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Journal Publications by year


2016 Journal Publications

"9-Fluorenylmethyl (Fm) disulfides: biomimetic precursors for persulfies," C. M. Park, B. A. Johnson, J. Duan, J. J. Park, J. J. Day, D. Gang, W. J. Qian, and M. Xian, Org Lett. 18 (5): 904-907 (2016).
PMID: 26870874, PMCID: PMC4782721

"A structures for lossless ion manipulations (SLIM) module for collision induced dissociation," I. K. Webb, S. V. Garimella, R. V. Norheim, E. S. Baker, Y. M. Ibrahim, and R. D. Smith, J Am Soc Mass Spectrom. 27 (7): 1285-1288 (2016).
PMID: 27098413, PMCID: PMC4899216

"Achieving high resolution ion mobility separations using traveling waves in compact multiturn structures for lossless ion manipulations," A. M. Hamid, S. V. Garimella, Y. M. Ibrahim, L. Deng, X. Zheng, I. K. Webb, G. A. Anderson, S. A. Prost, R. V. Norheim, A. V. Tolmachev, E. S. Baker, and R. D. Smith, Anal Chem. 88 (18): 8949-8956 (2016).
PMID: 27479234, PMCID: PMC5305179

"Advances in targeted proteomics and applications to biomedical research," T. Shi, E. Song, S. Nie, K. D. Rodland, T. Liu, W. J. Qian, and R. D. Smith, Proteomics, 16 (15-16): 2160-2182 (2016).
PMID: 27302376, PMCID: PMC5051956

"Capillary electrophoresis-nanoelectrospray ionization-selected reaction monitoring mass spectrometry via a true sheathless metal-coated emitter interface for robust and high-sensitivity sample quantification," X. Guo, T. L. Fillmore, Y. Gao, and K. Tang, Anal Chem. 88 (8): 4418-4425 (2016).
PMID: 27028594, PMCID: PMC4854437

"Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway," T. Shi, M. Niepel, J. E. McDermott, Y. Gao, C. D. Nicora, W. B. Chrisler, L. M. Markillie, V. A. Petyuk, R. D. Smith, K. D. Rodland, P. K. Sorger, W. J. Qian, and H. S. Wiley, Sci. Signal. 9 (436): rs6 (2016).
PMID: 27405981, PMCID: PMC5036860

"Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids," C. Wu, J. Duan, T. Liu, R. D. Smith, and W. -J. Qian, J Chromatogr B Analyt Technol Biomed Life Sci. 1021: 57-68 (2016).
PMID: 26868616, PMCID: PMC4862894

"FOXO/DAF-16 activation slows down turnover of the majority of proteins ion C. elegans," I. Dhondt, V. A. Petyuk, H. Cai, L. Vandemeulebroucke, A. Vierstraete, R. D. Smith, G. Depuydt, and B. P. Braeckman, Cell Rep. 16 (11): 3028-3040 (2016).
PMID: 27626670, PMCID: PMC5434875, NIHMS ID: NIHMS860021

"Free 25-hydroxyvitamin D: impact of vitamin D binding protein assays on racial-genotypic associations," C. M. Nielson, K. S. Jones, R. F. Chun, J. M. Jacobs, Y. Wang, M. Hewison, J. S. Adams, C. M. Swanson, C. G. Lee, D. Vanderschueren, S. Pauwels, A. Prentice, R. D. Smith, T. Shi, Y. Gao, A. A. Schepmoes, J. M. Zmuda, J. Lapidus, J. A. Cauley, R. Bouillon, I. Schoenmakers, and E. S. Orwoll, J. Clin Endocrinol Metab. 101 (5): 2226-2234 (2016).
PMID: 27007693, PMCID: PMC4870848

"Greatly increasing trapped ion populations for mobility separations using traveling waves in structures for lossless ion manipulations," L. Deng, Y. M. Ibrahim, S. V. Garimella, I. K. Webb, A. M. Hamid, R. V. Norheim, S. A. Prost, J. A. Sandoval, E. S. Baker, and R. D. Smith, Anal Chem. 88 (20): 10143-10150 (2016).
PMID: 27715008, PMCID: PMC5384881, NIHMS ID: NIHMS847974

