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bioRxiv · 10.1101/2025.04.07.647596

A modular, Galaxy-based immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of candidate cancer neoantigen peptides

Mehta, S.·Wagner, R.·Do, K. T.·Johnson, J. E.·Yu, F.·Jubenville, T.·Richards, K.·Coleman, S.·Popescu, F. E.·Nesvizhskii, A. I.·Largaespada, D. A.·Jagtap, P. D.·Griffin, T. J.
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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.

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Mehta, S., Wagner, R., Do, K. T., Johnson, J. E., Yu, F., Jubenville, T., Richards, K., Coleman, S., Popescu, F. E., Nesvizhskii, A. I., Largaespada, D. A., Jagtap, P. D., Griffin, T. J.. 2025-04-08. A modular, Galaxy-based immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of candidate cancer neoantigen peptides. https://doi.org/10.1101/2025.04.07.647596

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