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Journal Publications by year

2013 Journal Publications

"Activated CIpP kills persisters and eradicates a chronic biofilm infection," B. P. Conlon, E. S. Nakayasu, L. E. Fleck, M. D. LaFleur, V. M. Isabella, K. Coleman, S. N. Leonard, R. D. Smith, J. N. Adkins, and K. Lewis, Nature, 503 (7476): 365-370 (2013).
NIHMSID: 576642

"Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30," L. N. Anderson, D. E. Culley, B. A. Hofstad, L. M. Chauvigne-Hines, E. M. Zink, S. O. Purvine, R. D. Smith, S. J. Callister, J. M. Magnuson, and A. T. Wright, Mol Biosyst., 9 (12): 2992-3000 (2013).
NIHMSID: 537073

"Approach to cerebrospinal fluid (CSF) biomarker discovery and evaluation in HIV infection," R. W. Price, J. Peterson, D. Fuchs, T. E. Angel, H. Zetterberg, L. Hagberg, S. Spudich, R. D. Smith, J. M. Jacobs, J. N. Brown, and M. Gisslen, J Neuroimmune Pharmacol, 8 (5): 1147-1158 (2013).
PMCID: PMC3889225

"Assigning quantitative function to post-translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output," D. Pincus, C. J. Ryan, R. D. Smith, R. Brent, and O. Resnekov, PLoS One, 8 (3): e56544 (2013).
PMCID: PMC3595240

"Capillary isotachophoresis-nanoelectrospray ionization-selected reaction monitoring MS via a novel sheathless interface for high sensitivity sample quantification," C. Wang, C. S. Lee, R. D. Smith, and K. Tang, Anal Chem., 85 (15): 7308-7315 (2013).
PMCID: PMC3744340

"Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria," R. C. Taylor, B. J. Webb-Robertson, L. M. Markillie, M. H. Serres, B. E. Linggi, J. T. Aldrich, E. A. Hill, M. F. Romine, M. S. Lipton, and H. S. Wiley, Integr Biol, 5 (11): 1393-1406 (2013).
PMCID: PMC3968953

"A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MC proteomics experiments," M. M. Matzke, J. N. Brown, M. A. Gritsenko, T. O. Metz, J. G. Pounds, K. D. Rodland, A. K. Shukla, R. D. Smith, K. M. Waters, J. E. McDermott, and B. J. Webb-Robertson, Proteomics, 13 (3-4): 493-503 (2013).
PMCID: PMC3775642

"Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation duing Francisella infection," E. S. Nakayasu, R. Tempel, X. A Cambronne, V. A. Petyuk, M. B. Jones, M. A. Gritsenko, M. E. Monroe, F. Yang, R. D. Smith, J. N. Adkins, and F. Heffron, Mol Cell Proteomics, 12 (11): 3297-3309 (2013).
PMCID: PMC3820940

"Controlled dispensing and mixing of pico- to nanoliter volumes using on-demand droplet-based microfluidics," X. Sun, K. Tang, R. D. Smith, and R. T. Kelly, Microfluid Nanofluidics, 15 (1): 117-126 (2013).
PMCID: PMC3736999

"Determination of burn patient outcome by large-scale quantitative discovery proteomics," C. C. Finnerty, M. G. Jeschke, W. J. Qian, A. Kaushal, W. Xiao, T. Liu, M. A. Gritsenko, R. J. Moore, D. G. Camp, II, L. L. Moldawer, C. Elson, D. Schoenfeld, R. Gamelli, N. Gibran, M. Klein, B. Arnold, D. Remick, R. D. Smith, R. Davis, R. G. Tompkins, D. N. Herndon, Crit Care Med., 41 (6): 1421-1434 (2013).
PMCID: PMC3660437

"Disparate proteome responses of pathogenic and non pathogenic aspergilla to human serum measured by activity-based protein profiling (ABPP)," S. D. Wiedner, C. Ansong, B. J. Webb-Robertson, L. M. Pederson, S. Fortuin, B. A. Hofstad, A. K. Shukla, E. A. Panisko, R. D. Smith, and A. T. Wright, Mol Cell Proteomics, 12 (7): 1791-1805 (2013).
PMCID: PMC3708166

"Evaluation of selected binding domains for the analysis of ubiquitinated proteomes," E. S. Nakayasu, C. Ansong, J. N. Brown, F. Yang, D. Lopez-Ferrer, W. J. Qian, R. D. Smith, and J. N. Adkins, J Am Soc Mass Spectrom., 24 (8): 1214-1223 (2013).
PMCID: PMC3715598

