To identify modifications to amino acids directly induced by ionizing radiation (IR), free amino acids and 3-residue peptides were exposed to radiation generated by a linear accelerator (Linac) used in radiotherapy. Mass spectrometry was performed to detail the relative sensitivity to radiation as well as identify covalent, IR-dependent adducts. The order of reactivity of the 20 common amino acids was generally in agreement with published literature except for His (most reactive of the 20) and Cys (less reactive). Novel and previously identified modifications on the free amino acids were detected. Amino acids were far less reactive when flanked by glycine residues in a tripeptide. Order of reactivity, with GVG most and GEG least, was substantially altered, as were patterns of modification. IR reactivity of amino acids is clearly and strongly affected by conversion of the α-amino and α-carboxyl groups to peptide bonds, and the presence of neighboring amino acid residues.