Current status of cancer proteogenomics: a brief introduction

Abstract

Proteogenomics is a novel approach to understand the molecular backgrounds of diseases. In cancer research, proteomic studies have been conducted without using the genome data of individual samples. For example, a common public database has always been used to identify proteins by mass spectrometry. However, tumor genomes, even tumors of the same type of cancer, can differ considerably, and such differences affect the response to treatments. Thus, genomic backgrounds should be considered when identifying proteins by mass spectrometry. In cancer proteogenomics, a virtual proteome database is generated using the genome data of identical samples for the mass spectrometric identification of proteins reflecting genetic mutations, which are not common and not cited in the commonly used databases. Such proteins are candidate biomarkers and therapeutic targets. Although previous studies have reported software capable of translating genomic data to proteomic data, a standard protocol has not been established. In addition, the utility of proteogenomics has also not been established, and it is not self-evident that proteins with mutations unique to certain groups can be exploited for innovative treatments or to provide clues for the resolution of biological problems in cancers. Collaborative efforts by cancer researchers and specialists in mass spectrometry and bioinformatics are required for fruitful advancements.