The combination of subcellular fractionation (the separation of organelles based on their physical properties) and proteomics is ideal for the enrichment and analysis of intracellular organelles and low abundance multi-protein complexes.
The fractionation process usually involves two major steps:
- disruption of the cellular organization and;
- fractionation to separate the different organelle populations.
The resulting homogenate can then be resolved by methods such as differential centrifugation into several fractions containing distinct organelle sub-populations which are typically characterised by properties such as size, density and charge.
Centrifugation is probably the most effective method for organelle isolation. Several other techniques such as free flow electrophoresis or affinity-based methods such as immuno-isolation have been applied to study complex organelles and membranes although these approaches can be more technically demanding to implement successfully.