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

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 individualandapos 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 Project Narrative The detection of protein variants which differ from those predicted from the reference human genome sequence can make ideal candidates for the development of targeted treatments and diagnostics for many clinical conditions such as cancer This project proposes the development a first of its kind proteogenomics mass spectrometry search engine for the identification of protein variants making direct use of genomic data and ever growing public databases of genetic variation