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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.

2011 Journal Publications

Ansong C, N Tolic, SO Purvine, S Porwollik, MB Jones, H Yoon, SH Payne, JL Martin, MC Burnet, ME Monroe, P Venepally, RD Smith, S Peterson, F Heffron, M Mcclelland, and JN Adkins. 2011. "Experimental Annotation of Post-Translational Features and Translated Coding Regions in the Pathogen Salmonella Typhimurium." BMC Genomics, 12, 433.
PMCID: PMC3174948 - Abstract

Belov ME, S Prasad, DC Prior, WF Danielson, III, KK Weitz, YM Ibrahim, and RD Smith. 2011. "Pulsed Multiple Reaction Monitoring Approach to Enhancing Sensitivity of a Tandem Quadrupole Mass Spectrometer." Anal. Chem., 83(6), 2162–2171.
PMCID: PMC3059105 - Abstract

Dresang, LR, JR Teuton, H Feng, JM Jacob, DG Camp II, SO Purvine, MA Gritsenko, Z Li, RD Smith, B Sugden, PS Moore, and Y Chang. 2011. “Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes.” BMC Genomics, 12: Article No. 625.
PMCID: PMC3282826 - Abstract

Du X, SM Chowdhury, NP Manes, S Wu, MU Mayer, JN Adkins, GA Anderson, and RD Smith. 2011. "Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry." J. Proteome Res., 10(3), 923-931.
PMCID: PMC3048902 - Abstract

Frank AM, ME Monroe, AR Shah, JJ Carver, N Bandeira, RJ Moore, GA Anderson, RD Smith, and PA Pevzner. 2011. "Spectral Archives: Extending Spectral Libraries to Analyze both Identified and Unidentified Spectra." Nature Methods, 8(7), 587-591.
PMCID: PMC3128193 - Abstract

Ghazalpour A, B Bennett, VA Petyuk, L Orazco, R Hagopian, I Mungrue, CR Farber, J Sinsheimer, HM Kang, N Furlotte, C Park, PZ Wen, HM Brewer, KK Weitz, DG Camp, II, C Pan, R Yordanova, I Neuhaus, C Tilford, N Siemers, P Gargalovic, E Eskin, T Kirchgessner, DJ Smith, RD Smith, and AJ Lusis. 2011. "Comparative Analysis of Proteome and Transcriptome Variation in Mouse." PLoS Genetics, 7(6), e1001393.
PMCID: PMC3111477 - Abstract

Hossain M, DT Kaleta, EW Robinson, T Liu, R Zhao, JS Page, RT Kelly, RJ Moore, K Tang, DG Camp, II, W Qian, and RD Smith. 2011. "Enhanced Sensitivity for Selected Reaction Monitoring–Mass Spectrometry-based Targeted Proteomics using a Dual-Stage Electrodynamic Ion Funnel Interface." Mol. Cell. Proteomics, 10(2), M000062-MCP201.
PMCID: PMC3033664 - Abstract

Ibrahim YM, AA Shvartsburg, RD Smith, and ME Belov. 2011. "Ultrasensitive Identification of Localization Variants of Modified Peptides Using Ion Mobility Spectrometry ." Anal. Chem., 83(14), 5617–5623.
PMCID: PMC3136632 - Abstract

Kim JS, TL Fillmore, T Liu, EW Robinson, M Hossain, BL Champion, RJ Moore, DG Camp, II, RD Smith, and W Qian. 2011. "18O-Labeled Proteome Reference as Global Internet Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry." Mol. Cell. Proteomics, 10(12), M110.007302.
PMCID: PMC3237067 - Abstract on PubMed

Lee B, D Lopez-Ferrer, BC Kim, HB Na, YI Park, KK Weitz, MG Warner, T Hyeon, SW Lee, RD Smith, and J Kim. 2011. "Rapid and Efficient Protein Digestion using Trypsin Coated Magnetic Nanoparticles under Pressure Cycles." Proteomics, 11(2), 309-318.
PMCID: PMC3043614 - Abstract

Lopez-Ferrer D, K Petritis, EW Robinson, KK Hixson, Z Tian, JH Lee, SW Lee, N Tolic, KK Weitz, ME Belov, RD Smith, and L Pasa-Tolic. 2011. "Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics." Mol. Cell. Proteomics, 10(2), M110.001479.
PMCID: PMC3033671 - Abstract

