Onco-proteogenomics: a novel approach to identify cancer-specific mutations combining proteomics and transcriptome deep sequencing

Background The accumulation of somatic mutation is a common property in all cancer genomes. These mutations include several patterns of mutagenesis such as small insertions, chromosomal rearrangement and nucleotide substitutions. Consequently, the mutated genomes produce mutant transcriptome and, therefore, mutant proteins that give the cancer cell its oncogenic properties [1]. For such mutated proteins, however, mass spectrometrybased identification by shotgun proteomics is generally difficult because the identification is dependent on databases containing normal proteins or hybrid database with normal and mutated proteins. Here, we present ‘onco-proteogenomics, a novel proteogenomics approach to identify the cancer-related peptides (phosphoand non-phospho peptides) and proteins.