The potential of proteogenomics in oncology

Proteogenomics has been applied in multiple studies in humans and in many other model organisms (5-8) although these early works not always represent a coordinated contribution of genomic and proteomic data. Improvements of proteomic methods and the growing number of genomic data produced by NGS lead to a wider application of proteogenomic studies in the strictest sense of the word. A high number of reports on human proteome is focused on the identification of novel peptides and peptide variants by a proteogenomic approach (9-11). In particular, the most important applications of proteogenomics have been related to the oncology field for the detection of abnormal protein variants in different kind of tumors mainly thanks to the work of the NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) (11-13). The article “Proteogenomics connects somatic mutations to signaling in breast cancer” by Mertins et al. and with the collaboration of the CPTAC, published on June 2016 in Nature (14), finds its object in the understanding of how genomic changes drive the proteome and phosphoproteome to generate phenotypic characteristics. It is the second of three important papers on three different tumors (colorectal, breast and ovarian respectively) (11,13,14) previously analyzed by The Cancer Genome Atlas (TCGA). The general aim is integrating proteomic measurements with the genomic yielding a number of insights into the diseases (13).