"Fast and accurate database searches with MS-GF+ percolator," V. Granholm, S. Kim, J. C. Navarro, E. Sjolund, R. D. Smith, and L. Kall, J Proteome Res.. 13 (2): 890-897 (2014).
PMCID: PMC3975676

"The genome organization of thermotoga maritime reflects its lifestyle," H. Latif, J. A. Lerman, V. A. Portnoy, Y. Tarasova, H. Nagarajan, A. C. Schrimpe-Rutledge, R. D. Smith, J. N. Adkins, D. H. Lee, Y. Qiu, and K. Zengler, PLoS Genet, 9 (4): e1003485 (2013).
PMCID: PMC3636130

"Gray matter is targeted in first-attach multiple sclerosis," S. E. Schutzer, T. E. Angel, T. Liu, A. A. Schepmoes, F. Xie, J. Bergquist, L. Vecsei, D. Zadori, D. G. Camp, II, B. K. Holland, R. D. Smith, and P. K. Coyle, PLoS One, 8(9): e66117 (2013).
PMCID: PMC3769274

"High-definition differential ion mobility spectrometry with resolving power up to 500," A. A. Shvartsburg, T. A. Seim, W. F. Danielson, R. Norheim, R. J. Moore, G. A. Anderson, and R. D. Smith, Am Soc Mass Spectrom., 24 (1): 109-114 (2013).
PMCID: PMC3581339

"High-resolution differential ion mobility spectrometry of a protein," A. A. Shvartsburg and R. D. Smith, Anal Chem., 85 (1): 10-13 (2013).
PMCID: PMC3552553

"Identification of widespread adenosine nucleotide binding in mycobacterium tuberculosis," C. Ansong, C. Ortega, S. H. Payne, D. H. Haft, L. M. Chauvignè-Hines, M. P. Lewis, A. R. Ollodart, S. O. Purvine, A. K. Shukla, S. Fortuin, R. D. Smith, J. N. Adkins, C. Grundner, and A. T. Wright, Chem Biol, 20 (1): 123-133 (2013).
PMCID: PMC3558932

"Impact of pregnancy on the pharmacokinetics of dibenzo[def,p]chrysene in mice," S. R. Crowell, A. K. Sharma, S. Amin, J. J. Soelberg, N. C. Sadler, A. T. Wright, W. M. Baird, D. E. Williams, and R. A. Corley, Toxicol Sci., 135 (1): 48-62 (2013).
PMCID: PMC3748759

"In-source fragmentation and the sources of partially tryptic peptides in shotgun proteomics," J. S. Kim, M. E. Monroe, D. G. Camp II, R. D. Smith and W.-J. Qian, J. Proteome Res., 12 (2): 910-916 (2013).
PMCID: PMC3584699

"LC-IMS-MS feature finder: detecting multidimensional liquid chromatography, ion mobility and mass spectrometry features in complex datasets," K. L. Crowell, G. W. Slysz, E. S. Baker, B. L. LaMarche, M. E. Monroe, Y. M. Ibrahim, S. H. Payne, G. A. Anderson, and R. D. Smith, Bioinformatics, 29 (21): 2804-2805 (2013).
PMCID: PMC3799467

"Long-gradient separations coupled with selected reaction monitoring for highly sensitive, large scale targeted protein quantification in a single analysis," T. Shi, T. L. Fillmore, Y. Gao, R. Zhao, J. He, A. A. Schepmoes, C. D. Nicora, C. Wu, J. L. Chambers, R. J. Moore, J. Kagan, S. Srivastava, A. Y. Liu, K. D. Rodland, T. Liu, D. G. Camp, II, R. D. Smith, and W. J. Qian, Anal Chem., 85(19): 9196-9203 (2013).
PMCID: PMC3839867

"Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury," L. E. Gralinski, A. Bankhead, S. Jeng, V. D. Menachery, S. Proll, S. E. Belisle, M. Matzke, B. J. Webb-Robertson, M. L. Luna, A. K. Shukla, M. T. Ferris, M. Bolles, J. Chang, L. Aicher, K. M. Waters, R. D. Smith, T. O. Metz, G. L. Law, M. G. Katze, S. McWeeney, and R. S. Baric, MBio, 4 (4): e00271 (2013).
PMCID: PMC3747576

