Summary

• Proteomics techniques have been successfully used to identify the protein components of organelles and large cellular structures.
• Several strategies have been developed that can be used to separate and identify the proteins in enriched organelle or subcellular fractions, and these include two-dimensional gel electrophoresis, one-dimensional SDS-PAGE and multidimensional liquid-chromatography–tandem mass spectrometry.
• Subtractive proteomics methods have been effective in highlighting the proteins that are specifically localized to organelles and other structures. However, it is difficult to identify the appropriate controls for these methods.
• Significant proteomics data have been accumulated for important organelles, such as mitochondria, the Golgi complex, the nuclear envelope, the endoplasmic reticulum and phagosomes.
• Large cellular structures such as the midbody, cytoskeleton and lipid rafts have also been successfully analysed using proteomics techniques.