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Journal Publications by year


2014 Journal Publications

"Accounting for population variation in targeted proteomics," G. M. Fujimoto, M. E. Monroe, L. Rodriguez, C. Wu, B. MacLean, R. D. Smith, M. J. MacCoss, and S. H. Payne, J Proteome Res., 13 (1): 321-323 (2014).
PMCID: PMC3923399

"Advancing the high throughput identification of liver fibrosis protein signatures using multiplexed ion mobility spectrometry," E. S. Baker, K. E. Burnum-Johnson, J. M. Jacobs, D. L. Diamond, R. N. Brown, Y. M. Ibrahim, D. J. Orton, P. D. Piehowski, D. E. Purdy, R. J. Moore, W. F. Danielson, M. E. Monroe, K. L. Crowell, G. W. Slysz, M. A. Gritsenko, J. D. Sandoval, B. L. Lamarche, M. M. Matzke, B. J. Webb-Robertson, B. C. Simons, B. J. McMahon, R. Bhattacharya, J. D. Perkins, R. L. Carithers Jr., S. Strom, S. G. Self, M. G. Katze, G. A. Anderson, and R. D. Smith, Mol Cell Proteomics, 13 (4): 1119-1127 (2014).
PMCID: PMC3977189

"Antibody-independent targeted quantification of TMPRSS2-ERG fusion protein products in prostate cancer," J. He, X. Sun, T. Shi, A. A. Schepmoes, T. L. Fillmore, V. A. Petyuk, F. Xie, R. Zhao, M. A. Gritsenko, F. Yang, N. Kitabayashi, S. S. Chae, M. A. Rubin, J. Siddigui, J. T. Wei, A. M. Chinnaiyan, W. J. Qian, R. D. Smith, J. Kagan, S. Srivastava, K. D. Rodland, T. Liu, and D. G. Camp II, Mol Oncol., 8 (7): 1169-1180 (2014).
PMCID: PMC4183720

"Bayesian proteoform modeling improves protein quantification of global proteomic measurements," B. J. Webb-Robertson, M. M. Matzke, S. Datta, S. H. Payne, J. Kang, L. M. Bramer, C. D. Nicora, A. K. Shukla, T. O. Metz, K. D. Rodland, R. D. Smith, M. F. Tardiff, J. E. McDermott, J. G. Pounds, K. M. Waters, Mol Cell Proteomics, 13 (12): 3639-3646 (2014).
PMCID: PMC4256511

"Brain insulin lowers circulating BCAA levels by inducing hepatic BCAA catabolism," A. C. Shin, M. Fasshauer, N. Filatova, L. A. Grundell, E. Zielinski, J. Y. Zhou, T. Scherer, C. Lindtner, P. J. White, A. L. Lapworth, O. Ilkayeva, U. Knippschild, A. M. Wolf, L. Scheja, K. L. Grove, R. D. Smith, W. J. Qian, C. J. Lynch, C. B. Newgard, and C. Buettner, Cell Metab., 20 (5): 898-909 (2014).
PMCID: PMC4254305

"Characterization of individual mouse cerebrospinal fluid proteomes," J. S. Smith, T. E. Angel, C. Chavkin, D. J. Orton, R. J. Moore, and R. D. Smith, Proteomics, 14 (9): 1102-1106 (2014).
PMCID: PMC4044923

"Characterization of ion dynamics in structures for lossless ion manipulations," A. V. Tolmachev, I. K. Webb, Y. M. Ibrahim, S. V. Garimella, X. Zhang, G. A. Anderson, and R. D. Smith, Anal Chem., 86 (18): 9162-9168 (2014).
PMCID: PMC4175726

"Cytomegalovirus pp65 limits dissemination buy is dispensable for persistence," D. Malouli, S. G. Hansen, E. S. Nakayasu, E. E. Marshall, C. M. Hughes, A. B. Ventura, R. M. Gilbride, M. S. Lewis, G. Xu, C. Kreklywich, N. Whizin, M. Fischer, A. W. Legasse, K. Viswanathan, D. Siess, D. G. Camp II, M. K. Axthelm, C. Kahl, V. R. DeFilippis, R. D. Smith, D. N. Streblow, L. J. Picker, and K. Früh, J Clin Invest., 124 (5): 1928-1944 (2014).
PMCID: PMC4002596

"Detecting and removing data artifacts in hadamard transform ion mobility-mass spectrometry measurements," S. A. Prost, K. L. Crowell, E. S. Baker, Y. M. Ibrahim, B. H. Clowers, M. E. Monroe, G. A. Anderson, R. D. Smith, and S. H. Payne, J Am Soc Mass Spectrom., 25 (12): 2020-2027 (2014).
PMCID: PMC4223016

