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Publications

Journal Publications by year


Acknowledgments

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

Portions of this research were supported by the NIH National Center for Research Resources (RR18522), 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.

2006 Journal Publications

Baas T, CR Baskin, DL Diamond, A García-Sastre, H Bielefeldt-Ohmann, TM Tumpey, MJ Thomas, VS Carter, TH Teal, N Van Hoeven, S Proll, JM Jacobs, ZR Caldwell, MA Gritsenko, RR Hukkanen, DG Camp II, RD Smith, and MG Katze. 2006. "Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics." Journal of Virology 80(21):10813-10828.
Download the supplemental data corresponding to this article - 1 Excel file (845 KB) (registration required).

Callister SJ, RC Barry, JN Adkins, ET Johnson, WJ Qian, BJ Webb-Robertson, RD Smith, and MS Lipton. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5(2):277-286.
PMCID: PMC1992440 - Abstract

Diamond DL, SC Proll, JM Jacobs, EY Chan, DG Camp II, RD Smith, and MG Katze. 2006. "HepatoProteomics: Applying Proteomic Technologies to the Study of Liver Function and Disease." Hepatology 44(2):299-308.
Abstract on PubMed

Ibrahim, Y, K Tang, AV Tolmachev, AA Shvartsburg, and RD Smith. 2006. “Improving Mass Spectrometer Sensitivity using a High-Pressure Electrodynamic Ion Funnel Interface.” J Am Soc Mass Spectrom., 17(9), 1299-1305.
PMCID: PMC1785296 - Abstract

Jaitly N, ME Monroe, VA Petyuk, TR Clauss, JN Adkins, and RD Smith. 2006. "Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline." Analytical Chemistry 78(21):7397-7409.
Abstract on PubMed

Kelly RT, JS Page, Q Luo, RJ Moore, DJ Orton, K Tang, and RD Smith. 2006. "Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry." Analytical Chemistry 78(22):7796-7801.
PMCID: PMC1769309 - Abstract

Kiebel GR, KJ Auberry, N Jaitly, DA Clark, ME Monroe, ES Peterson, N Tolic, GA Anderson, and RD Smith. 2006. "PRISM: A Data Management System for High-Throughput Proteomics." Proteomics 6 (6):1783-1790.
Abstract on PubMed

Koeniger, SL, SI Merenbloom, SJ Valentine, MF Jarrold, HR Udseth, RD Smith, and DE Clemmer. 2006. “An IMS-IMS Analogue of MS-MS.” Anal Chem, 78(12), 4161-4174.
Abstract on PubMed

Liu T, WJ Qian, HM Mottaz, MA Gritsenko, AD Norbeck, RJ Moore, SO Purvine, DG Camp, and RD Smith. 2006. "Evaluation of Multiprotein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry." Molecular & Cellular Proteomics 5(11):2167-2174.
PMCID: PMC1850944 - Abstract

Liu T, W-J Qian, MA Gritsenko, W Xiao, LL Moldawer, A Kaushal, ME Monroe, SM Varnum, RJ Moore, SO Purvine, RV Maier, RW Davis, RG Tompkins, DG Camp II, and RD Smith. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome and the Inflammation and the Host Response to Injury Large Scale Collaborative Research Program." Molecular & Cellular Proteomics 5(10):1899-1913.

Luo Q, K Tang, F Yang, A Elias, Y Shen, RJ Moore, R Zhao, KK Hixson, SS Rossie, and RD Smith. 2006. "More Sensitive and Quantitative Proteomic Measurements Using Very Low Flow Rate porous Silica Monolithic LC Columns with Electrospray Ionization-Mass Spectrometry." Journal of Proteome Research 5(5):1091-1097.
Abstract on PubMed

Metz TO, JM Jacobs, MA Gritsenko, G. Fontes, W.-J. Qian, D. Camp II, V. Poitout, RD Smith. 2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5(12):3345-3354.
Download the supplemental data corresponding to this article - 1 Excel file (5.2 MB) (registration required).

Page JS, AV Tolmachev, K Tang, and RD Smith. 2006. "Theoretical and Experimental Evaluation of the Low m/z Transmission of an Electrodynamic Ion Funnel." Journal of the American Society for Mass Spectrometry 17(4):586-592.
PMCID: PMC1829303

Patwardhan AJ, EF Strittmatter, DG Camp, II, RD Smith, and M Pallavicini. 2006. "Quantitative Proteome Analysis of Breast Cancer Cell Lines using 18O-Labeling and an Accurate Mass and Time Tag Strategy." Proteomics 6(9):2903-2915 (2006). doi:10.1002/pmic200500582
Abstract on PubMed

Petritis K, LJ Kangas, B Yan, ME Monroe, EF Strittmatter, W Qian, JN Adkins, RJ Moore, Y Xu, MS Lipton, DG Camp II, and RD Smith. 2006. "Improved Peptide Elution Time Prediction for Reversed-Phase Liquid Chromatography-MS by Incorporating Peptide Sequence Information." Analytical Chemistry 78(14):5026-5039.
Abstract on PubMed

Qian WJ, JM Jacobs, T Liu, DG Camp, and RD Smith. 2006. "Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications." Molecular & Cellular Proteomics 5(10):1727-1744.
PMCID: PMC1781927 - Abstract

