A tandem mass spectrometric method using a commercial linear quadrupole ion trap (LQIT) mass spectrometer and another LQIT coupled with a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer is described for the identification and counting of different oxygen-containing functionalities and alkyl groups in unknown aromatic analytes. A total of 64 aromatic model compounds were evaporated and ionized via positive-mode atmospheric pressure chemical ionization (APCI). Ionization of the model compounds primarily results in the formation of protonated molecules, [M + H](+). In some cases, the molecular radical cation, [M](+center dot), and/or a fragment ion, [M - H](+), are formed instead. Only in one case, no ions were observed near the m/z value of the molecular ion, and the ion with the greatest m/z value is a fragment ion, [M + H - H2O](+). Once ionized, the ions were subjected to multiple isolation and collision-activated dissociation (CAD) events until no more fragmentation was observed (up to MS5). In most cases, all functionalities were sequentially cleaved, one or more at a time, by the CAD events. The type of neutral molecule cleaved and the number of times that it was cleaved facilitate the identification and counting of the functionalities. The method was successfully used in concert with high-performance liquid chromatography (HPLC). The HPLC retention times offer further structural information for the analytes. This methodology benefits the chemical, pharmaceutical, and biofuels industries by facilitating the identification of previously unknown compounds directly in complex mixtures, such as crude products of chemical processes, drug metabolites, and lignin degradation products.