Collaborative Proteomics Research for Kentucky: A Standard Bioinformatics Infrastructure for Proteomics Data at the University of Kentucky and University of Louisville

Abstract: This proposal requests funds to establish a Collaborative Research Development Program (CRDP) to support the development of a core team of proteomic scientists at UK and UofL. To establish this team, a critical need is to implement standards and innovation for the analysis and comparison of proteomics data. A standardized, validated informatics infrastructure will provide researchers with a foundation onto which the data analysis tools required for technology innovations can be implemented and creates access for non-proteomic specialists throughout the Commonwealth. Technology advances in mass spectrometry (MS) make it the essential tool for the study of the primary structure of proteins and therefore the central technology for proteomics. Three MS facilities and three independent MS labs, active in proteomics, have been established at Kentucky's research universities since 2001, but access to the MSfacilities has been limited for some of the most promising applications. Protein identification in complex mixtures and analysis of protein expression are not provided as a service to researchers due to the complexities of data analysis. The nature of these complexities has to do with comparing data that can be generated by a variety of instrumentation and software. This also creates a challenge for innovation as there is no accepted baseline from which to extend data analysis. Recent initiatives are providing standards that will give practitioners and editors alike an appreciation of the necessary level of information to ensure the integrity of assignments and thus preserve the accuracy of scientific records. The UK MSfacility has a working implementation of a data analysis pipeline based on a similar initiative from the Institute for Systems Biology (a major genomics research institute formally associated with the University of Washington). The goal of this CROPwill be to extend the scope of the UK MSfacility's analysis pipeline to include _allproteomics facilities in Kentucky, thereby achieving the baseline infrastructure required to obtain additional funding from technology innovation and creating increased access to Kentucky's proteomic resources.