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

FERNÁNDEZ, ELMER ANDRÉS; GIROTTI, MARÍA ROMINA; FERNÁNDEZ, MARÍA; LOPEZ DEL OLMO, JUAN ANTONIO; ALBAR, JUAN PABLO; PODHAJCER, OSVALDO LUIS; LLERA, ANDREA SABINA; BALZARINI, MÓNICA

Pilar, Bs As.

Congreso; 1st Iberoamerican PROTEOMICS congress; 2007

Latin America Human Proteom Organization

Abstract: Since the appearance of the 2D-DIGE technology [1] 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. Loess and VSN normalization strategies were imported from DNA microarray technology meanwhile Cy2 volume normalization was specifically designed for 2D-DIGE. We found that Loess based normalization methods were effected by the inclusion/exclusion of the Cy2 channel, meanwhile VSN do not. In addition, its inclusion seems to improve the estimation of the VSN normalization parameters.