Identification of non-canonical peptides with moPepGen Article Swipe

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Proteogenomics Computational biology Biology RNA Gene Unobservable Identification (biology) Proteome Germline Genetics Somatic cell Transcriptome Open reading frame Genome Genomics Gene expression Peptide sequence Epistemology Philosophy Botany

Chenghao Zhu , Lydia Liu , Annie Ha , Takafumi N. Yamaguchi , Helen He Zhu , Rupert Hugh-White , Julie Livingstone , Yash Patel , Thomas Kislinger , Paul C. Boutros ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.1038/s41587-025-02701-0 · OA: W4411328709

Proteogenomics is limited by the challenge of modeling the complexities of gene expression. We create moPepGen, a graph-based algorithm that comprehensively generates non-canonical peptides in linear time. moPepGen works with multiple technologies, in multiple species and on all types of genetic and transcriptomic data. In human cancer proteomes, it enumerates previously unobservable noncanonical peptides arising from germline and somatic genomic variants, noncoding open reading frames, RNA fusions and RNA circularization.