Choi, Seunghyuk Ju, Shinyeong Lee, Jinwon Na, Seungjin Lee, Cheolju Paek, Eunok 2024-01-19T18:31:16Z 2024-01-19T18:31:16Z 2021-09-05 2020-01 1535-3893 https://pubs.kist.re.kr/handle/201004/119124 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 translated UTR (tUTR) 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 the H1299 cell line mass spectrometry (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 contexts of annotated initiation sites. It is also worth noting that our approach can detect translated amino acid sequences as well as provide evidence for UTR translation, while ribosome profiling provides only the translation evidence. For previously reported stop codon readthrough in MDH1 gene, we could confirm the amino acid inserted during the readthrough. English AMER CHEMICAL SOC PROTEIN-SYNTHESIS TRANSLATION Proteogenomic Approach to UTR Peptide Identification Article 10.1021/acs.jproteome.9b00498 1 JOURNAL OF PROTEOME RESEARCH, v.19, no.1, pp.212 - 220 JOURNAL OF PROTEOME RESEARCH 19 1 212 220 scie scopus 000506722100020 2-s2.0-85076243898 Biochemical Research Methods Biochemistry & Molecular Biology Article PROTEIN-SYNTHESIS TRANSLATION proteogenomics peptide identification tandem mass spectrometry untranslated regions non-AUG start codons translational readthrough