A reference DNA sequence (10 codons) is translated with the standard genetic code, then its monoisotopic peptide mass is predicted from residue masses. A simulated tandem mass spectrometer "detects" peptides by their mass-to-charge ratio (m/z), and proteogenomics matches these observed masses back to genome-predicted peptides — including ones altered by point mutations — to flag novel biomarkers or non-canonical proteoforms.
M(peptide) = Σ residue_mass(aa_i) + M(H2O)
m/z = (M(peptide) + z·M(H+)) / z
Δppm = (m/z_obs − m/z_ref) / m/z_ref × 1e6
novel if |Δppm| > tolerance_ppm
- Mutation rate — per-codon probability of a single-base substitution each time you mutate the sequence, altering translated residues (or truncating via a stop codon).
- Charge state (z) — the ionization charge assumed by the detector; changes the observed m/z for the same peptide mass.
- MS tolerance — the ppm mass-accuracy window used to call a spectral match vs. a novel (variant) peptide.
- Mutate / Reset / Auto-Scan — regenerate a variant sequence, restore the wild-type reference, or continuously fire peptides at the detector.
Real proteogenomics pipelines build custom protein databases from DNA/RNA sequencing (including patient-specific SNPs, indels and splice junctions) and search MS spectra against them to discover variant peptides invisible to standard reference databases — powering cancer neoantigen discovery and biomarker validation.