"Detecting differential protein expression in large-scale population proteomics," S. Y. Ryu, W. J. Qian, D. G. Camp, R. D. Smith, R. G. Tompkins, R. W. Davis, and W. Xiao, Bioinformatics, 30 (19): 2741-2746 (2014).
PMCID: PMC4173009

"Differential ion mobility separations in up to 100% helium using microchips," A. A. Shvartsburg, Y. M. Ibrahim, R. D. Smith, J Am Soc Mass Spectrom., 25 (3): 480-489 (2014).
PMCID: PMC4031910

"Expediting SRM assay development for large-scale targeted proteomics experiments," C. Wu, T. Shi, J. N. Brown, J. He, Y. Gao, T. L. Fillmore, A. K. Shukla, R. J. Moore, D. G. Camp II, K. D. Rodland, W. J. Qian, T. Liu, and R. D. Smith, J Proteome Res., 13 (10): 4479-4487 (2014).
PMCID: PMC4184450

"Experimental evaluation and optimization of structures for lossless ion manipulations for ion mobility spectrometry with time-of-flight mass spectrometry," I. K. Webb, S. V. Garimella, A. V. Tolmachev, T. C. Chen, X. Zhang, R. V. Norheim, S. A. Prost, B. LaMarche, G. A. Anderson, Y. M. Ibrahim, and R. D. Smith, Anal Chem., 86 (18): 9169-9176 (2014).
PMCID: PMC4165449

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

"GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization," S. R. Kronewitter, S. G. Slysz, I. Marginean, C. D. Hagler, B. L. LaMarche, R. Zhao, M. Y. Harris, M. E. Monroe, C. A. Polyukh, K. L. Crowell, T. L. Fillmore, T. S. Carlson, D. G. Camp II, R. J. Moore, S. H. Payne, G. A. Anderson, and R. D. Smith, Anal Chem., 86 (13): 6268-6276 (2014).
PMCID: PMC4082388

"HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa," W. Jonkers, A. C. Leeder, C. Anson, Y. Wang, F. Yang, T. L. Starr, D. G. Camp II, R. D. Smith, and N. L. Glass, PLoS Genet., 10 (11): e1004783 (2014).
PMCID: PMC4238974

"High and low doses of ionizing radiation induce different secretome profiles in a human skin model," Q. Zhang, M. Matzke, A. A. Schepmoes, R. J. Moore, B. J. Webb-Robertson, Z. Hu, M. E. Monroe, W. J. Qian, R. D. Smith, and W. F. Morgan, PLoS One, 9 (3): e92332 (2014).
PMCID: PMC3958549

"High sensitivity combined with extended structural coverage of labile compounds via nanoelectrospray ionization at subambient pressures," J. T. Cox, S. R. Kronewitter, A. K. Shukla, R. J. Moore, R. D. Smith and K. Tang, Anal Chem., 86 (19): 9504-9511 (2014).
PMCID: PMC4188276

"A highly sensitive targeted mass spectrometry assay for quantification of AGR2 protein in human urine and serum," T. Shi, Y. Gao, S. I. Quek, T. L. Fillmore, C. D. Nicora, D. Su, R. Zhao, J. Kagan, S. Srivastava, K. D. Rodland, T. Liu, R. D. Smith, D. W. Chan, D. G. Camp, II, A. Y. Liu, and W. J. Qian, J. Proteome Res., 13 (2): 875-882 (2014).
PMCID: PMC3975687

"The identification of novel potential injury mechanisms and candidate biomarkers in renal allograft rejection by quantitative proteomics," T. K. Sigdel, N. Salomonis, C. D. Nicora, S. Ryu, J. He, V. Dinh, D. J. Orton, R. J. Moore, S. C. Hsieh, H. Dai, M. Thien-Vu, W. Xiao, R. D. Smith, W. J. Qian, D. G. Camp II, and M. M. Sarwal, Mol Cell Proteomics, 13 (2): 621-631 (2014).
PMCID: PMC3916658

"Implementation of dipolar resonant excitation for collision induced dissociation with ion mobility/time-of-flight MS," I. K. Webb, T. C. Chen, W. F. Danielson, Y. M. Ibrahim, K. Tang, G. A. Anderson, and R. D. Smith, J Am Soc Mass Spectrom., 25 (4): 563-571 (2014).
PMCID: PMC4113219

