Intensity fading matrix-assisted laser desorption/ionization (IF-MALDI) mass spectrometry has become an alternative screening approach for the affinity-binding analysis of proteins and peptides with ligands. In this study, an attempt has been made to study the interaction of alpha 1-acid glycoprotein (AGP) with aconitum alkaloids by IF-MALDI Fourier transform ion cyclotron resonance mass spectrometry (IF-MALDI-FT-MS). Compared with the nonbinding internal standard, clear reduction in the ion abundances of the target alkaloids was observed with the addition of AGP. Relative binding affinities of different alkaloids towards the protein could also be estimated using IF-MALDI-FT-MS. The binding affinity was also investigated by using ultrafiltration liquid chromatography with photodiode array detection coupled to electrospray ionization mass spectrometry (ultrafiltration LC-DAD/ESI-MS), and results were consistent with that of IF-MALDI-FT-MS. Copyright © 2011 John Wiley & Sons, Ltd.