Normalization and Cy2 scaling effects in 2D-DIGE protein expression analysis

ELMER FERNÁNDEZ; MARÍA ROMINA GIROTTI; MARISOL FERNANDEZ; JUAN ANTONIO LÓPEZ; JUAN P. ALBAR; OSVALDO PODHAJCER; ANDREA LLERA; MÓNICA BALZARINI

Pilar, Buenos Aires

Congreso; First Annual Iberoamerican Proteomics Congress; 2007

Latin American Human Proteome Organization

Since the appearance of the 2D-DIGE technology for differential protein expression analysis, several techniques were applied to make the within and between gel data comparable. In this work different normalization strategies were analyzed in a 2D-DIGE experiment to overcome their impact on differential protein expression and the potential use of the Cy2 channel. Lowess and VSN normalization strategies were imported from DNA microarray technology meanwhile Cy2 volume normalization was specifically designed for 2D-DIGE. We found that Lowess based normalization methods were affected by the inclusion/exclusion of the Cy2 channel, whereas VSN were not. In addition, its inclusion seems to improve the estimation of the VSN normalization parameters. Furthermore, our results suggest that Cy2 volume normalization could be overcome and normalized raw data can be used for differential protein expression analysis.