"Mixed-isotope labeling with LC-IMS-MS for characterization of protein-protein interactions by chemical cross-linking," E. D. Merkley, E. S. Baker, K. L. Crowell, D. J. Orton, T. Taverner, C. Ansong, Y. M. Ibrahim, M. C. Burnett, J. R. Cort, G. A. Anderson, R. D. Smith, and J. N. Adkins, J Am Soc Mass Spectrom, 24 (3): 444-449 (2013).
PMCID: PMC3594340

"MultiAlign: A multiple LC-MS analysis tool for integrated omics analysis," B. L. LaMarche, K. L. Crowell, N. Jaitly, V. A. Petyuk, A. R. Shah, A. D. Polpitiya, J. D. Sandoval, G. R. Kiebel, M. E. Monroe, S. J. Callister, T. O. Metz, G. A. Anderson, and R. D. Smith, BMC Bioinformatics, 14: 49 (2013).
PMCID: PMC3599190

"Multi-omic data integration links deleted in breast cancer 1 (DBC1) degradation in chromatin remodeling in inflammatory response," E. S. Nakayasu, R. N. Brown, C. Ansong, M. A. Sydor, S. Imtiaz, C. Mihai, R. Sontag, K. K. Hixson, M. E. Monroe, T. J. Sobreira, G. Orr, V. A. Petyuk, F. Yang, R. D. Smith, and J. N. Adkins, Mol Cell Proteomics, 12 (8): 2136-2147 (2013).
PMCID: PMC3734575

"A multi-omic systems approach to elucidating Yersinia virulence mechanisms," C. Ansong, A. C. Schrimpe-Rutledge, H. D. Mitchell, S. Chauhan, M. B. Jones, Y. M. Kim, K. McAteer, B. L. Deatherage Kaiser, J. L. Dubois, H. M. Brewer, B. C. Frank, J. E. McDermott, T. O. Metz, S. N. Peterson, R. D. Smith, V. L. Motin, and J. N. Adkins, Mol Biosyst, 9 (1): 44-54 (2013).
PMCID: PMC3518462

"A multi-omic view of host-pathogen-commensal interplay in Salmonella-mediated intestinal infection," B. L. Deatherage Kaiser, J. Li, J. A. Sanford, Y. M. Kim, S. R. Kronewitter, M. B. Jones, C. T Peterson, S. N. Peterson, B. C. Frank, S. O. Purvine, J. N. Brown, T. O. Metz, R. D. Smith, F. Heffron, and J. N. Adkins, PLoS One, 8(6):e67155 (2013).
PMCID: PMC3694140

"A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses," H. D. Mitchell, A. J. Eisfeld, A. C. Sims, J. E. McDermott, M. M. Matzke, B. J. Webb-Robertson, S. C. Tilton, N. Tchitchek, L. Josset, C. Li, A. L. Ellis, J. H. Chang, R. A. Heegel, M. L. Luna, A. A. Schepmoes, A. K. Shukla, T. O. Metz, G. Neumann, A. G. Benecke, R. D. Smith, R. S. Baric, Y. Kawaoka, M. G. Katze, and K. M. Waters, PLoS One, 8 (7): e69374 (2013).
PMCID: PMC3723910

"Pyrethroid activity-based probes for profiling cytochrome P450 activities associated with insecticide interactions," H. M. Ismail, P. M. O’Neill, D. W. Hong, R. D. Finn, C. J. Henderson, A. T. Wright, B. F. Cravatt, J. Hemingway, M. J. Paine, Proc Natl Acad Sci, 110(49): 19766-19771 (2013).
PMCID: PMC3856776

"Quantitative site-specific reactivity profiling of S-nitrosylation in mouse skeletal muscle using cysteinyl peptide enrichment coupled with mass spectrometry," D. Su, A. K. Shukla, B. Chen, J. S. Kim, E. Nakayasu, Y. Qu, U. Aryal, K. Weitz, T. R. Clauss, M. E. Monroe, D. G. Camp II, D. J. Bigelow, R. D. Smith, R. N. Kulkarni, and W. J. Qian, Free Radic Biol Med., 57: 68-78 (2013).
PMCID: PMC3771501

