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Journal Publications by year


2018 Journal Publications

"High-Fat Diets Alter the Modulatory Effects of Xenobiotics on Cytochrome P450 Activites," N. C. Sadler, B-J M. Webb-Rovertson, T. R. Clauss, J. G. Pounds, R. Corley, A. T. Wright. Chemical Res. Toxicology, 2018 May 21; 31(5):308-318. doi: 10.1021/acs.chemrestox.8b00008
PMID: 29688711, PMCID: PMC7075635

"Micropuncture of Bowman's Space in Mice Facilitated by 2 Photon Microscopy," K. Matsushita, K. Golgotiu, D. J. Orton, R. D. Smith, K. D. Rodland, P. D. Piehowski, M. P. Hutchens. Journal of visualized experiments: JoVE, 2018 Oct 11; (140):58206. doi: 10.3791/58206
PMID: 30371667, PMCID: PMC6235460

"Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells," T. Shi, M. J. Gaffrey, T. L. Fillmore, C. D. Nicora, L. Yi, P. Zhang, A. K. Shukla, H. S. Wiley, K. D. Rodland, T. Liu, R. D. Smith, W. J. Qian. Commun Biol, 2018 Aug 6; 1:103. doi: 10.1038/s42003-018-0107-6
PMID: 30271983, PMCID: PMC6123794

"Proteome Profiling of 1 to 5 Spoked Circulating Tumore Cells Isolated From Whole Blood Using Immunodensity Enrichment, Laser Capture, Microdissection, Nanodroplet Sample Processing, and Ultasensitive nanoLC-MS," Y. Zhu, J. Podolak, R. Zhao, A. K. Shukla, R. J. Moore, F. V. Thomas, R. T. Kelly. Anlaytical Chemistry, 2018 Oct 16; 90(20):11756-11759. doi: 10.1021/acs.analchem.8b03268
PMID: 30269481, PMCID:PMC6686195

"Distinguishing enantiomeric amino acids with chiral cyclodextrin adducts and structures for lossless ion manipulations," G. Nagy, C. D. Chouinard, I. K. Attah, I. K. Webb, S. V. B. Garimella, Y. M. Ibrahim, E. S. Baker, R. D. Smith. Electrophoresis, 2018 Dec; 39(24):3148-3155. doi: 10.1002/elps.201800294
PMID: 30168603, PMCID: PMC6294673

"Nanowell-mediated multidimensional separations combining nanoLC with SLIM IM-MS for rapid, high-peak-capacity proteomic analyses," M. Dou, C. D. Chouinard, Y. Zhu, G. Nagy, A. V. Liyu, Y. M. Ibrahim, R. D. Smith, R. T. Kelly, Anal Bioanal Chem, 2019 Aug; 411(21):5363-5372. doi: 10.1007/s00216-018-1452-5
PMID: 30397757, PMCID:PMC6500776

"Using Skyline to Analyze Data-Containing Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry Dimensions," B. X. MacLean, B. S. Pratt, J. D. Egertson, M. J. MacCoss, R. D. Smith, E. S. Baker. Journal of the American Society for Mass Spectrometry, 2018 Nov; 29(11):2182-2188. doi: 10.1007/s13361-018-2028-5
PMID: 30047074, PMCID:PMC6191345

"A systems perspective of heterocellular signaling," A. Wells, H. S. Wiley. Essays Biochem, 2018 Oct 26; 62(4):607-617. doi: 10.1042/EBC20180015
PMID: 30139877, PMCID: PMC6309864

"Unraveling the isomeric heterogeneity of glycans: ion mobility separations in structures for lossless ion manipulations," G. Nagy, I. K. Attah, S. V. B. Garimella, K. Tang, Y. M. Ibrahim, E. S. Baker, R. D. Smith. Chemical communications (Cambridge, England), 2018 Oct 25; 54(83):11701-11704. doi: 10.1039/c8cc06966b
PMID: 30264832, PMCID: PMC6191335