"Hepatic cytochrome P450 activity, abundance, and expression throughout human development," N. C. Sadler, P. Nandhikonda, B. J. Webb-Robertson, C. Anson, L. N. Anderson, J. N. Smith, R. A. Corley, and A. T. Wright, Drug Metab Dispos. 44 (7): 984-991 (2016).
PMID: 27084891, PMCID: PMC4931891

"Host-pathogen interactions: A cholera surveillance system," A. T. Wright, Nat Chem Biol. 12 (4): 203-204 (2016).
PMID: 26900864

"Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes," Y. Hasin-Brumshtein, A. H. Khan, F. Hormozdiari, C. Pan, B. W. Parks, V. A. Petyuk, P. D. Piehowski, A. Brummer, M. Pellegrini, X. Xiao, E. Eskin, R. D. Smith, A. J. Lusis and D. J. Smith, eLife 5: e15614 (2016).
PMID: 27623010, PMCID: PMC5053804

"Identification of novel host interactors of effectors secreted by Salmonella and Citrobacter," R. L. Sontag, E. S. Nakayasu, R. N. Brown, G. S. Niemann, M. A. Sydor, O. Sanchez, C. Ansong, S. Y. Lu, H. Choi, D. Valleau, K. K. Weitz, A. Savchenko, E. D. Cambronne, and J. N. Adkins, mSystems, 1 (4) 2016.
PMID: 27822540, PMCID: PMC5069955

"Integrated omics analysis of pathogenic host responses during pandemic H1N1 influenza virus infection: the crucial role of lipid metabolism," J. Tisoncik-Go, D. J. Gasper, J. E. Kyle, A. J. Eisfeld, C. Selinger, M. Hatta, J. Morrison, M. J. Korth, E. M. Zink, Y. M. Kim, A. A. Schepmoes, C. D. Nicora, S. O. Purvine, K. K. Weitz, X. Peng, R. R. Green, S. C. Tilton, B. J. Webb-Robertson, K. M. Waters, T. O. Metz, R. D. Smith, Y. Kawaoka, M. Suresh, L. Josset, and M. G. Katze, Cell Host Microbe 19 (2): 254-266 (2016).
PMID: 26867183, PMCID: PMC5271177

"Integrated proteogenomic characterization of human high-grade serous ovarian cancer," H. Zhang, T. Liu, Z. Zhang, S. H. Payne, B. Zhang, J. E. McDermott, J. Y. Zhou, V. A. Petyuk. L. Chen, D. Ray, S. Sun, F. Yang, L. Chen, J. Wang, P. Shah, S. W. Cha, P. Aiyetan, S. Woo, Y. Tian, M. A. Gritsenko, T. R. Clauss, C. Choi, M. E. Monroe, S. Thomas, S. Nie, C. Wu, R. J. Moore, K. H. Yu, D. L. Tabb, D. Fenyo, V. Bafna, Y. Wang, H. Rodriguez, E. S. Boja, T. Hiltke, R. C. Rivers, L. Sokoll, H. Zhu, IeM. Shih, L. Cope, A. Pandey, B. Zhang, M. P. Snyder, D. A. Levine, R. D. Smith, D. W. Chan, K. D. Rodland, and CPTAC Investigators, Cell 166 (3): 755-765 (2016).
PMID: 27372738, PMCID: PMC4967013

"Large-scale and deep quantitative proteome profiling using isobaric labeling coupled with two-dimensional LC-MS/MS," M. A. Gritsenko, Z. Xu, T. Liu, and R. D. Smith, Methods Mol Biol. 1410: 237-247 (2016).
PMID: 26867748, PMCID: PMC5292933

"Mining the human urine proteome for monitoring renal transplant injury," T. K. Sigdel, Y. Gao, J. He, A. Wang, C. D. Nicora, T. L. Fillmore, T. Shi, B. J. Webb-Robertson, R. D. Smith, W. J. Qian, O. Salvatierra, D. G. Camp II, and M. M. Sarwal, Kidney Int. 89 (6): 1244-1252 (2016).
PMID: 27165815, PMCID: PMC5221536

