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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Kyle, Jennifer E; Aly, Noor; Zheng, Xueyun et al. (2018) Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry. Bioanalysis 10:279-289
Gralinski, Lisa E; Sheahan, Timothy P; Morrison, Thomas E et al. (2018) Complement Activation Contributes to Severe Acute Respiratory Syndrome Coronavirus Pathogenesis. MBio 9:
Menachery, Vineet D; Gralinski, Lisa E; Mitchell, Hugh D et al. (2018) Combination Attenuation Offers Strategy for Live Attenuated Coronavirus Vaccines. J Virol 92:
Menachery, Vineet D; Schäfer, Alexandra; Burnum-Johnson, Kristin E et al. (2018) MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape. Proc Natl Acad Sci U S A 115:E1012-E1021
Agnihothram, Sudhakar; Menachery, Vineet D; Yount Jr, Boyd L et al. (2018) Development of a Broadly Accessible Venezuelan Equine Encephalitis Virus Replicon Particle Vaccine Platform. J Virol 92:
Thackray, Larissa B; Handley, Scott A; Gorman, Matthew J et al. (2018) Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections. Cell Rep 22:3440-3453.e6
Couvillion, Sneha P; Zhu, Ying; Nagy, Gabe et al. (2018) New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. Analyst :
White, James P; Xiong, Shanshan; Malvin, Nicole P et al. (2018) Intestinal Dysmotility Syndromes following Systemic Infection by Flaviviruses. Cell 175:1198-1212.e12
Wojcik, Roza; Webb, Ian K; Deng, Liulin et al. (2017) Lipid and Glycolipid Isomer Analyses Using Ultra-High Resolution Ion Mobility Spectrometry Separations. Int J Mol Sci 18:
Burnum-Johnson, Kristin E; Kyle, Jennifer E; Eisfeld, Amie J et al. (2017) MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. Analyst 142:442-448

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