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Experimental window exposure

Explore delivery assumptions with the MHCtools exposure model. This analysis leaves vaccine ranking and products unchanged.

Run

Start with an enriched --output-epitopes file containing native antigen contexts and saved per-allele scores. The command evaluates all admitted, target-containing SLP windows in the length range, before ranking or count limits.

Save this minimal profile.json; kinetics remain unassessed until supplied:

{
  "scenario": "IM SLP comparison; kinetics not supplied",
  "times_hours": [0, 1, 2, 4, 8, 24, 48],
  "administration": "IM"
}

vaxrank-window-exposure --input-epitopes native.tsv --profile profile.json \
  --min-length 20 --max-length 30 --n-term free --c-term free \
  --output-dir window-exposure

Outputs: request.json, exposure.json, cores.csv and report.md. The request also works with mhctools vaccine-windows.

Interpret

  • Free linear peptides default to 1 µg per window. Supply the actual terminal chemistry; modified peptides remain unassessed by the current engine.
  • Missing context, scores or admission appear as coverage gaps. No new prediction or source reconstruction occurs; provenance and admission records are retained.
  • Supply explicit kinetic rates and cleavage assessments under kinetics. Per-window overrides use candidates[window_id].
  • The tracked interval is the saved scored ligand. A shorter documented core uses core_intervals with prediction ID, allele, source and zero-based, half-open coordinates within that ligand. Affinity alone does not identify a shorter core. Original ligand scores and provenance remain recorded.
  • APC arrival, blood persistence and pMHC exposure are different outputs. Core marginals cannot be summed as unique dose fractions; weighted means require numerical assessments for every contributing core.

For rates, units and sensitivity examples, see the MHCtools window guide. For mRNA, use the full-construct model with the actual encoded construct, transcript dose and delivery assumptions. The SLP command does not infer an RNA sequence from a protein window.