Posttranscriptional modifications are characteristic structural features of RNA molecules. To study the functional roles played by RNA modifications, it is necessary to identify the genes and enzymes that are responsible for their biosynthesis. Many uncharacterized genes for RNA modifications still remain buried in the genomes of model organisms. We describe here a systematic genomewide screening method that uses a reverse genetic approach combined with mass spectrometry, which we have named "ribonucleome analysis," to identify uncharacterized genes that are involved in generating RNA modifications.