The PeptideXme Platform

Multi-omics discovery, structural immunology, and functional T-cell modulation

Multi-omics Discovery

Integrated long-read transcriptomics (PacBio Iso-Seq / Oxford Nanopore), immunopeptidomics (LC-MS/MS), and computational filtering to systematically identify patient-specific alternative splicing– and fusion-derived MHC class I peptides beyond somatic mutations.

Long-read RNA-seq Immunopeptidomics (MS/MS) rMATS SUPPA2 ImmunoPepper ISOTOPE SNAF

Structural Immunology

Precision targeting at the level of peptide-MHC-TCR interactions. 3D structural modeling of peptide-MHC complexes and TCR-pMHC docking to quantify binding energies and predict recognition potential.

AlphaFold2 ESMFold ColabFold TCRmodel ImmuneBuilder Rosetta FoldX

Functional T-cell Modulation

Validation of immunogenicity and TCR recognition of prioritized neoepitopes in autologous patient-derived T cells. Elucidation of regulatory mechanisms controlling expression of immunogenic AS-derived peptides.

Autologous T-cell assays TCR-seq Single-cell RNA-seq Intracellular cytokine staining

Computational Immunostructural Engineering

Rational engineering of neoepitopes combined with displacement of antagonistic self-peptides. Peptide enhancement via computational mutagenesis and ProteinMPNN to convert transient immune activation into durable, precision-guided anti-tumor immunity.

ProteinMPNN Computational mutagenesis Competitive binding modeling In silico mutational scanning

PeptideXme vs. Mutation-Only Approaches

Feature Mutation-Only Platforms PeptideXme
Neoantigen sources Somatic SNVs, indels Somatic mutations + AS-derived + fusion-derived + non-canonical
Transcriptomics Short-read RNA-seq (expression only) Long-read + short-read RNA-seq (full isoform resolution)
Immunopeptidomics Prediction only Direct MS validation of presented peptides
Structural modeling Binding affinity prediction 3D peptide-MHC-TCR structural modeling + binding energy
Peptide engineering None Rational peptide enhancement + self-peptide displacement
TME characterization Limited (gene signatures) Full immune profiling (scRNA-seq, TCR repertoire, TME deconvolution)