"Mitotic protein kinase CDK1 phosphorylation of mRNA translation regulator 4E-BP1 Ser83 may contribute to cell transformation," C. Velasquez, E. Cheng, M. Shuda, P. J. Lee-Oesterreich, L. Pogge von Strandmann, M. A. Gritsenko, J. M. Jacobs, P. S. Moore, and Y. Chang, Proc Natl Acad Sci USA 113 (30): 8466-8471 (2016).
PMID: 27402756, PMCID: PMC4968757

"Mobility-selected ion trapping and enrichment using structures for lossless ion manipulations," T. C. Chen, Y. M. Ibrahim, I. K. Webb, S. V. Gaimella, X. Zhang, A. M. Hamid, L. Deng, W. E. Karnesky, S. A. Prost, J. A. Sandoval, R. V. Norheim, G. A. Anderson, A. V. Tolmechev, E. S. Baker, and R. D. Smith, Anal Chem. 88 (3): 1728-1733 (2016).
PMID: 26752262, PMCID: PMC4793926

"Multi-species identification of polymorphic peptide variants via propagation in spectral networks," S. Na, S. H. Payne, and N. Bandeira, Mol Cell Protoemics 15 (11): 3501-3512 (2016).
PMID: 27609420, PMCID: PMC5098046

"Quantitative profiling of protein S-Glutathionylation reveals redocx-dependent regulation of macrophage function during nanoparticle-induced oxidative stress," J. Duan, V. K. Kodali, M. J. Gaffrey, J. Guo, R. K. Chu, D. G. Camp II, R. D. Smith, B. D. Thrall, and W. -J. Qian, ACS Nano. 10 (1): 524-538 (2016).
PMID: 26700264, PMCID: PMC4762218

"Quantitative profiling of protein S-Glutathionylation reveals redox-dependent regulation of macrophage function during nanoparticle-induced oxidative stress," J. Duan, V. K. Kodali, M. J. Gaffrey, J. Guo, R. K. Chu, D. G. Camp, R. D. Smith, B. D. Thrall, and W. J. Qian, ACS Nano. 10 (1): 524-538 (2016).
PMID: 26700264, PMCID: PMC4762218

"Role of cytochrome P450 hydroxylase in the decreased accumulation of vitamin E in muscle from turkeys compared to that from chickens," D. M. Perez, M. P. Richards, R. S. Parker, M. E. Berres, A. T. Wright, M. Sifri, N. C. Sadler, N. Tatiyaborwomtham, and N. Li, J Agric Food Chem. 64 (3): 671-680 (2016).
PMID: 26653675, PMCID: PMC4753779

"SerpinB1 promotes pancreatic β cell proliferation," A. El Ouaamari, E. Dirice, N. Gedeon, J. Hu, J. Y. Zhou, J. Shirakawa, L. Hou, J. Goodman, C. Karampelias, G. Qian, J. Boucher, R. Martinez, M. A. Gritsenko, D. F. De Jesus, S. Kahraman, S. Bhatt, R. D. Smith, H. D. Beer, P. Jungtrakoon, A. B. Goldfine, C. W. Liew, A. Doria, O. Andersson, W. J. Qian, E. Remold-O’Donnell, and R. N. Kulkarni, Cell Metab. 23 (1): 194-205 (2016).
PMID: 26701651, PMCID: PMC4715773

"Simultaneous proteomic discovery and targeted monitoring using liquid chromatography, ion mobility spectrometry, and mass spectrometry," K. E. Burnum-Johnson, S. Nie, C. P. Casey, M. E. Monroe, D. J. Orton, Y. M. Ibrahim, M. A. Gritsenko, T. R. Clauss, A. K. Shukla, R. J. Moore, S. O. Purvine, T. Shi, W. Qian, T. Liu, E. S. Baker, and R. D. Smith, Mol Cell Proteomics 15 (12): 3694-3705 (2016).
PMID: 27670688, PMCID: PMC5141281

"SNaPP: simplified nanoproteomics platform for reproducible global proteomic analysis of nanogram protein quantities," E. L. Huang, P. D. Piehowski, D. J. Orton, R. J. Moore, W. –J. Qian, C. P. Casey, X. Sun, S. K. Dey, K. E. Burnum-Johnson, and R. D. Smith, Endocrinology 157 (3): 1307-1314 (2016).
PMID: 26745641, PMCID: PMC4769369

