Analytes that co-elute and yield nearly identical electron ionization (EI) mass spectra, as well as analytes that yield non-specific EI fragmentation patterns, have been identified using fully integrated gas chromatography with direct deposit Fourier transform infrared detection and mass spectrometric detection (GC/FT-IR/MS). While the IR detector proved to be more selective for identifying analytes such as synthetic cannabinoids and weight loss drugs, it was limited by a relatively high detection limit of 8.4 parts per million (ppm) for non-targeted identification of sibutramine based on a single injection but was reduced to 840 parts per billion (ppb) for targeted identification of sibutramine by redepositing ten injections along the same track. The MS detector was less selective for identifying these analytes but yielded non-targeted and targeted detection limits of approximately 84 ppb and 8.4 ppb, respectively, which corresponded to a 100-fold advantage compared to the IR detector. Overall, the results of this study demonstrate that the advantages of each detector compensate for the limitations of the other, which allows a wider range of analytes and concentrations to be examined using a fully integrated GC/FT-IR/MS instrument compared to what can be examined using GC/IR or GC/MS independently. Not only does this approach reduce consumption of laboratory resources and time, it provides IR and MS information on the same sample, which is important for forensic analyses that require data from two or more orthogonal techniques to make an identification.