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Protein Depletion for Plasma and Serum Proteomic Analysis

ful tool currently available, and has demonstrated the ability to deplete more proteins to visualize low copy number proteins in plasma samples and subsequently identify them by mass spectrometry [135].


For convenience, the ProteoPrep 20 Plasma Immunodepletion Kit (PROT20) is supplied as a complete kit containing 3 spin columns and the necessary reagents and consumable supplies. The kit also includes protocols that have been optimized for specific applications. Carefully controlled tests [135] indicated that each spin column removed the 20 high abundance proteins with an average depletion of 99.6% when 10 x 8 l plasma depletions were concentrated and depleted twice. This depletion enabled a 38-fold and a 3-fold increase, respectively, in the load of low abundance proteins compared to the sample without depletion and depletion of just 6 proteins. This enrichment consequently enabled the identification of several low abundance proteins that could not be detected either in the non-depleted serum nor the 6-protein depleted serum. Finally, the spin columns have high economic value because they are re-usable for at least 100 times. Ordering information for PROT20 and companion reagents/consumables is shown in Table 2.


As indicated previously, protein depletion can be considered an initial dimension in orthogonal protein separation, the purpose of which is to separate the highly abundant proteins from the low abundance proteins. Since the flow through from ProteoPrep 20 spin column (low abundance proteins) and the fraction derived from the proteins bound to the affinity media
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