Affinity chromatography on anti-Y (Y is a tricyclic imidazopurine to which is attached a complex four-carbon side chain) antibody immobilized to Sepharose was used to determine the proportion of rat liver tRNAPhe species containing the peroxy Y-nucleoside. Unfractionated Unfractionated mammalian tRNA was aminoacylated with labeled phenylalanine. The phenylalanyl-tRNA was then chemically acetylated to yield N-acetylphenylalanyl-tRNA. When this preparation was applied to the antibody column, between 6-10% of the radioactivity was not bound to the column, indicating a deficiency of peroxy Y-nuceloside in a minor isoaccepting tRNAPhe species. In contrast to normal tissues (including embryonic tissue), about 85% of the tRNAPhe from mouse neuroblastoma C-1300 or N-18 tumors lack the peroxy Y-base, a property which is not affected by tumor age. Rat liver labeled N-acetylphenylalanyl-tRNA preparations were resolved on Plaskon chromatography (RPC-5) into two minor peaks closely followed by a mojor component. A high proportion of the two minor tRNAPhe species was unable to bind to anti-Y antibodies. Upon mild acid treatment, the minor and major tRNAPhe species eluted simultaneously from Plaskon columns, at a much reduced salt concentration. These results would indicate that the two minor tRNAPhe species from rat liver as well as the major component contain a tricyclic imidazopurine base that differs from each other in its side chain. About 85% of the N-acetylphenylalanyl-tRNA from neuroblastoma was resolved by Plaskon chromatography as an early eluting peak. The position of this major neuroblastoma tRNAPhe species was not altered by mild acid treatment, and its elution position from the column almost coincides with that of acid-treated normal rat liver tRNAPhe. The latter results would suggest that most of the tRNAPhe chains from neuroblastoma lack the tricyclic imidazopurine of normal rat liver tRNAPhe, but are very close if not identical in primary nucleotide sequence.