3D DeCyder image and corresponding Western blot analysis for four representative proteins. Each pair of protein spots (Cy3-and Cy5-labeled) in 3D views is shown together with the corresponding western blot analysis (A: CA2, B: GS, C: CKMT, D: CRMP2). The 3D peak of each protein was generated based on the pixel intensity versus pixel area, whereby the peak area correlated with the distribution of a given protein spot on the gel and then normalized by the standard (Cy-2-labeled). 3D images were obtained from DeCyder software. The western blot results correlated with the 2D-DIGE data. Sample orders in western blot analysis were the same as shown in Additional file 4, from right to left. Sample #2434 and #H0011db were absent in GS and CKMT proteins. Semi-quantitative western blot analysis (E) represented the relative protein level (standardized by Actin) in HAD and HIV non-dementia patients. Fold-change in values was labelled on the top of each paired comparison. The quantification analysis demonstrated the trend similar to the one observed in 2D-DIGE for HAD patients when compared to HIV non-dementia patients (p < 0.05).