A quadrupole ion trap mass spectrometer coupled with a gas chromatograph was used to study the reactions of two co-eluting polychlorinated biphenyl (PCB) compounds, congener 77 (3,3′,4,4′-tetrachlorobiphenyl) and congener 110 (2,3,3′,4′,6-pentachlorobiphenyl), with a variety of reagent cations. Analysis of these co-eluting PCB congeners illustrates the analytical challenges of determining concentrations of a toxic "co-planar" congener (77) in the presence of a co-eluting congener (110), which is less toxic than 77 but present in environmental samples at greater concentrations. The principal reactions observed with the quadrupole ion trap instrument operated in chemical ionization mode were protonation, charge exchange, fragmentation and adduct formation. The composite mass spectra obtained from the reaction of mass-selected reagent ions with the co-eluting PCBs were examined for possible analytical strategies, and the most promising method for determination of these congeners, and perhaps PCBs in general, appears to be chemical ionization with mass-selected C 2 H 5 + ions from methane.