Development of a Proteogenomic Search Engine for Direct Mass Spectrometric Identification of Variant Proteins Using Genomic Data

Spectragen Informatics, Llc, Bainbridge Island WA

Investigators

Abstract

Project Summary / Abstract Next-generation sequencing (NGS) technologies are uncovering a wealth of information regarding genetic differences at the DNA-level. These differences can be either inheritable or occur in somatic cells during the course of an individual's lifetime. In rare but important cases, these differences occur in coding regions, giving rise to mutated protein forms. Such proteins can have aberrant activity and lead to diseases such as cancer. While genomic data provides circumstantial evidence, mass spectrometry can confirm the presence of such proteins in patient samples. However, software used for the identification of proteins by mass spectrometry does not routinely make use of variant information, such as that stored in dbSNP. Our application proposes to solve this problem by enabling direct input of NGS data files and searching of public variant databases. This software would be a first-of-its-kind ?proteogenomics? search engine which will be used to simply and accurately identify variants at the protein-level, enabling the further design of targeted therapies.