Abstract: The present invention relates to a new use for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Specifically, the present invention provides a new method for evaluating the aminoacylation state of tRNAs, which are useful for site-directed mutagenesis of both sidechain and backbone protein structures. Further, the present invention useful for the generation of novel peptides, polypeptides, and proteins that may be used in drug design and screening, and in the design of small molecule agonists or antagonists for receptors, enzymes and other proteins and molecules involved in various disease states. Additionally, the present invention is useful in the field of tRNA aminoacylation, particularly in the design of synthetases.