The integration of genomics and proteomics has led to the emergence of proteogenomics, a field of research successfully applied to the characterization of cancer samples. The diagnosis, prognosis and response to therapy of cancer patients will largely benefit from the identification of mutations present in their genome. The current state of the art of high throughput experiments for genome-wide detection of somatic mutations in cancer samples has allowed the development of projects such as the TCGA, in which hundreds of cancer genomes have been sequenced. This huge amount of data can be used to generate protein sequence databases in which each entry corresponds to a mutated peptide associated with certain cancer types. In this chapter, we describe a bioinformatics workflow for creating these databases and detecting mutated peptides in cancer samples from proteomic shotgun experiments. The performance of the proposed method has been evaluated using publicly available datasets from four cancer cell lines.
Keywords: Cancer research; Proteogenomics; SAP detection; TCGA project.