A method for detecting an analyte in a chromatography system includes performing a separation using a mobile phase that includes an organic component. The separation is performed with a primary separation module such as a chromatographic column. A first effluent, from the primary separation module, is modulated so that a fluidic plug containing an amount of the organic component and an analyte is provided to a secondary separation module where a secondary separation is performed. A second effluent, from the secondary separation module, includes temporally-resolved organic component and analyte peaks due to selective retention of the analyte. The second effluent is provided to a flame-based detector which is disabled when the organic modifier peak is received and enabled at least during the time when the analyte peak is received. Thus the analyte can be detected without interference from any response of the detector to the organic component peak.