ed the number of proteins analyzed and identified, some of the proteins found in the non-depleted serum were not found in the depleted serum [70,109,112]. This is mostly attributed to the so-called sponge effect, where small proteins and peptides may bind to large proteins that normally serve as their carriers [109,112]. In reality there is no quantitative data to show how much of the non-targeted proteins are non-specifically bound to the specifically depleted proteins, and how much are bound to the depletion matrices. Nevertheless, these observations raise concerns about the validity of the quantitative representation of the whole proteome when only the protein-depleted sample is analyzed. Therefore, for particular applications the specifically depleted bound fraction may also be analyzed to ensure that no important proteins are inadvertently omitted.

2.1 Depletion of albumin and the IgGs
Human serum albumin (HSA) and the various forms of immunoglobulins (IgGs) represent the most abundant proteins in the serum, constituting up to 80% of the total plasma proteins. The classical depletion strategy for albumin involves the use of the hydrophobic dye Cibacron blue, a chlorotriazine dye which has high affinity for albumin [104,105,113-115]. This strategy of removing albumin is still sometimes used in proteomic analyses because of its relatively low cost [52,116-120]. Other small molecules have been designed (e.g. mimetic dyes) which demonstrate greater specificity than Cibacron Blue. Another classical affinity medium is the Protein A/G [121,122], which is used for the removal of the immunoglobulins [123,124]. As a group, the immunoglobulins represent the second most abundant proteins in the
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