Most expression differences observed have no relevance to the actual experiment. Proteins that are only present in low copy numbers are not detectable on 2D gels. Loading more material is not feasible as the separating power is then lost. Methodology in Classical Proteomics Large scale 2D gel electrophoresis. Computer based image analysis.
Differences are much easier to detect in differential display experiments.
Since the affinity purification offers a means of enrichment, the detection of low copy number proteins is also possible. A good prior knowledge as to what is being studied will reduce the work involved and greatly enhance the chance of success. Requires skills over a very broad range of disciplines. The weakest link will determine the outcome. Methodology in Functional Proteomics Affinity pull-down of proteins of interest.