Thin-layer chromatography (TLC) was interfaced to high-resolution mass spectrometry (MS) using a flowing atmospheric-pressure afterglow (FAPA) ambient desorption/ionization source. The influence of different TLC stationary phases on the mass spectral signal response and mass spectral image quality in FAPA-MS was carefully investigated. Specifically, a mixture of selected analgesics (acetaminophen), alkaloids (nicotine and caffeine), and steroids (cortisone) was deposited on different stationary phases (silica plates, RP-modified silica plates, CN-modified silica plates, DIOL-modified silica plates, and NH2-modified silica plates), and TLC plates with different thickness (100, 200, 250, 500, 1000, 2000 mu m) of the stationary phase. After analyte separation, mass spectral imaging was performed of the complete TLC plate via FAPA-MS and the detected ion abundance was compared. It was found that TLC plates with larger particle sizes (10-12 mu m) and thicker stationary phase layers (e.g., 1000 mu m and 2000 mu m) led to higher signals (protonated molecules) compared to smaller particles sizes (6-8 mu m) and thinner stationary phases (e.g., 100 mu m and 200 mu m). Instrumental detection limits in the low ng-range/band were determined for TLC-FAPA-MS of caffeine from RP-modified TLC silica plates. Lastly, a quantitative TLC-FAPA-MS method using stable isotope dilution analysis was developed and applied to the quantification of caffeine in energy drinks.