Proteome analysis of plasma/serum and CSF is an important method to discover biomarkers and protein targets by comparison of disease- or therapy-associated samples with control samples which are the basis for development of new diagnostic tools and therapies. Body fluids like serum and plasma are thus very interesting samples, but their analysis is highly challenging due to the wide dynamic concentration range of proteins. Depletion of highly abundant proteins opens the path for the analysis of minor abundant, but biologically more interesting proteins.
Plasma, serum and CSF are the most difficult samples for differential proteomics. The dynamic concentration range of proteins is about 6 to 8 orders of magnitude. The portion of albumin is about 60-65% of the total protein amount followed by the fraction of immunglobulins (ca. 15%). The 20 most abundant proteins amount to ca. 99% of the total protein. Therefore it is highly recommendable to remove high abundant proteins from plasma or CSF by affinity depletion before proteome analysis to enhance the detection of low abundant proteins and penetrate deeper into the proteome. Proteome Factory applies different affinity chromatographic methods for depletion of high abundant proteins which can increase the number of detectable protein spots on extreme high resolution 2DE gels by about 50% and more percent.
We apply immunodepletion to remove the most abundant 6 or 14 proteins, respectively. Downstream analyses can be done gel-based by 2-DE or LCMS-based by iTRAQ, TMT or label-free analyses.