"Reduced insulin/insulin-like growth factor-1 signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegan," G. Depuydt, F. Xie, V. A. Petyuk, N. Shanmugam, A. Smolders, I Dhondt, H. M. Brewer, D. G. Camp, II, R. D. Smith, and B. P. Braeckman, Mol Cell Proteomics, 12(12): 3624-3639 (2013).
PMCID: PMC3861712

"Resin-assisted enrichment of N-terminal peptides for characterizing protolytic processing," J. S. Kim, Z. Dai, U. K. Aryal, R. J. Moore, D. G. Camp, II, S. E. Baker, R. D. Smith, and W. J. Qian, Anal Chem., 85(14): 6826-6832 (2013).
PMCID: PMC3782086

"RNA type III secretion signals that require Hfq," G. S. Niemann, R. N. Brown, I. T. Mushamiri, N. T. Nguyen, R. Taiwo, A. Stufkens, R. D. Smith, J. N. Adkins, J. E. McDermott, F. Heffron, J Bacteriol., 195(10): 2119-2125 (2013).
PMCID: PMC3650527

"Separation of protein conformers by differential ion mobility in hydrogen-rich gases," A. A. Shvartsburg and R. D. Smith, Anal Chem., 85(14): 6967-6973 (2013).
PMCID: PMC3749073

"Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes," Q. Zhang, T. L. Fillmore, A. A. Schepmoes, T. R. Clauss, M. A. Gritsenko, P. W. Mueller, M. Rewers, M. A. Atkinson, R. D. Smith, T. O. Metz, J Exp Med., 10 (1): 191-203 (2013).
PMCID: PMC3549705

"Sources of technical variability in quantitative LC-MS proteomics: human brain tissue sample analysis," P. D. Piehowski, V. A. Petyuk, D. J. Orton, F. Xie, R. J. Moore, M. Ramirez-Restrepo, A. Engel, A. P. Lieberman, R. L. Albin, D. G. Camp, II, R. D. Smith, and A. J. Myers, J. Proteome Res.., 12(5): 2128-2137 (2013).
PMCID: PMC3695475

"Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice," N. Tchitchek, A. J. Eisfeld, J. Tisoncik-Go, L. Josset, L. E. Gralinski, C. Becavin, S. C. Tilton, B. J. Webb-Robertson, M. T. Ferris, A. L. Totura, C. Li, G. Neumann, T. O. Metz, R. D. Smith, K. M. Waters, R. Baric, Y. Kawaoka, and M. G. Katze, BMC Syst Biol., 7: 69 (2013).
PMCID: PMC3750405

"STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results," P. D. Piehowski, V. A. Petyuk, J. D. Sandoval, K. E. Burnum, G. R. Kiebel, M. E. Monroe, G. A. Anderson, D. G. Camp, II, and R. D. Smith, Proteomics, 13(5): 766-770 (2013).
PMCID: PMC3676282

"Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion," T. Shi, X. Sun, Y. Gao, T. L. Fillmore, A. A. Schepmoes, R. Zhao, J. He, R. J. Moore, J. Kagan, K. D. Rodland, T. Liu, A. Y. Liu, R. D. Smith, K. Tang, D. G. Camp, II, and W. J. Qian, J. Proteome Res., 12(7): 3353-3361 (2013).
PMCID: PMC3733379

"Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typhimurium in response to infection-like conditions," C. Ansong, S. Wu, D. Meng, X. liu, H. M. Brewer, B. L. Deatherage Kaiser, E. S. Nakayasu, J. R. Cort, P. Pevzner, R. D. Smith, F. Heffron, J. N. Adkins, and L. Paša-Tolić, Proc Natl Acad Sci, 110 (25): 10153-10158 (2013).
PMCID: PMC3690903

"Trauma-associated human neutrophil alterations revealed by comparative proteomics profiling," J. Y. Zhou, R. K. Krovvidi, Y. Gao, H. Gao, B. O. Petritis, A. K. De, C. L. Miller-Graziano, P. E. Bankey, V. A. Petyuk, C. D. Nicora, T. R. Clauss, R. J. Moore, T. Shi, J. N. Brown, A. Kaushal, W. Xiao, R. W. Davis, R. V. Maier, R. G. Tompkins, W. J. Qian, D. G. Camp, II, and R. D. Smith, Proteomics Clin Appl., 7(7-8): 571-583 (2013).
PMCID: PMC3737403


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Portions of this research were supported by the NIH National Institute of General Medical Sciences (GM103493), and the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory). Pacific Northwest National Laboratory is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RLO-1830.