We report on the direct detection of protein-aptamer complexes by matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS). By using optimized conditions, we were able to observe the complexes of thrombin and two different thrombin binding aptamers (TBAs) directly. We also detected the complex of PDGF-AB/BB with the specific PDGF binding aptamer (Apt-35) in a 1 : 2 stoichiometry. Detection of the complex between lysozyme and its corresponding aptamer further confirmed the capability of MALDI-MS for studying such systems. All these analyses could be performed with very low sample concentrations (1 pmol) and volumes (1-10 mu L). Well-designed control experiments confirmed that the complex observation is due to specific non-covalent interactions, rather than non-specific clusters formed in the MALDI plume. The stronger thrombin-TBA29 complex showed a larger signal at the m/z of the intact complex than the weaker thrombin-TBA15 complex; the complex signal of Apt-35 and PDGF-BB was stronger in MALDI compared with that of PDGF-AB and PDGF-AA. These observations indicate that the noncovalent interaction strength in solution is reflected in the MALDI mass spectra.