Schoenherr RM, KS Kelly-Spratt, CW Lin, JR Whiteaker, T Liu, T Holzman, I Coleman, LC Feng, TD Lorentzen, AL Krasnoselsky, P Wang, Y Liu, KE Gurley, LM Amon, AA Schepmoes, RJ Moore, DG Camp, II, LA Chodosh, RD Smith, PS Nelson, M McIntosh, C Kemp, and AG Paulovich. 2011. "Proteome and Transcriptome Profiles of a Her2/Neu-driven Mouse Model of Breast Cancer." Proteomics - Clinical Applications, 5(3-4), 179-188.
PMCID: PMC3069718 - Abstract

Schutzer SE, TE Angel, T Liu, AA Schepmoes, TRW Clauss, JN Adkins, DG Camp, II, BK Holland, J Bergquist, PK Coyle, RD Smith, BA Fallon, and B Natelson. 2011. "Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome." PLoS One, 6(2), e17287.
PMCID: PMC3044169 - Abstract

Shen Y, N Tolic, F Xie, R Zhao, SO Purvine, AA Schepmoes, RJ Moore, GA Anderson, and RD Smith. 2011. "Effectiveness of CID, HCD, and ETD with FT MS/MS for Degradomic-Peptidomic Analysis: Comparison of Peptide Identification Methods." J. Proteome Res., 10(9), 3929-3943.
PMCID: PMC3166380 - Abstract

Shukla AK, R Zhang, DJ Orton, R Zhao, TRW Clauss, RJ Moore, and RD Smith. 2011. "Formation of Iron Complexes from Trifluoroacetic Acid Based Liquid Chromatography Mobile Phases as Interference Ions in Liquid Chromatography/Electrospray Ionization Mass Spectrometric Analysis." Rapid Commun. Mass Spectrom., 25(10):1452-1456.
PMCID: 3120053

Shvartsburg AA, and RD Smith. 2011. "Accelerated High-Resolution Differential Ion Mobility Separations Using Hydrogen." Anal. Chem., 83(23), 9159-9166.
PMCID: PMC3234991 - Abstract

Shvartsburg AA, D Singer, RD Smith, and R Hoffmann. 2011. "Ion Mobility Separation of Isomeric Phosphopeptides from a Protein with Variant Modification of Adjacent Residues." Anal. Chem., 83(13), 5078-5085.
PMCID: PMC3139565 - Abstract

Shvartsburg AA, G Isaac, N Leveque, RD Smith, and TO Metz. 2011. "Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry." J. Am. Soc. Mass Spectr., 22(7), 1146-1155.
PMCID: PMC3187568 - Abstract

Shvartsburg AA, AJ Creese, RD Smith, and HJ Cooper. 2011. "Separation of a Set of Peptide Sequence Isomers Using Differential Ion Mobility Spectrometry." Anal. Chem., 83(18), 6918-6923.
PMCID: PMC3173593 - Abstract

Shvartsburg AA, and RD Smith. 2011. "Ultrahigh-Resolution Differential Ion Mobility Spectrometry Using Extended Separation Times." Anal. Chem., 83(1), 23-29.
PMCID: PMC3012152 - Abstract

Smallwood, HS, D López-Ferrer, and TC Squier. 2011. “Aging Enhances Production of Reactive Oxygen Species and Bactericidal Activity in Peritoneal Macrophages by Up-Regulating Classical Activation Pathways.” Biochemistry, 50(45), 9911-9922.
PMCID: PMC3241613 - Abstract

Stanley JR, JN Adkins, GW Slysz, ME Monroe, SO Purvine, YV Karpievitch, GA Anderson, RD Smith, and AR Dabney. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Anal. Chem., 83(16), 6135-6140
PMCID: PMC3212438 - Abstract

Sun X, RT Kelly, WF Danielson, III, N Agrawal, K Tang, and RD Smith. 2011. "Hydrodynamic Injection with Pneumatic Valving for Microchip Electrophoresis, with Total Analyte Utilization." Electrophoresis, 32(13), 1610-1618.
PMCID: PMC3124583 - Abstract

