Detection of neoantigens (complexes of altered peptides and HLA molecules). DNA sequencing yields information about changes in the amino acid composition that arise from somatic mutations, insertions, deletions, and translocations (gene fusions). Schischlik et al show that mRNA sequencing provides similar results plus additional information about splice variants that arise from mutations in genes encoding mRNA splicing factors. Direct identification of neoantigens involves elution of peptides from HLA molecules and sequencing by MS. A unique feature of MS is the ability to detect peptides with tumor-specific posttranslational modifications such as phosphorylation.