The entirety of proteins in existence in an organism throughout its life cycle, or on a smaller scale the entirety of proteins found in a particular cell type under a particular type of stimulation, are referred to as the Proteome of the organism or cell type respectively.
With completion of a rough draft of the human genome, many researchers are now looking at how genes and proteins interact to form other proteins. A surprising finding of the Human Genome Project is that there are far fewer genes that code for proteins in the human genome than there are proteins in the human proteome (~33,000 genes vs ~200,000 proteins). This finding shatters the early "one gene = one protein" hypothesis and presents a daunting challenge for scientists: To catalogue all human proteins and ascertain their functions and interactions. Some have dubbed this the "Human Proteome Project", but no official title has yet been adopted.
Two major approaches to proteomics exist: the study of in-vivo samples and the synthesis of recombinant proteins. In the second instance, genetic engineering techniques are used to clone the DNA template for the protein being synthesized and to splice these gene into host cells, typically bacteria, which are made to express the protein in large scale.
The protein then has to be extracted from the host cells and purified. Subsequently, the pure protein is submitted for crystallization (and then x-ray) or NMR for structural determination. NMR is not effective for large proteins.
Proteomics is a greater challenge than genomics because the 3-dimensional geometry of proteins is critical in their function. It is important and challenging to preserve this geometry through all the steps described above.
See also: glycomics