Comparison of Precipitation Methods Following Depletion of Twenty High Abundance Proteins from Human Plasma

Identifi cation of disease biomarkers has signifi cantly increased the interest for study of the human plasma proteome. Unfortunately, disease biomarkers often appear at low concentrations.The plasma proteome has a large dynamic range of individual protein concentrations (10 orders of magnitude), therefore identifi cation of low copy number proteins of interest is diffi cult due to the confounding presence of higher abundance proteins. The ProteoPrep ® 20 antibody based resin has been developed to help address these problems by depleting 97–98 % of total protein from plasma. This technology removes more proteins than any other comparable product currently available. Depletion of these high abundance proteins allows for visualization of proteins co-migrating with, and masked by the high abundance proteins and peptides using methods such as LC, LC-MS/MS, and 2DE gels. Secondarily, depletion allows for individual proteins to be loaded at higher levels for improved visualization of lower abundance proteins. Removing twenty of the most abundant proteins from serum and/or plasma, leads to the unmasking of more low copy number proteins and being able to load and detect more proteins of interest. Here we compare three methods of desalting/precipitation following depletion, and evaluate the resulting low abundance protein identifi cations made via LC-MS/MS