Sacksteder CA, WJ Qian, TV Knyushko, H Wang, MH Chin, G Lacan, WP Melega, DG Camp II, RD Smith, DJ Smith, TC Squier, and DJ Bigelow. 2006. "Endogenously Nitrated Proteins in Mouse Brain: Links to Neurodegenerative Disease." Biochemistry 45(26):8009-8022.
Abstract on PubMed

Shvartsburg AA, F Li, K Tang, and RD Smith. 2006. "Characterizing the Structures and Folding of Free Proteins Using 2-D Gas-Phase Separations: Observation of Multiple Unfolded Conformers." Analytical Chemistry 78(10):3304-3315.
Abstract on PubMed

Shvartsburg AA, SV Mashkevich, and RD Smith. 2006. "Feasibility of Higher-Order Differential Ion Mobility Separations Using New Asymmetric Waveforms." Journal of Physical Chemistry A 110(8):2663-2673.
PMCID: PMC3173260 - Abstract

Shvartsburg AA, F Li, K Tang, and RD Smith. 2006. "High-Resolution Field Asymmetric Waveform Ion Mobility Spectrometry Using New Planar Geometry Analyzers." Analytical Chemistry 78(11):3706-3714.
PMCID: PMC1785295 - Abstract

Shvartsburg AA, T Bryskiewicz, RW Purves, K Tang, R Guevremont, and RD Smith. 2006. "Field Asymmetric Waveform Ion Mobility Spectrometry Studies of Proteins: Dipole Alignment in Ion Mobility Spectrometry." Journal of Physical Chemistry B 110(43):21966-21980.
Abstract on PubMed

Simpson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Mottaz, AN Vilkov, GA Anderson, MS Lipton, and RD Smith. 2006. "Using Size Exclusion Chromatography-RPLC and RPLC-CIEF as Two-Dimensional Separation Strategies for Protein Profiling." Electrophoresis 7(13):2722-2733.

Smallwood HS, L Shi, and TC Squier. 2006. "Increases in Calmodulin Abundance and Stabilization of Activated Inducible Nitric Oxide Synthase Mediate Bacterial Killing in RAW 264.7 Macrophages." Biochemistry 45(32):9717-9726.
Abstract on PubMed

Smith RD. 2006. "Future Directions for Electrospray Ionization for Biological Analysis Using Mass Spectrometry." Biotechniques 41(2):147-148.

Smith, RD, K Tang, and Y Shen. 2006. “Ultra-Sensitive and Quantitative Characterization of Proteomes.” Mol Biosyst., 2(5), 221-230.
Abstract on PubMed

Tolmachev AV, ME Monroe, N Jaitly, VA Petyuk, JN Adkins, and RD Smith. 2006. "Mass Measurement Accuracy in Analyses of Highly Complex Mixtures Based Upon Multidimensional Recalibration." Analytical Chemistry 78(24):8374-8385.
Abstract on PubMed

Valentine SJ, MD Plasencia, X Liu, M Krishnan, S Naylor, HR Udseth, RD Smith, and DE Clemmer. 2006. "Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry." Journal of Proteome Research 5(11):2977-2984.
Abstract on PubMed

Wang HX, W Qian, MH Chin, VA Petyuk, RC Barry, T Liu, MA Gritsenko, HM Mottaz, RJ Moore, DG Camp, II, AH Khan, D Smith, and RD Smith 2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5(2):361-369.
Abstract on PubMed(free in PMC)

Waters KM, JG Pounds, and BD Thrall. 2006. "Data Merging for Integrated Microarray and Proteomic Analysis." Briefings in Functional Genomics & Proteomics 5(4):261-272.
Abstract on PubMed

Zhang, H, P Loriaux, J Eng, D Campbell, A Keller, P Moss, R Bonneau, N Zhang, Y Zhou, B Wollscheid, K Cooke, EC Yi, H Lee, ER Pesking, J Zhang, RD Smith, and R Aebersold. 2006. “UniPep—A Database for Human N-linked Glycosites: a Resource for Biomarker Discovery.” Genome Biol., 7(8), R73.
PMCID: PMC1779586 - Abstract

Zimmer JS, ME Monroe, W Qian, and RD Smith. 2006. "Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach." Mass Spectrometry Reviews 25(3):450-482.
Abstract on PubMed

Book Chapters

Jacobs JM and RD Smith. 2006. "Proteomic Analyses Using High-Efficiency Separations and Accurate Mass Measurements." In Separation Methods in Proteomics. Editors GB Smejkal and ALazareu, CRC Taylor and Francis Group, Boca Raton, Florida, Chapter 20, pp. 363-385.

Liu T, WJ Qian, DG Camp II, and RD Smith. 2006. "The Use of Quantitative Cysteinyl-Peptide Enrichment Technology for High-Throughput Quantitative Proteomics." In Quantitative Proteomics by Mass Spectrometry (Methods in Molecular Biology Series Vol. 359), S Sechi, Editor. Humana Press, Totowa, New Jersey, Chapter 7, pp. 107-124.
Abstract on PubMed

Streblow DN, SM Varnum, RD Smith, and JA Nelson. 2006. "A Proteomics Analysis of Human Cytomegalovirus Particles." In Cytomegaloviruses: Molecular Biology and Immunology. MJ Raeddehase and N Lemmermann, Editors. Caister Academic Press, Wymondham, United Kingdom, Chapter 5, pp. 91-110.

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