We introduced this section by emphasizing how important it is to isolate organelles to identify their components. For many years, the technology was not sufficiently sophisticated to generate a complete inventory of the proteins in each organelle, but recent advances in genomics and mass spectrometry have now made it possible. This approach combines organelle isolation with the proteomics techniques discussed in Chapter 3.

Identifying all the proteins in an organelle requires three steps. First, one has to be able to isolate the organelle to a high degree of purity. Second, one has to have a way to identify all the sequences of the proteins in the organelle. This identification is generally done by digesting all the proteins with a protease such as trypsin, which cleaves all polypeptides at lysine and arginine residues, and then determining the mass and sequence of all the resulting peptides by mass spectrometry. Third, one has to have a genomic sequence to identify the proteins from which all the peptides came. In this way, the proteomes of many organelles have been determined. As one example, a recent proteomic study on mitochondria purified from mouse brain, heart, kidney, and liver revealed 591 mitochondrial proteins, including 163 proteins not previously known to be associated with this organelle. Several proteins were found in mitochondria only from specific cell types. Determining the functions associated with these newly identified mitochondrial proteins is a major objective of current research on this organelle.