This subproject is one of many research subprojects utilizing the resources provided by a Shared Instrumentation Grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the grant, which is not necessarily the institution for the investigator. DESCRIPTION (provided by applicant): The goal of this proposal is to secure funds to purchase a multi-tiered proteomic compute (MFC) cluster for University of Washington Health Sciences Center-based principal investigators engaged in biomedical research. The MPC will be located in the School of Pharmacy Mass Spectrometry (SOP MS) facility in the Health Sciences Center, which serves as a fee-for-service operation for UW Pi's wishing to conduct proteomic experiments, and is the only such facility on the UW campus. The SOP MS facility currently has a 10-node compute cluster for processing mass spectrometry-based proteomic experiments, but none for protein folding. The MPC will expand this capability 20-fold. Both traditional hypothesis-driven protein chemistry research and hypothesis-generating research enabled by proteomic techniques will utilize the MPC cluster. All aspects of proteomic and protein chemistry-based research will be supported. For example, we will use it to: 1) fold individual proteins de novo, 2) fold entire proteomes de novo, 3) elucidate protein-protein interactions via chemical cross-linking, 4) map out sub- cellular protein locations, 5) search for multiple anticipated post-translation modifications (PTM's) on individual proteins, 6) search MS-based proteomic data for multiple unsuspected PTM's, and 7) define proteomes. Initially, the MPC cluster will be for support of researchers in the Schools of Pharmacy, Medicine, and Public Health; eventually, however, any PI on campus or from the Seattle region utilizing the SOP MS facility will be given access to the compute power. Initial projects include the following areas of biomedical research: 1) acute respiratory distress syndrome (ARDS) and other lung injury diseases under investigation at the UW- affiliated Harbor view Medical Center, 2) prions and prion folding, 3) Apolipoprotein PTM's, 4) protein-protein cross-linking, 5) vaccine candidates and therapeutic targets in Gram-negative organisms, 6) sub cellular mapping of proteins under conditions of drug-induced liver disease, and 8) toxic-proteomics.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biomedical Research Support Shared Instrumentation Grants (S10)
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Special Emphasis Panel (ZRG1-BST-D (30))
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University of Washington
Schools of Pharmacy
United States
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Cheng, Chin Jung; Daggett, Valerie (2014) Molecular dynamics simulations capture the misfolding of the bovine prion protein at acidic pH. Biomolecules 4:181-201
Jung, Sunhee; Smith, Jennifer J; von Haller, Priska D et al. (2013) Global analysis of condition-specific subcellular protein distribution and abundance. Mol Cell Proteomics 12:1421-35
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Hengel, Shawna M; Goodlett, David R (2012) A Review of Tandem Mass Spectrometry Characterization of Adenosine Diphosphate-Ribosylated Peptides. Int J Mass Spectrom 312:114-121
McCully, Michelle E; Beck, David A C; Daggett, Valerie (2012) Multimolecule test-tube simulations of protein unfolding and aggregation. Proc Natl Acad Sci U S A 109:17851-6
Moore, Eli K; Nunn, Brook L; Goodlett, David R et al. (2012) Identifying and tracking proteins through the marine water column: insights into the inputs and preservation mechanisms of protein in sediments. Geochim Cosmochim Acta 83:324-359
Merkley, Eric D; Daggett, Valerie; Parson, William W (2012) A temperature-dependent conformational change of NADH oxidase from Thermus thermophilus HB8. Proteins 80:546-55
Ting, Ying S; Shaffer, Scott A; Jones, Jace W et al. (2011) Automated lipid A structure assignment from hierarchical tandem mass spectrometry data. J Am Soc Mass Spectrom 22:856-66
Panchaud, Alexandre; Jung, Sunhee; Shaffer, Scott A et al. (2011) Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem 83:2250-7

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