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Publications

Journal Publications by year


2015 Journal Publications

"An optimized informatics pipeline for mass spectrometry-based peptidomics," C. Wu, M. E. Monroe, Z. Xu, G. W. Slysz, S. H. Payne, K. D. Rodland, T. Liu, and R. D. Smith, J Am Soc Mass Spectrom. 26 (12): 2002-2008 (2015).
PMID: 26015166, PMCID: PMC4655184

"Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods," J. He, A. A. Schepmoes, T. Shi, C. Wu, T. L. Fillmore, Y. Gao, R. D. Smith, W. J. Qian, R. D. Rodland, T. Liu, D. G. Camp II, A. Rastogi, S. H. Tan, W. Yan, A. A. Mohamed, W. Huang, S. Banerjee, J. Kagan, S. Srivastava, D. G. McLeod, S. Srivastava, G. Petrovics, A. Dobi, and A. Srinivasan, J Transl Med. 13: 54 (2015).
PMID: 25889691, PMCID: PMC4342100

"Changes in serine hydrolase activity associated with Mycobacterium tuberculosis replication," C. Ortega, L. N. Anderson, A. Frando, N. C. Sadler, R. W. Brown, R. D. Smith, A. T. Wright, and C. Grundner, Chemistry and Biology 8: 156 (2015).
PMID: 26853625, PMCID: PMC4803444

"Characterization of traveling wave ion mobility separations in structures for lossless ion manipulations," A. M. Hamid, Y. M. Ibrahim, S. V. Garimella, I. K. Webb, L. Deng, T. C. Chen, G. A. Anderson, S. A. Prost, R. V. Norheim, A. V. Tolmachev, and R. D. Smith, Anal Chem. 87 (22): 11301-11308 (2015).
PMID: 26510005, PMCID: PMC4748841

"Compensatory islet response to insulin resistance revealed by quantitative proteomics," A. El Ouaamari, J. Y. Zhou, C. W. Liew, J. Shirakawa, E. Dirice, N. Gedeon, S. Kahraman, D. F. De Jesus, S. Bhatt, J. S. Kim, T. R. Clauss, D. G. Camp II, R. D. Smith, W. -J. Qian, and R. N. Kulkarni, J Proteome Res. 14 (8): 3111-3122 (2015).
PMID: 26151086, PMCID: PMC4615688

"Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes," Z. Xu, C. Wu, F. Xie, G. W. Slysz, N. Tolic, M. E. Monroe, V. A. Petyuk, S. H. Payne, G. M. Fujimoto, R. J. Moore, T. L. Fillmore, A. A. Schepmoes, D. A. Levine, R. R. Townsend, S. R. Davies, S. Li, M. Ellis, E. Boja, R. Rivers, H. Rodriguez, K. D. Rodland, T. Liu, and R. D. Smith, J. Proteome Res. 14 (1): 422-433 (2015).
PMID: 25350482, PMCID: PMC4286152

"Correcting systematic bias and instrument measurement drift with mzRefinery," B. C. Gibbons, M. C. Chambers, M. E. Monroe, D. L. Tabb, and S. H. Payne, Bioinformatics 31 (23): 3838-3840 (2015).
PMID: 26243018, PMCID: PMC4653383

"Deficient expression of aldehyde dehydrogenase 1A1 is consistent with increased sensitivity of Gorlin syndrome patients to radiation carcinogenesis," A. T. Wright, T. Magnaldo, R. L. Sontag, L. N. Anderson, N. C. Sadler, P. D. Piehowski, Y. Gache, and T. J. Weber, Mol Carcinog. 54 (6): 473-484 (2015).
PMID: 24285572, PMCID: PMC4782972

"Development of a new ion mobility (quadrupole) time-of-flight mass spectrometer," Y. M. Ibrahim, E. S. Baker, W. F. Danielson, R. V. Norheim, D. C. Prior, G. A. Anderson, M. E. Belov, and R. D. Smith, Int J Mass Spectrom. 377: 655-622 (2015).
PMID: 26185483, PMCID: PMC4501404