Sun X, RT Kelly, K Tang, and RD Smith. 2011. "Membrane-Based Emitter for Coupling Microfluidics with Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry." Anal. Chem., 83(4), 5797-5803.
PMCID: PMC3139426 - Abstract

Tang K, JS Page, I Marginean, RT Kelly, and RD Smith. 2011. "Improving Liquid Chromatography-Mass Spectrometry Sensitivity using a Subambient Pressure Ionization with Nanoelectrospray (SPIN) Interface." J. Am. Soc. Mass Spectr., 22(8), 1318-1325.
PMCID: PMC3187566 - Abstract

Tolmachev AV, EW Robinson, S Wu, RD Smith, and L Pasa-Tolic. 2011. "Trapping Radial Electric Field Optimization in Compensated FTICR Cells." J. Am. Soc. Mass Spectr., 22(8), 1334-1342.
PMCID: PMC21953187 - Abstract on PubMed

Wang Y, F Yang, MA Gritsenko, Y Wang, TRW Clauss, T Liu, Y Shen, ME Monroe, D Lopez-Ferrer, T Reno, RJ Moore, RL Klemke, DG Camp, II, and RD Smith. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11(10), 2019-2026.
PMCID: PMC3120047 - Abstract

Wang Y, F Yang, Y Fu, X Huang, W Wang, X Jiang, MA Gritsenko, R Zhao, ME Monroe, OC Pertz, SO Purvine, DJ Orton, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry, 286(20), 18190-18201.
PMCID: PMC3093891 - Abstract

Wu, S, N Tolic, Z Tian, EW Robinson, and L Pasa-Tolic. 2011. “An Integrated Top-Down and Bottom-Up Strategy for Characterization of Protein Isoforms and Modification.” Methods Mol Biol., 694, 291-304.
Abstract on PubMed

Xie F, T Liu, W Qian, VA Petyuk, and RD Smith. 2011. "Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics." Journal of Biological Chemistry, 286(29), 25443-25449.
PMCID: PMC3138289 - Abstract

Yoon H, C Ansong, JE McDermott, MA Gritsenko, RD Smith, F Heffron, and JN Adkins. 2011. "Systems Analysis of Multiple Regulator Perturbations Allows Discovery of Virulence Factors in Salmonella." BMC Systems Biology, 5, 100.
PMCID: PMC3213010 - Abstract

Zhang H, KE Burnum, ML Luna, BO Petritis, JS Kim, W Qian, RJ Moore, A Heredia-Langner, BJM Webb-Robertson, BD Thrall, DG Camp, II, RD Smith, JG Pounds, and T Liu. 2011. "Quantitative Proteomics Analysis of Adsorbed Plasma Proteins Classifies Nanoparticles with Different Surface Properties and Size." Proteomics, 11(23), 4569-4577.
PMCID: PMC3252235 - Abstract

Zhang Q, ME Monroe, AA Schepmoes, TRW Clauss, MA Gritsenko, D Meng, VA Petyuk, RD Smith, and TO Metz. 2011. "Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects." J. Proteome Res., 10(7), 3076-3088.
PMCID: PMC3128674 - Abstract

Zhou J, GP Dann, CW Liew, RD Smith, RN Kulkarni, and W Qian. 2011. "Unraveling Pancreatic Islet Biology by Quantitative Proteomics." Expert Review of Proteomics, 8(4), 495-504.
PMCID: PMC3160816 - Abstract


2011 Book Chapters

Lopez-Ferrer D, KK Hixson, ME Belov, and RD Smith. 2011. "Ultra-Fast Sample Preparation for High-Throughput Proteomics." Chapter 8 in Sample Preparation in Biological Mass Spectrometry, ed. AR Ivanov and AV Lazarev, pp. 125-139. Springer, Dordrecht, Germany.

Qian W, BO Petritis, CD Nicora, and RD Smith. 2011. "Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics." Chapter 3 in Gel-Free Proteomics, Methods and Protocols: Methods in Molecular Biology, vol. 753, ed. K Gevaert and J Vandekerckhove, pp. 43-54. Humana Press Inc., Totowa, NJ.
View Abstract on PubMed

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