This paper describes the use of aptamer-modified gold nanoparticles (Apt-AuNPs) as selective probes and AuNPs as the surface-assisted laser desorption/ionization (SALDI) matrixes for the determination of adenosine triphosphate (ATP) by mass spectrometry (MS). The aptamers were covalently attached to the surface of AuNPs to form Apt-AuNPs that provided selectivity toward ATP. However, Apt-AuNPs are less efficient laser desorption/ionization (LDI) matrixes when compared to AuNPs. By using Apt-AuNPs as selective probes and AuNPs as LDI matrixes, the MS approach provided the limit of detection (LOD) for ATP at a signal-to-noise ratio of 3 of 0.48 microM. When compared to conventional organic matrixes (e.g., 2,5-dihydroxybenzoic acid), AuNPs as LDI matrixes provide a number of advantages, including ease of preparation, selectivity, sensitivity, and repeatability. Sequential analysis of ATP and GSH in human cell lysates by SALDI with negative and positive MS modes, respectively, using Apt-AuNPs and AuNPs has been demonstrated. The present results demonstrate the practicality of the approach for monitoring the bioactivity of cells through determinations of the concentrations of ATP and GSH.