"Spatial ion peak compression and its utility in ion mobility spectrometry," S. V. Garimella, Y. M. Ibrahim, K. Tang, I. K. Webb, E. S. Baker, A. V. Tolmachev, T. C. Chen, G. A. Anderson, and R. D. Smith, J Am Soc Mass Spectrom. 27 (6): 1128-1135 (2016).
PMID: 27052738, PMCID: PMC4955798

"Spatially-resolved proteomics: rapid quantitative analysis of laser capture microdissected alveolar tissue samples," G. Clair, P. D. Piehowski, T. Nicola, J. A. Kitzmiller, E. L. Huang, E. M. Zink, R. L. Sontag, D. J. Orton, R. J. Moore, J. P. Carson, R. D. Smith, J. A. Whitsett, R. A. Corley, N. Ambalavanan, and C. Ansong, Sci Rep. 6: 39223 (2016).
PMID: 28004771, PMCID: PMC5177886

"Squeezing of ion populations and peaks in traveling wave ion mobility separations and structures for lossloss ion manipulations using compression ratio ion mobility programming (CRIMP), S. V. B. Garimella, A. M. Hamid, L. Deng, Y. M. Ibrahim, I. K. Webb, E. S. Baker, S. A. Prost, R. V. Norheim, G. A. Anderson, and R. D. Smith, Anal Chem. 88 (23): 11877-11885 (2016).
PMID: 27934097, PMCID: PMC5470847, NIHMS ID: NIHMS861889

"Surprising impact of remote groups on the folding—unfolding and dimer-chain equilibria of bifunctional H-bonding unimers," R. Liu, S. Chen, E. S. Baker, R. D. Smith, X. C. Zeng, and B. Gong, Chem Commun (Camb)., 52 (19): 3773-3776 (2016).
PMID: 27003741, PMCID: PMC5168931

"Systematic survey of serine hydrolase activity in mycobacterium tuberculosis defines changes associated with persistence," C. Ortega, L. N. Anderson, A. Frando, N. C. Sadler, R. W. Brown, R. D. Smith, A. T. Wright, and C. Grundner, Cell Chem Biol. 23 (2): 290-298 (2016).
PMID: 26853625, PMCID: PMC4803444

"The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification," H. Wang, T. Shi, W. –J. Qian, T. Liu, J. Kagan, S. Srivastava, R. D. Smith, K. D. Rodland, and D. G. Camp II, Expert Rev Proteomics 13 (1): 99-114 (2016).
PMID: 26581546, PMCID: PMC4822694

"The current state of the art of quantitative phosphoproteomics and its applications to diabetes research," C. Y. Chan, M. A. Gritsenko, R. D. Smith, and W. Qian, Expert Rev Proteomics 13 (4): 421-433 (2016).
PMID: 26960075, PMCID: PMC4939282

"The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity," S. H. Payne, M. E. Monroe, C. C. Overall, G. R. Kiebel, M. Degan, B. C. Gibbons, G. M. Fujimoto, S. O. Purvine, J. N. Adkins, M. S. Lipton, and R. D. Smith, Sci Data 2: 150041 (2016).
PMID: 26306205, PMCID: PMC4540001

"Ultra-high resolution ion mobility separations utilizing traveling waves in a 13 m serpentine path length structures for lossless ion manipulations module," L. Deng, Y. M. Ibrahim, A. M. Hamid, S. V. Garimella, I. K. Webb, X. Zheng, S. A. Prost, J. A. Sandoval, R. V. Norheim, G. A. Anderson, A. V. Tolmachev, E. S. Baker, and R. D. Smith, Anal Chem. 88 (18): 8957-8964 (2016).
PMID: 27531027, PMCID: PMC5340421

"Uncovering biologically significant lipid isomers with liquid chromatography, ion mobility spectrometry and mass spectrometry," J. E. Kyle, X. Zhang, K. K. Weitz, M. E. Monroe, Y. M. Ibrahim, R. J. Moore, J. Cha, X. Sun, E. S. Lovelace, J. Wagoner, S. J. Polyak, T. O. Metz, S. K. Dey, R. D. Smith, K. E. Burnum-Johnson, and E. S. Baker, Analyst 141 (5): 1649-1659 (2016).
PMID: 26734689, PMCID: PMC4764491

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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