A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates

Abstract Characterizing tumor-specific neoantigen peptides, derived from genomic or transcriptomic aberrations and presented to the immune system, is critical for immuno-oncology studies. To this end, the modular iPepGen immunopeptidogenomics pipeline provides these functions: (1) Neoantigen prediction and protein database generation from genomic or transcriptomic sequencing data; (2) Peptide identification (3) Verification from immunopeptidomic mass spectral data; (4) Neoantigen classification and visualization; (5) Candidate prioritization for further study. Easy access via a publicly available, scalable cloud-based gateway coupled with online, interactive training materials streamlines the adoption by cancer researchers who require immunopeptidogenomic analysis tools but lack advanced computational expertise and resources. Competing Interest Statement A.I.N. and F.Y. receive royalties from the University of Michigan for the sale of MSFragger, IonQuant, and diaTracer software licenses to commercial entities. All license transactions are managed by the University of Michigan Innovation Partnerships office, and all proceeds are subject to the university's technology transfer policy. D.A.L. is the co-founder and co-owner of NeoClone Biotechnologies, Inc., Discovery Genomics, Inc. (recently acquired by Immusoft, Inc.), B-MoGen Biotechnologies, Inc. (recently acquired by Bio-Techne Corporation), and Luminary Therapeutics, Inc. The business of all these companies is unrelated to the contents of this abstract. Footnotes The new version incorporates changes made to the existing workflow, added newer versions of tools and adds features with new capabilities.