"Improving ion mobility measurement sensitivity by utilizing helium in an ion funnel trap," Y. M. Ibrahim, S. V. Garimella, A. V. Tolmachev, E. S. Baker, and R. D. Smith, Anal. Chem., 86 (11): 5295-5299 (2014).
PMCID: PMC4051256

"Improving the sensitivity of mass spectrometry by using a new sheath flow electrospray emitter array at subambient pressures," J. T. Cox, I. Marginean, R. T. Kelly, R. D. Smith, and K. Tang, J Am Soc Mass Spectrom., 25 (12): 2028-2037 (2014).
PMCID: PMC4177967

"LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism," G. Depuydt, F. Xie, V. A. Petyuk, A. Smolders, H. M. Brewer, D. G. Camp II, R. D. Smith, and B. P. Braeckman, J Proteome Res., 13 (4): 1938-1956 (2014).
PMCID: PMC3993954

"Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani," J. L. Martin, P. A. Yates, R. Soysa, J. F. Alfaro, F. Yang, K. E. Burnum-Johnson, V. A. Petyuk, K. K. Weitz, D. G. Camp II, R. D. Smith, P. A. Wilmarth, L. L. David, G. Ramasamy, P. J. Myler, N. S. Carter, PLoS Pathog., 10 (2): e1003938 (2014).
PMCID: PMC3937319

"A method to determine lysine acetylation stoichiometries," E. S. Nakayasu, S. Wu, M. A. Sydor, A. K. Shukla, K. K. Weitz, R. J. Moore, K. K. Hixson, J. S. Kim, V. A. Petyuk, M. E. Monroe, L. Pasa-Tolic, W. J. Qian, R. D. Smith, J. N. Adkins, and C. Ansong, Int J Proteomics, 2014: 730725 (2014).
PMCID: PMC4131070

"Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid," S. W. Hyung, P. D. Piehowski, R. J. Moore, D. J. Orton, A. A. Schepmoes, T. R. Clauss, R. K. Chu, T. L. Fillmore, H. Brewer, T. Liu, R. Zhao, and R. D. Smith, Anal Bioanal Chem., 406 (28): 7117-7125 (2014).
PMCID: PMC4208972

"Mobility-resolved ion selection in uniform drift field ion mobility spectrometry/mass spectrometry: dynamic switching in structures for lossless ion manipulations," I. K. Webb, S. V. Garimella, A. V. Tolmachev, T. C. Chen, X. Zhang, J. T. Cox, R. V. Norheim, S. A. Prost, B. LaMarche, G. A. Anderson, Y. M. Ibrahim, and R. D. Smith, Anal Chem., 86 (19): 9632-9637 (2014).
PMCID: PMC4188271

"Mycobacterium tuberculosis Ser/Thr protein kinase B mediates an oxygen-dependent replication switch," C. Ortega, R. Liao, L. N. Anderson, T. Rustad, A. R. Ollodart, A. T. Wright, D. R. Sherman, C. Grundner, PLoS Biol, 12(1): e1001746 (2014).
PMCID: PMC3883633

"Optimization for peptide sample preparation for urine peptidomics," T. K. Sigdel, C. D. Nicora, S. C. Hsieh, H. Dai, W. J. Qian, D. G. Camp, and M. M. Sarwal, Clin Proteomics, 11 (1): 7 (2014).
PMCID: PMC3944950

"Organelle-specific activity-based protein profiling in living cells," S. D. Wiedner, L. N. Anderson, N. C. Sadler, W. B. Chrisler, V. K. Kodali, R. D. Smith, and A. T. Wright, Angew Chem Int Ed, 53 (11): 2919-2922 (2014).
PMCID: PMC4023867

"Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses," V. D. Menachery, A. J. Eisfeld, A. Schäfer, L. Josset, A. C. Sims, S. Proll, S. Fan, C. Li, G. Neumann, S. C. Tilton, J. Chang, L. E. Gralinski, C. Long, R. Green, C. M. Williams, J. Weiss, M. M. Matzke, B. J. Webb-Robertson, A. A. Schepmoes, A. K. Shukla, T. O. Metz, R. D. Smith, K. M. Waters, M. G. Katze, Y. Kawaoka, and R. S. Baric, MBio., 5 (3): e01174-14 (2014).
PMCID: PMC4030454

"Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens," A. Zaborin, J. R. Defazio, M. Kade, B. L. Kaiser, N. Belogortseva, D. G. Camp II, R. D. Smith, J. N. Adkins, S. M. Kim, A. Alverdy, D. Goldfeld, M. A. Firestone, J. H. Collier, B. Jabri, M. Tirrell, O. Zaborina, J. C. Alverdy, Antimicrob Agents Chemother, 58 (2): 966-977 (2014).
PMCID: PMC3910877

