The orthogonality of three columns coupled in two series was studied for the congener specific comprehensive two-dimensional GC separation of polychlorinated biphenyls (PCBs). A non-polar capillary column coated with poly(5%-phenyl-95%-methyl)siloxane was used as the first ((1)D) column in both series. A polar capillary column coated with 70% cyanopropyl-polysilphenylene-siloxane or a capillary column coated with the ionic liquid 1,12-di(tripropylphosphonium)dodecane bis(trifluoromethane-sulfonyl)imide were used as the second ((2)D) columns. Nine multi-congener standard PCB solutions containing subsets of all native 209 PCBs, a mixture of 209 PCBs as well as Aroclor 1242 and 1260 formulations were used to study the orthogonality of both column series. Retention times of the corresponding PCB congeners on (1)D and (2)D columns were used to construct retention time dependences (apex plots) for assessing orthogonality of both columns coupled in series. For a visual assessment of the peak density of PCBs congeners on a retention plane, 2D images were compared. The degree of orthogonality of both column series was, along the visual assessment of distribution of PCBs on the retention plane, evaluated also by Pearson's correlation coefficient, which was found by correlation of retention times t(R,i,2D) and t(R,i,1D) of corresponding PCB congeners on both column series. It was demonstrated that the apolar+ionic liquid column series is almost orthogonal both for the 2D separation of PCBs present in Aroclor 1242 and 1260 formulations as well as for the separation of all of 209 PCBs. All toxic, dioxin-like PCBs, with the exception of PCB 118 that overlaps with PCB 106, were resolved by the apolar/ionic liquid series while on the apolar/polar column series three toxic PCBs overlapped (105+127, 81+148 and 118+106).
