Proteogenomic approach to UTR peptides identification

Recent sequencing technologies have highlighted translation of untranslated regions (UTRs) in genomes although it remains unknown whether the translated products persist in a cell. Here we propose a proteogenomic approach to UTR identification at the proteome level, which has been challenging due to the lack of corresponding sequences required for peptide-spectrum matching. We address the challenge with constructing tUTR (translated UTR) database, consisting of all hypothetical sequences that can be translated from UTR by assuming non-AUG initiation at near-cognate start codons and stop codon readthrough. In the analysis of H1299 cell line MS/MS dataset, the tUTR DB-based proteogenomic approach enabled the detection of 52 5’-UTR and 9 3’-UTR peptides from 45 and 9 genes, respectively. The identified UTR peptides were validated via high spectral similarity with their synthetic peptides. The 5’-UTR peptides pointed out alternative initiation sites with non-AUG start codons, which exactly conformed to Kozak ...