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What Is a Neoantigen? A Practical Guide for Experimental Researchers

By Lociven · NeoantigenLab · July 2026 If you work in cancer immunology, you have heard the word neoantigen more times than you can count. It appears in grant proposals, immunotherapy papers, and tumor board discussions. But the explanations are usually either too shallow ("mutated peptides the immune system can recognize") or buried in computational methods papers that assume you already know what a VCF file is. This post is for the wet-lab side of the room — the researchers who understand tumor biology and immunology but want a clear picture of what neoantigens are, where they come from, and why the field cares so much about them. Figure 1. Most somatic mutations do not become immunogenic neoantigens. Each step — coding region, MHC binding, processing, T cell recognition — acts as a filter. The core idea A neoantigen is a peptide fragment, derived from a tumor-specific somatic mutation, that can be presented on the surface of a cancer cell via MHC molecule...
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NetMHCpan Explained: How MHC Binding Prediction Works and How to Read the Output

By Lociven · NeoantigenLab · July 2026 You run NetMHCpan on your mutant peptide list and get back a table full of percentile ranks, EL scores, and BA scores. One peptide shows 0.48% rank. Another shows 2.1%. What does that mean, and which one should you follow up on? NetMHCpan is the most widely used MHC-I binding prediction tool in neoantigen research. Most papers cite it, most pipelines include it, and most wet-lab researchers who encounter its output don't fully understand what it's predicting. This post explains the model, the output, and where interpretation goes wrong. What NetMHCpan predicts NetMHCpan predicts the binding affinity between a peptide and an MHC class I molecule. More precisely, it predicts two things: Binding affinity (BA) : Estimated IC50 in nM — the concentration of peptide needed to displace 50% of a reference ligand from the HLA molecule. Lower IC50 = stronger binder. The common threshold is IC50 < 500 nM for "weak binder,...
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Tumor Mutational Burden (TMB): What It Measures, What It Doesn't, and How to Interpret It

By Lociven · NeoantigenLab · July 2026 Your pathology report comes back with a TMB of 14 mut/Mb. The oncologist asks whether this patient is likely to respond to pembrolizumab. What do you actually say? Tumor mutational burden has become one of the most frequently cited biomarkers in solid tumor immunotherapy — and one of the most frequently misunderstood. This post explains what TMB measures, how it is calculated, what the FDA approval actually covers, and what it cannot tell you. What TMB measures — and what it doesn't TMB is a count of somatic mutations per megabase of coding sequence sequenced. That is all it is. It does not measure: Whether any of those mutations produce peptides that bind HLA Whether those peptides are actually presented on tumor cell surfaces Whether the patient has T cells that recognize them Whether the tumor microenvironment is immunologically accessible TMB is a proxy. More mutations → more potential neoantigens → higher p...
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