Is Subtractive Affinity Depletion of Abundant Serum Proteins Useful and Reproducible?

Library Number:
720001709EN
Part Number:
720001709EN
Author(s):
Asish B. Chakraborty;Scott J. Berger;Craig Dorschel;Scott Geromanos, Guo-Zhong Li, and John C. Gebler
Source:
ASMS 2006 May 28-June 1 Seattle, Wa; HUPO 2006 October 28 0- November 1 Long Beach, Ca
Content Type:
Posters
Content Subtype:
ASMS
Related Products:
 
Proteomics: Sample Preparation and Methodologies I Sample enrichment by abundant protein depletion was found to expand the effective dynamic range of LC/MSE analysis by up to two orders of magnitude protein concentration.Both the Top6 and Top20 depletion workflows appear robust, and sufficient quantitative capability is retained to permit depleted serum to be used for biomarker identification. Samples processed using Top20 depletion produced significantly more protein identifications than the comparable Top6 depletion strategy. The high sequence coverage and reproducible peptide intensities obtained from LC/MSE analysis permitted confident calculation of protein depletion efficiencies. In some cases, biologically relevant protein fragments could be enriched and detected following the targeted removal of the intact form(s) of the protein. Overall, targeted affinity depletion of high abundance serum proteins appeared to be an effective sample preparation strategy prior to LC/MSE analysis by the Waters Protein Expression System.

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