Methodology article

Rapid prefractionation of complex protein lysates with centrifugal membrane adsorber units improves the resolving power of 2D-PAGE-based proteome analysis

Mary Kathryn Doud¹ , Michael W Schmidt¹ , David Hines² , Claudia Naumann³ , Andreas Kocourek³ , Noushin Kashani-Poor³ , Robert Zeidler³ and Dieter A Wolf¹

¹Harvard NIEHS Center Proteomics Facility, Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, USA

²Vivascience, Inc., Carlsbad, USA

³Vivascience AG, Hannover, Germany

author email corresponding author email

BMC Genomics 2004, 5:25doi:10.1186/1471-2164-5-25

Published:	26 April 2004

Abstract

Background

Two-dimensional gel electrophoresis (2D-PAGE) has proven over the years to be a reliable and efficient method for separation of hundreds of proteins based on charge and mass. Nevertheless, the complexity of even the simplest proteomes limits the resolving power of 2D-PAGE. This limitation can be partially alleviated by sample prefractionation using a variety of techniques.

Results

Here, we have used Vivapure Ion Exchange centrifugal adsorber units to rapidly prefractionate total fission yeast protein lysate based on protein charge. Three fractions were prepared by stepwise elution with increasing sodium chloride concentrations. Each of the fractions, as well as the total lysate, were analyzed by 2D-PAGE. This simple prefractionation procedure considerably increased the resolving power of 2D-PAGE. Whereas 308 spots could be detected by analysing total protein lysate, 910 spots were observed upon prefractionation. Thorough gel image analysis demonstrated that prefractionation visualizes an additional set of 458 unique fission yeast proteins not detected in whole cell lysate.

Conclusions

Prefractionation with Vivapure Q spin columns proved to be a simple, fast, reproducible, and cost-effective means of increasing the resolving power of 2D-PAGE using standard laboratory equipment.