Here, we establish a sequence-resolved mouse liver small-RNA epitranscriptomic database by integrating nucleoside-level modification discovery with complementary RNase T1 and RNase A LC–MS/MS oligonucleotide mapping, enabling high-confidence modification-site annotation across tRNAs, 5S and 5.8S rRNAs, miRNAs, snRNAs, and snoRNAs.