PeptideXme

Precision Neoantigen Discovery

PeptideXme is your personal cancer genomic, epigenetic, and immune passport, built before cancer happens. We combine your genetic mutations, gene fusions, alternative splicing, epigenetic and immune characteristics to build your personalized molecular profile and identify potential neoantigens and peptide targets. The vision is to create a lifelong molecular profile that can help you understand your cancer biology, monitor changes over time, and prepare for more personalized prevention and treatment.

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The PeptideXme Pipeline

Discover

Multi-omics neoantigen discovery from long-read transcriptomics, immunopeptidomics, and computational filtering

Engineer

Rational peptide design and structural immunology modeling of peptide-MHC-TCR interactions

Report

Patient-specific reports with ranked neoantigen candidates, immune profiling, and therapeutic recommendations

Beyond Somatic Mutations

Mutation-derived neoantigens are limited in HCC and insufficient to explain inter-patient variability in immunotherapy response. Alternative splicing events and gene fusions generate individualized transcriptomic diversity capable of producing tumor-specific peptides independent of mutation burden.

  • Alternative splicing–derived neoepitopes: tumor-specific peptides from aberrant splice junctions, invisible to exome-only approaches
  • Fusion-derived neoepitopes: novel peptides at gene fusion breakpoints, validated by long-read transcriptomics
  • Immunopeptidomics validation: direct MS identification of MHC-I presented peptides, confirming actual presentation
  • Computational immunostructural engineering: rational peptide enhancement and self-peptide displacement design

Initial Focus: Hepatocellular Carcinoma

HCC remains a leading cause of cancer-related mortality worldwide. The liver's intrinsic immune tolerance and the adaptive immunosuppressive TME limit durable immunotherapy responses. PeptideXme targets this challenge with precision neoantigen discovery — and the platform architecture is extensible to other cancer types.