"Enhancing biological analyses with three dimensional field asymmetric ion mobility, low field drift tube ion mobility and mass spectrometry (╬╝FAIMS/IMS-MS) separations," X. Zhang, Y. M. Ibrahim, T. C. Chen, J. E. Kyle, R. V. Norheim, M. E. Monroe, R. D. Smith, and E. S. Baker, Analyst 140 (20): 6955-6963 (2015).
PMID: 26140287, PMCID: PMC4586386

"Enhancing bottom-up and top-down proteomic measurements with ion mobility separations," E. S. Baker, K. E. Burnum-Johnson, Y. M. Ibrahim, D. J. Orton, M. E. Monroe, R. T. Kelly, R. J. Moore, X. Zhang, R. Theberge, C. E. Costello, and R. D. Smith, Proteomics 15 (16): 2766-2776 (2015).
PMID: 26046661, PMCID: PMC4534090

"Global analysis of Salmonella alternative sigma factor E on protein translation," J. Li, E. S. Nakayasu, C. C. Overall, R. C. Johnson, A. S. Kidwai, J. E. McDermott, C. Ansong, and F. Heffron, J Proteome Res. 14 (4): 1716-1726 (2015).
PMID: 25686268, PMCID: PMC4476319

"Identification of Salmonella Typhimurium Deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis," E.S. Nakayasu, M. A. Sydor, R. N. Brown, R. L. Sontag, T. J. Sobreira, G. W. Slysz, D. R. Humphrys, T. Skarina, O. Onoprienko, R. Di Leo, B. L. Deatherage Kaiser, C. Ansong, E. D. Cambronne, R. D. Smith, A. Savchenko, and J. N. Adkins, J Proteome Res. 14 (9): 4029-4038 (2015).
PMID: 26147956, PMCID: PMC4561012

"Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer," Y. Chen, F. E. Leach III, N. K. Kaiser, X. Dang, Y. M. Ibrahim, R. V. Norheim, G. A. Anderson, R. D. Smith, and A. G. Marshall, J Mass Spectrom. 50 (1): 280-284 (2015).
PMID: 25601704, PMCID: PMC4300554

"Ion manipulations in structures for lossless ion manipulations (SLIM): computational evaluation of a 90┬░ turn and a switch," S. V. Garimella, Y. M. Ibrahim, I. K. Webb, A. B. Ispen, T. C. Chen, A. V. Tolmachev, E. S. Baker, G. A. Anderson, and R. D. Smith, Analyst 140 (20): 6845-6852 (2015).
PMID: 26289106, PMCID: PMC4587302

"Ion trapping, storage, and ejection in structures for lossless ion manipulations," X. Zhang, S. V. Garimella, S. A. Post, I. K. Webb, T. C. Chen, K. Tang, A. V. Tolmachev, R. V. Norheim, E. S. Baker, G. A. Anderson, Y. M. Ibrahim, and R. D. Smith, Anal. Chem. 87 (12): 6010-6016 (2015).
PMID: 25971536, PMCID: PMC4523076

"Lipidomic and proteomic analysis of Caenorhabdit is elegans lipid droplets and identification of ACS-4 as a lipid droplet-associated protein," T. L. Vrablik, V. A. Petyuk, E. M. Larson, R. D. Smith, and J. L. Watts, Biochim Biophys Acta 1851 (10): 1337-1345 (2015).
PMID: 26121959, PMCID: PMC4561591

"On the ionization and ion transmission efficiencies of different ESI-MS interfaces," J. T. Cox, I. Marginean, R. D. Smith, and K. Tang, J Am Soc Mass Spectrom. 26 (1): 55-62 (2015).
PMID: 25267087, PMCID: PMC4276539

