Bioinformatics solutions for confident identification and targeted quantification of proteins using tandem mass spectrometry

Proteins are the structural supports, signal messengers and molecular workhorses that underpin living processes in every cell. Understanding when and where proteins are expressed, and their structure and functions, is the realm of proteomics. Mass spectrometry (MS) is a powerful method for identifying and quantifying proteins, however, very large datasets are produced, so researchers rely on computational approaches to transform raw data into protein information. This project develops new bioinformatics solutions to support the next generation of proteomic MS research. Part I introduces the state of the art in proteomic bioinformatics in industry and academia. The business history and funding mechanisms are examined to fill a notable gap in management research literature, and to explain events at the sponsor, GlaxoSmithKline. It reveals that public funding of proteomic science has yet to come to fruition and exclusively high-tech niche bioinformatics businesses can succeed in the current climate. Next, a comprehensive review of repositories for proteomic MS is performed, to locate and compile a summary of sources of datasets for research activities in this project, and as a novel summary for the community. Part II addresses the issue of false positive protein identifications produced by automated analysis with a proteomics pipeline. The work shows that by selecting a suitable decoy database design, a statistically significant improvement in identification accuracy can be made. Part III describes development of computational resources for selecting multiple reaction monitoring (MRM) assays for quantifying proteins using MS. A tool for transition design, MRMaid (pronounced „mermaid‟), and database of pre-published transitions, MRMaid-DB, are developed, saving practitioners time and leveraging existing resources for superior transition selection. By improving the quality of identifications, and providing support for quantitative approaches, this project brings the field a small step closer to achieving the goal of systems biology.