"Spatially Resolved Proteome Mapping of Laser Capture Microdissected Tussue with Automated Smaple Transfer to Nanodroplets,", Y. Zhu, M. Dou, P. D. Piehowski, Y. Liang, F. Wang, R. K. Chu, W. B. Chrisler, J. N. Smith, K. C. Schwarz, Y. Shen, S. K. Shukla, R. J. Moore, R. D. Smith, W. J. Qian, R. T. Kelly. Mol Cell Proteomics, 2018 Sep; 17(9):1864-1874. doi: 10.1074/mcp.TIR118.000686
PMID: 29941660, PMCID: PMC6126383

"Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection," S. L. Stevens, T. Liu, F. R. Bahjat, V. A. Petyuk, A. A. Schepmoes, R. L. Sontag, M. A. Gritsenko, C. Wu, S. Wang, A. K. Shukla, J. M. Jacobs, R. D. Smith, K. D. Rodland, G. Alexander West, S. G. Kohama, C. Glynn, M. P. Stenzel-Poore. Transl Stroke Res, 2019 Aug;10(4):440-448. doi: 10.1007/s12975-018-0670-7.
PMID: 30341719, PMCID: PMC6474839

"Improved Sensitivity and Separations for Phosphopeptides using Online Liquid Chromotography Coupled with Structures for Lossless Ion Manipulations Ion Mobility-Mass Spectrometry," C. D. Chouinard, G. Nagy, I. K. Nagy, T. Shi, E. S. Baker, S. A. Prost, T. Liu, Y. M. Ibrahim, R. D. Smith. Anal Chem, 2018 Sep 18; 90(18):10889-10896. doi: 10.1021/acs.analchem.8b02397
PMID: 30118596, PMCID: PMC6211290

"Rapid Ion Mobility Separations of Bile Acid Isomers Using Cyclodextrin Adducts and Structures for Lossless Ion Manipulations," C. D. Chouinard, G. Nagy, I. K. Webb, S. V. B. Garimella, E. S. Baker, Y. M Ibrahim, R. D. Smith. Analytical Chemistry, 2018 Sep 18;90(18):11086-11091. doi: 10.1021/acs.analchem.8b02990
PMID: 30102518, PMCID: PMC6191033

"Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS," Y. Zhu, G. Clair, W. B. Chrisler, Y. Shen, R. Zhao, A. K. Shukla, R. J. Moore, R. S. Misra, G. S. Pryhuber, R. D. Smith, C. Ansong, R. T. Kelly. Angewandte Chemie (International ed. in English), 2018 Sep 17;57(38):12370-12374. doi: 10.1002/anie.201802843
PMID: 29797682, PMCID: PMC6261339

"The human brainome: network analysis identifies HSPA2 as a novel Alzheimer's disease target," V. A. Petyuk, R. Chang, M. Ramirez-Restrepo, N. D. Beckmann, M. Y. R. Henrion, P. D. Piehowski, K. Zhu, S. Wang, J. Clarke, M. J. Huentelman, F. Xie, V. Andreev, A. Engel, T. Guettoche, L. Navarro, P. De Jager, J. A. Schneider, C. M. Morris, I. G. McKeith, R. H. Perry, S. Lovestone, R. L. Woltjer, T. G. Beach, L. I. Sue, G. E. Serrano, A. P. Lieberman, R. L. Albin, I. Ferrer, D. C. Mash, C. M. Hulette, J. F. Ervin, E. M. Reiman, J. A. Hardy, D. A. Bennett, E. Schadt, R. D. Smith, A. J. Myers. Brain: a journal of neurology, 2018 Sep 1;141(9):2721-2739. doi: 10.1093/brain/awy215
PMID: 30137212, PMCID: PMC6136080

"Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data," B. A. Stanfill, E. S. Nakayasu, L. M. Bramer, A. M. Thompson, C. K. Ansong, T. R. Clauss, M. A. Gritsenko, M. E. Monroe, R. J. Moore, D. J. Orton, P. D. Piehowski, A. A. Schepmoes, R. D. Smith, B. M. Webb-Robertson, T. O. Metz. Molecular & cellular proteomics (MCP), 2018 Sep; 17(9):1824-1836. doi: 10.1074/mcp.RA118.000648
PMID: 29666158, PMCID: PMC6126382

"Mass spectrometry-based proteomics for system-level characterization of biological responses to engineered nanomaterials," B. A. Stanfill, E. S. Nakayasu, L. M. Bramer, A. M. Thompson, C. K. Ansong, T. Analytical and Bioanalytical Chemistry, 2018 Sep; 410(24):6067-6077. doi: 10.1007/s00216-018-1168-6
PMID: 29947897, PMCID: PMC6119095

"A Customizable Flow Injection System for Automated, High Throughput, and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements," Orton DJ, Tfaily MM, Moore RJ, LaMarche BL, Zheng X, Fillmore TL, Chu RK, Weitz KK, Monroe ME, Kelly RT, Smith RD, Baker ES. Anal Chem, 2018 Jan 2; 90(1):737-744. doi: 10.1021/acs.analchem.7b02986.
PMID: 29161511, PMCID: PMC5764703

"A Global Survey of ATPase Activity in Plasmodium falciparum Asexual Blood Stages and Gametocytes," Ortega C, Frando A, Webb-Robertson BJ, Anderson LN, Fleck N, Flannery EL, Fishbaugher M, Murphree TA, Hansen JR, Smith RD, Kappe SHI, Wright AT, Grundner C. Mol Cell Proteomics, 2018 Jan; 17(1):111-120. doi: 10.1074/mcp.RA117.000088.
PMID: 29079720, PMCID: PMC5750841

"A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer Using Structures for Lossless Ion Manipulations," Prabhakaran A, Hamid AM, Garimella SVB, Valenzuela BR, Ewing RG, Ibrahim YM, Smith RD. J Am Soc Mass Spectrom 29 (2): 342-351 (2018). doi: 10.1007/s13361-017-1841-6.
PMID: 29235041, PMCID: PMC5815952

"An algorithm to correct saturated mass spectrometry ion abundances for enhanced quantitation and mass accuracy in omic studies," A. Bilbao, B. C. Gibbons, G. W. Slysz, K. L. Crowell, M. E. Monroe, Y. M. Ibrahim, R. D. Smith, S. H. Payne, E. S. Baker, Int J Mass Spectrom, 2018 Apr;427:91-99. doi: 10.1016/j.ijms.2017.11.003
PMID: 29706793, PMCID: PMC5920534

"Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry," J. E. Kyle, N. Aly, X. Zheng, K. E. Burnum-Johnson, R. D. Smith, E. S. Baker. Bioanalysis, 2018 Mar 1; 10(5):279-289. doi: 10.4155/bio-2017-0245
PMID: 29494212, PMCID: PMC6040087

"Fatiguing contractions increase protein S- glutathionylation occupancy in mouse skeletal muscle," P. A. Kramer, J. Duan, M. J. Gaffrey, A. K. Shukla, L. Wang, T. K. Bammler, W. J. Qian, D. J. Marcinek, Redox Biol, 2018 Jul; 17:367-376. doi: 10.1016/j.redox.2018.05.011
PMID: 29857311, PMCID: PMC6007084

"High-throughput serum proteomics for the identification of protein biomarkers of mortality in older men," E. S. Orwoll, J. Wiedrick, J. Jacobs, E. S. Baker, P. Piehowski, V. Petyuk, Y. Gao, T. Shi, R. D. Smith, D. C. Bauer, S. R. Cummings, C. M. Nielson, J. Lapidus, Osteoporotic Fractures in Men Study (MrOS) Research Group, Aging Cell, 2018 Apr; 17(2):e12717. doi: 10.1111/acel.12717
PMID: 29399943, PMCID: PMC5847880

"MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape," Menachery VD, Schäfer A, Burnum-Johnson KE, Mitchell HD, Eisfeld AJ, Walters KB, Nicora CD, Purvine SO, Casey CP, Monroe ME, Weitz KK, Stratton KG, Webb-Robertson BM, Gralinski LE, Metz TO, Smith RD, Waters KM, Sims AC, Kawaoka Y, Baric RS. Proc Natl Acad Sci USA, 115 (5): E1012-E1021 (2018). doi: 10.1073/pnas.1706928115.
PMID: 29339515, PMCID: PMC5798318

"Moonshot Objectives: Catalyze New Scientific Breakthroughs-Proteogenomics," K. D. Rodland, P. Piehowski, R. D. Smith. Cancer Journal, May/Jun 2018;24(3):121-125. doi: 10.1097/PPO.0000000000000315
PMID: 29794536, PMCID: PMC5975970

"Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells," Zhu Y, Piehowski PD, Zhao R, Chen J, Shen Y, Moore RJ, Shukla AK, Petyuk VA, Campbell-Thompson M, Mathews CE, Smith RD, Qian WJ, Kelly RT. Nat Commun, 9 (1): 882 (2018). doi: 10.1038/s41467-018-03367-w.
PMID: 29491378, PMCID: PMC5830451

"Pyroptosis by caspase11/4-gasdermin-D pathway in alcoholic hepatitis in mice and patients," Khanova E, Wu R, Wang W, Yan R, Chen Y, French SW, Llorente C, Pan SQ, Yang Q, Li Y, Lazaro R, Ansong C, Smith RD, Bataller R, Morgan T, Schnabl B, Tsukamoto H. Hepatology, 2018 May; 67(5):1737-1753. doi: 10.1002/hep.29645.
PMID: 29108122, PMCID: PMC5906140

"Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry," P. Mertins, L. C. Tang, K. Krug, D. J. Clark, M. A. Gritsenko, L. Chen, K. R. Clauser, T. R. Clauss, P. Shah, M. A. Gillette, V. A. Petyuk, S. N. Thomas, D. R. Mani, F. Mundt, R. J. Moore, Y. Hu, R. Zhao, M. Schnaubelt, H. Keshishian, M. E. Monroe, Z. Zhang, N. D. Udeshi, D. Mani, S. R. Davies, R. R. Townsend, D. W. Chan, R. D. Smith, H. Zhang, T. Liu, S. A. Carr, Nat Protoc, 13(7):1632-1661 (2018).
PMID: 29988108, PMCID: PMC6211289

"Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples," Int J Mass Spectrom, 427:4-10 (2018).
PMID: 29576737, PMCID: PMC5863755

"Targeted Brain Proteomics Uncover Multiple Pathways to Alzheimer's Dementia," Yu L, Petyuk VA, Gaiteri C, Mostafavi S, Young-Pearse T, Shah RC, Buchman AS, Schneider JA, Piehowski PD, Sontag RL, Fillmore TL, Shi T, Smith RD, De Jager PL, Bennett DA. Ann Neurol, (2018). doi: 10.1002/ana.25266.
PMID: 29908079

"Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR- MAPK Pathway," L. Yi, T. Shi, M. A. Gritsenko, C. Y. X'avia Chan, T. L. Fillmore, B. M. Hess, A. C. Swensen, T. Liu, R. D. Smith, H. S. Wiley, W. J. Qian. Anal Chem, 2018 Apr 17; 90(8):5256-5263. doi: 10.1021/acs.analchem.8b00071
PMID: 29584399, PMCID: PMC5912210

"Urinary Virome perturbations in kidney transplantation," Sigdel TK, Mercer N, Nandoe S, Nicora CD, Burnum-Johnson K, Qian WJ, Sarwal MM. Front Med (Lausanne), 5: 72 (2018). doi: 10.3389/fmed.2018.00072.
PMID: 29725592, PMCID: PMC5916966

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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