"Orthogonal injection ion funnel interface providing enhanced performance for selected reaction monitoring-triple quadrupole mass spectrometry," T. C. Chen, T. L. Fillmore, S. A. Prost, R. J. Moore, Y. M. Ibrahim, and R. D. Smith, Anal Chem. 87 (14): 7326-7331 (2015).
PMID: 26107611, PMCID: PMC4776758

"Peptide-centric proteome analysis: an alternative strategy for the analysis of tandem mass spectrometry data," Y. S. Ting, J. D. Egertson, S. H. Payne, S. Kim, B. MacLean, L. Kall, R. Aebersold, R. D. Smith, W. S. Noble, and M. J. MacCoss, Molecular and Cellular Proteomics, 14, 2301-2307 (2015).
PMID: 26217018, PMCID: PMC4563716

"Perturbations in the urinary exosome in transplant rejection," T. K. Sigdel, Y. W. Ng, S. Lee, C. D. Nicora, W. J. Qian, R. D. Smith, D. G. Camp II, and M. M. Sarwal, Front Med (Lausanne), 1: 57 (2015).
PMID: 25593928, PMCID: PMC4292055

"Preserved DNA damage checkpoint pathway protects against complications in long-standing type 1 diabetes," S. Bhatt, M. K. Gupta, M. Khamaisi, R. Martinez, M. A. Gritsenko, B. K. Wagner, P. Guye, V. Busskamp, J. Shirakawa, G. Wu, C. W. Liew, T. R. Clauss, I. Valdez, A. El Ouaamari, E. Dirice, T. Takatani, H. A. Keenan, R. D. Smith, G. Church, R. Weiss, A. J. Wagers, W. -J. Qian, G. L. King, and R. N. Kulkarni, Cell Metab. 22 (2): 239-252 (2015).
PMID: 26244933, PMCID: PMC4589213

"Proteomic analysis reveals down-regulation of surfactant protein B in murine type II pneumocytes infected with influenza A virus," L. P. Kebaabetswe, A. K. Haick, M. A. Gritsenko, T. L. Fillmore, R. K. Chu, S. O. Purvine, B. J. Webb-Robertson, M. M. Matzke, R. D. Smith, K. M. Waters, T. O. Metz, and T. A. Miura, Virology 438: 96-107 (2015).
PMID: 25965799, PMCID: PMC4516596

"Rectangular ion funnel: a new ion funnel interface for structures for lossless ion manipulations," T. C. Chen, I. K. Webb, S. A Prost, M. B. Harrer, R. V. Norheim, K. Tang, Y. M. Ibrahim, and R. D. Smith, Anal. Chem. 87 (1): 716-722 (2015).
PMID: 25409343, PMCID: PMC4287841

"Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry," B. J. Webb-Robertson, H. K. Wilberg, M. M. Matzke, J. N. Brown, J. Wang, J. E. McDermott, R. D. Smith, K. D. Rodland, T. O. Metz, J. G. Pounds, and K. M. Waters, J Proteome Res. 14 (5): 1993-2001 (2015).
PMID: 25855118, PMCID: PMC4776766

"Sensitive targeted quantification of ERK phosphorylation dynamics and stoichiometry in human cells without affinity enrichment," T. Shi, Y. Gao, M. J. Gaffrey, C. D. Nicora, T. L. Fillmore, W. B. Chrisler, M. A. Gritsenko, C. Wu, J. He, K. J. Bloodsworth, R. Zhao, D. G. Camp II, T. Liu, K. D. Rodland, R. D. Smith, H. S. Wiley, and W. -J. Qian, Anal Chem. 87 (2): 1103-1110 (2015).
PMID: 25517423, PMCID: PMC4365449

"Subunit compositions of Arabidopsis RNA polymerases I and III reveal Pol I- and Pol III-specific forms of the AC40 subunit and alternative forms of the C53 subunit," T. S. Ream, J. R. Haag, F. Pontvianne, C. D. Nicora, A. D. Norbeck, L. Pasa-Tolic, and C. S. Pikaard, Nucleic Acids Res. 43 (8): 4163-4178 (2015).
PMCID: PMC4417161

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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