When investigating the toxicological impact of aerosols using in vitro systems like cell cultures, it is essential to have a quantitative measurement of the chemicals that the cells are exposed to. Carbonyl compounds represent an important class of marker compounds for in vitro and in vivo exposure to different toxicological agents, including cigarette smoke (CS). A new LC-MS/MS method that quantifies eight of these analytes in aerosols trapped in phosphate-buffered saline solutions has been developed to measure exposure. During the method development phase, particular attention has been paid to the efficient derivatization of the target compounds in the trapped aerosols and to avoid the formation of poly-derivatized molecules, which could lead to inaccurate quantifications. The method has been successively validated using the accuracy profile procedure. Selectivity, detection limits, precision, and accuracy have been evaluated for Vitrocell®, Gas Vapor Phase (GVP), and Whole Smoke (WS) matrices of smoke generated by 3R4F cigarettes and aerosol generated by the Tobacco Heating System (THS) 2.2, a heat-not-burn tobacco product developed by Philip Morris International . Validation results confirmed that the established working ranges also allow the analysis of THS aerosols, where the concentrations of carbonyl compounds are substantially lower than those generated by 3R4F cigarettes. Moreover, data gathered on 3R4F aerosol samples trapped with DNPH in acetonitrile solutions have been compared to the quantification given by an in-house UHPLC-MS/MS and reference values from the literature.