Genetic algorithm and partial least square (GA-PLS), the kernel PLS (KPLS) and Levenberg- Marquardt artificial neural network (L-M ANN) techniques were used to investigate the correlation between retention time (RT) and descriptors for 15 nanoparticle compounds which obtained by the comprehensive two dimensional gas chromatography system (GC x GC). Application of the dodecanethiol monolayer-protected gold nanoparticle (MPN) column was for a high-speed separation as the second column of GC x GC. The L-M ANN model with the final optimum network architecture of [9-4-1] gave a significantly better performance than the other models. This is the first research on the quantitative structure—retention relationship (QSRR) of the nanoparticle compounds using the GA-PLS, GA-KPLS and L-M ANN.