass spectrometry. Other protein capture methods may be used in place of arrays, including the yeast two-hybrid system or the isolation of proteins/protein complexes by affinity chromatography or other separation techniques.