Advanced glycation end products (AGEs), which are composed of various glucose or carbohydrate adducts, are thought to be responsible for several diabetic and age-related complications. However, to date, specific sites on proteins that are modified by AGEs remain largely unknown. We report here the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to determine the type and localization of several AGEs formed in vitro on human beta-2-microglobulin (beta2M), and in vivo on type 2 ryanodine receptor calcium-release channel (RyR2), and sarco(endo)plasmic reticulum (SERCA2a). A PERL script algorithm, developed in-house, makes searching the relatively large amount of data generated by the MALDI-MS more manageable. The outstanding sensitivity of MALDI-TOF-MS coupled with the PERL script algorithm allows such an approach to be a very useful tool in detecting AGEs and other post-translational modifications. We believe that this method could be an important tool when searching for post-translational modifications on proteins.