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

Project Summary / Abstract Mass spectrometry-based proteomics, used in conjunction with genomics, has been called proteogenomics. Recent exponential increases in variant identification by next-generation sequencing (NGS) is redefining the concept of the human genome/proteome. Our project is the commercialization of a first-to-market proteomic database search engine for mass spectrometry capable of directly reading NGS data for the identification of mutilations from individual samples or from curated resources. Such an offering has the potential to bring together these two fields, enabling validation of mutations at the protein-level. Mutated proteins have been shown to make ideal targets for drug therapies and diagnostics in cancer. Our software will provide an intuitive user experience, approachable by scientists who may not be expert both proteomic and genomic data analysis. Since the search engine is guided by prior knowledge, performance exceeds current practice. The software will come complete with a full array of post-processing validation, and visualization tools.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” search engine for the identification of protein variants by mass spectrometry, making direct use of genomic data and ever-growing public and private databases of genetic variation.