LTQ-Orbitrap XL for protein identification and biomarker discovery

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DESCRIPTION (provided by applicant): The current proposal will help to expand the Institute for Systems Biology's (ISB's) Proteomics facility by providing capital to purchase an LTQ-Orbitrap XL with electron transfer dissociation (ETD) capability. Currently the Proteomics facility's focus is on the application of novel approaches to systematically characterize and quantify proteins and their modifications in cells, tissues, and in macromolecular assemblies. This will allow for the detection of dynamic changes in protein expression profiles or protein complex composition that are characteristic for biological processes or medical conditions. Numerous collaborations exist between the facility and NIH supported biomedical researchers that are outlined in this proposal covering areas as diverse as the innate immune system, the search for biomarkers of disease such as diabetes, prostate and bladder cancer, and basic mechanisms of gene regulation, DNA repair, chromosome segregation, and cellular differentiation. This is being accomplished, in part, through the development of a novel proteomic strategy that first attempts to comprehensively map the proteomic space, to collect the data from proteome mapping in a database and to use the prior information for robust, fast and reproducible proteome analysis. This represents a significant departure from the traditional proteomics approaches in which in every experiment the proteins in a sample are identified de novo without using prior knowledge from other proteomics experiments. It has become apparent that the novel strategy is essential to reach the goal of comprehensive, quantitative proteome analysis using mass spectrometry. Access to the requested instrument would greatly accelerate our ability to complete the proteome maps because it can be expected that precursors that are difficult to fragment by CAD would be amenable to fragmentation by ETD. Furthermore, the combination of high mass accuracy and mass resolution with ETD fragmentation technology enables the characterization of larger peptides and improves the confidence of peptide identification. Altogether, these characteristics of the Orbitrap with ETD will significantly enhance our ability to comprehensively characterize proteomes, subproteomes and individual proteins. ETD technology is not currently available at ISB and the limited access to instruments that possess high mass accuracy/resolution with the ability to perform electron transfer reactions in the Seattle area will not meet our requirements. PUBLIC HEALTH RELEVANCE Proteins play a major role in executing virtually all cellular functions. As such, the ability to comprehensively characterize their dynamic expression levels, modification states, and molecular interactions in normal and perturbed systems provides information that is essential to understand the molecular underpinnings of cellular function in health and disease. The requested instrumentation provides the technology that will allow us to attain our ambitious goal of comprehensive proteome characterization.