The Proteomics, Metabolomics, and Lipidomics Core will be located at Pacific Northwest National Laboratory (PNNL). PNNL OMICs Core measurements will be based upon world-class mass spectrometry (MS)-based platforms and the availability of unique capabilities and resources. Ultra-sensitive proteomics analyses will be performed using the accurate mass and time (AMT) tag approach together with high resolution mass spectrometry, a process that offers high OMIC coverage, high quantitative precision, and high sensitivity with small sample-size requirements. Quantification of global phosphopeptide measurements will be obtained using ITRAQ stable isotope labeling. The global metabolomics and lipidomics components of this Core will utilize GC-MS and LC-MS, respectively. These studies will enhance our understanding of the host response to infection by evaluating changes in the abundance for the broad range of host proteins, metabolites, and lipid molecules that directly carry out biological functions. Based on the results of complementary transcriptomics (analyzed in parallel outside of this Core) and global MS-based OMICs data or a priori knowledge of the biological systems under study, we will also then employ multiplexed targeted MS-based analyses for quantifying a defined number of substrates and/or products of corresponding encoded proteins. These targeted proteomics, metabolomics and lipidomics analyses will provide accurate absolute quantification based on stable-isotope dilution where feasible

Public Health Relevance

The broad molecular profiles for influenza, Ebola, and West Nile viral infection generated by this OMICs Core and provided to the Computational Modeling Core is expected to enable under this Program new mechanistic insights into host-pathogen interactions and thereby aid in our ability to combat global health concerns attributed to these viral infections.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
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Special Emphasis Panel (ZAI1-EC-M)
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University of Wisconsin Madison
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Nakayasu, Ernesto S; Nicora, Carrie D; Sims, Amy C et al. (2016) MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses. mSystems 1:
Gorman, Matthew J; Poddar, Subhajit; Farzan, Michael et al. (2016) The Interferon-Stimulated Gene Ifitm3 Restricts West Nile Virus Infection and Pathogenesis. J Virol 90:8212-25
Zhang, Rong; Miner, Jonathan J; Gorman, Matthew J et al. (2016) A CRISPR screen defines a signal peptide processing pathway required by flaviviruses. Nature 535:164-8
Bowen, James R; Ferris, Martin T; Suthar, Mehul S (2016) Systems biology: A tool for charting the antiviral landscape. Virus Res 218:2-9
Wang, Mingxun; Carver, Jeremy J; Phelan, Vanessa V et al. (2016) Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 34:828-37
Kyle, Jennifer E; Zhang, Xing; Weitz, Karl K et al. (2016) Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry. Analyst 141:1649-59
Burnum-Johnson, Kristin E; Nie, Song; Casey, Cameron P et al. (2016) Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry. Mol Cell Proteomics 15:3694-3705
Hyde, Jennifer L; Diamond, Michael S (2015) Innate immune restriction and antagonism of viral RNA lacking 2׳-O methylation. Virology 479-480:66-74
Totura, Allison L; Whitmore, Alan; Agnihothram, Sudhakar et al. (2015) Toll-Like Receptor 3 Signaling via TRIF Contributes to a Protective Innate Immune Response to Severe Acute Respiratory Syndrome Coronavirus Infection. MBio 6:e00638-15
Lazear, Helen M; Diamond, Michael S (2015) New insights into innate immune restriction of West Nile virus infection. Curr Opin Virol 11:1-6

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