Proteogenomics is the study of how information about the DNA in a cell or organism relates to the proteins made by that cell or organism. This includes understanding how genes control when proteins get made and what changes occur to proteins after they are made that may switch them on and off.

Genetic variant detection has important implications for confirming the presence of somatic or germline mutations, which may be important drivers of cancer and other diseases and differentiated from ancestral variation. Mutations in cancer hallmark genes make ideal candidates for new targeted drug development for known and emerging variants. Variant detection also has applications in forensics which involve protein measurements.

Proteome software have developed Scaffold Variants to enable the detection of genetic variation directly from MS/MS proteomic data.