"Picoelectrospray ionization mass spectrometry using narrow-bore chemically etched emitters," I. Marginean, K. Tang, R. D. Smith, and R. T. Kelly, J Am Soc Mass Spectrom., 25 (1): 30-36 (2014).
PMCID: PMC3945158

"Polysialylated N-glycans identified in human serum through combined developments in sample preparation, separations, and electrospray ionization-mass spectrometry," S. R. Kronewitter, I. Marginean, J. T. Cox, R. Zhao, C. D. Hagler, A. K. Shukla, T. S. Carlson, J. N. Adkins, D. G. Camp II, R. J. Moore, K. D. Rodland, and R. D. Smith, Anal Chem., 86 (17): 8700-8710 (2014).
PMCID: PMC4151788

"Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea," J. N. Brown, H. M. Brewer, C. D. Nicora, K. K. Weitz, M. J. Morris, A. J. Skabelund, J. N. Adkins, R. D. Smith, J. H. Cho, and R. Gelinas, BMC Med Genomics, 7: 58 (2014).
PMCID: PMC4193960

"Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data," S. Woo, S. W. Cha, S. Na, C. Guest, T. Liu, R. D. Smith, K. D. Rodland, S. Payne, and V. Bafna, Proteomics, 14 (23-24): 2719-2730 (2014).
PMCID: PMC4256132

"The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation," Y. Xiong, S. T. Coradetti, X. Li, M. A. Gritsenko, T. Clauss, V. Petyuk, D. Camp, R. Smith, J. H. Cate, F. Yang, and N. L. Glass, Fungal Genet Biol., 72: 21-33 (2014).
PMCID: PMC4247816

"Proteomic analysis of saliva in HIV-positive heroin addicts reveals proteins correlated with cognition," S. S. Dominy, J. N. Brown, M. I. Ryder, M. Gritsenko, J. M. Jacobs, and R. D. Smith, PLoS One, 9(4): e89366 (2014).
PMCID: PMC3981673

"Proteomic approaches for site-specific O-GlcNAcylation analysis," S. Wang, F. Yang, D. G. Camp II, K. Rodland, W.J. Qian, T. Liu, and R. D. Smith, Bioanalysis, 6 (19): 2571-2580 (2014).
PMCID: PMC4275047

"Proteomic identification and quantification of S-glutathionylation in mouse macrophages using resin-assisted enrichment and isobaric labeling," D. Su, M. J. Gaffrey, J. Guo, K. E. Hatchell, R. K. Chu, T. R. Clauss, J. T. Aldrich, S. Wu, S. Purvine, D. G. Camp, II, R. D. Smith, B. D. Thrall, and W. J. Qian, Free Radic Biol Med., 67: 460-470 (2014).
PMCID: PMC3945121

"Quantitative analysis of human salivary gland-derived intact proteome using top-down mass spectrometry," S. Wu, J. N. Brown, N. Tolic, D. Meng, X. Liu, H. Zhang, R. Zhao, R. J. Moore, P. Pevzner, R. D. Smith, and L. Pasa-Tolic, Proteomics, 14 (10): 1211-1222 (2014).
PMID: 24591407 (In process)

"Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications," J. Guo, M. J. Gaffrey, D. Su, T. Liu, D. G. Camp II, R. D. Smith, and W. J. Qian, Nat Protoc., 9 (1): 64-75 (2014).
PMCID: PMC4038159

"Signatures for mass spectrometry data quality," B. G. Amidan, D. J. Orton, B. L. Lamarche, M. E. Monroe, R. J. Moore, A. M. Venzin, R. D. Smith, L. H. Sego, M. F. Tardiff, and S. H. Payne, J Proteome Res., 13 (4): 2215-2222 (2014).
PMCID: PMC4104976

"Simulation of electric potentials and ion motion in planar electrode structures for lossless ion manipulations (SLIM)," S. V. Garimella, Y. M. Ibrahim, I. K. Webb, A. V. Tolmachev, X. Zhang, S. A. Prost, G. A. Anderson, and R. D. Smith, J Am Soc Mass Spectrom., 25 (11): 1890-1896 (2014).
PMCID: PMC4198429

"The succinated proteome," E. D. Merkley, T. O. Metz, R. D. Smith, J. W. Baynes, N. Frizzell, Mass Spectrom Rev., 33 (2): 98-109 (2014).
PMCID: PMC4038156

Acknowledgments

All publications that result from utilization of the Resource must acknowledge NIGMS grant support. Please include the following acknowledgment statement:

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.

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