Understanding the full complexity of proteins in cancer is a major challenge for scientists. Many proteins are made in unusual ways that don’t follow the standard rules we learn in biology class. These “non-canonical” peptides can be important in disease, but they are often missed in typical genetic and protein studies. A team of researchers from UCLA has developed a new computational tool called moPepGen to help find these hidden proteins.

moPepGen is a graph-based algorithm that takes genetic and RNA sequencing data and predicts a wide range of non-standard peptides quickly and efficiently. It works across different species and with various types of genomic data. In human cancer samples, moPepGen identified many non-canonical peptides, including those created by uncommon events like RNA fusions, circular RNA, and genetic mutations. These findings could improve how we detect and understand cancer, helping researchers build better diagnostic tools and treatments.

moPepGen is a graph-based algorithm that uncovers non-canonical peptides with variant combinations

a, moPepGen algorithm schematic. moPepGen is a graph-based algorithm that generates databases of non-canonical peptides that harbor genomic and transcriptomic variants (for example, single-nucleotide variant (SNV), small insertion and deletion (INDEL), RNA editing, alternative splicing, gene fusion and circular RNA (circRNA)) from coding transcripts, as well as from novel open reading frames of noncoding transcripts. C-term, C terminus; N-term, N terminus. b,c, moPepGen achieves linear runtime complexity when fuzz testing with SNVs only (b) and with SNVs and indels (c), based on 1,000 simulated test cases in each panel. d, A variant peptide from SYNPO2 that harbors a small deletion and an SNV. Fragment ion mass spectrum from peptide-spectrum match (PSM) of the non-canonical peptide harboring two variants (top, both) is compared against the canonical peptide theoretical spectra (left, theoretical spectra at the bottom) and against the variant peptide theoretical spectra (right, bottom). Fragment ion matches are colored, with b-ions in blue and y-ions in red. e–g, A somatic SNV D1249N in AHNAK was detected in DNA sequencing of a prostate tumor (CPCG0183) at chr11:62530672 (e), in RNA sequencing (f) and as the non-canonical peptide MDIDAPDVEVQGPNWHLK (g). RNA-Seq, RNA sequencing; WGS, whole-genome sequencing. h,i, Fragment ion mass spectrum from PSM of the canonical peptide MDIDAPDVEVQGPDWHLK (h) and the non-canonical peptide (i). m/z, mass-to-charge ratio.