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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.

2010 Journal Publications

Ahn, H-K, BC Kim, S-H Jun, MS Chang, D Lopez-Ferrer, RD Smith, MB Gu, S-W Lee, B Soo Kim, and J Kim. 2010. "Robust Trypsin Coating on Electrospun Polymer Nanofibers in Rigorous Conditions and its uses for Protein Digestion," Biotechnol. Bioeng., 107, 917-923.
Abstract on PubMed

Angel, TE, BJ Luft, X Yang, CD Nicora, DG Camp II, JM Jacobs, and RD Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One, 5, 11, e13800.
Abstract on PubMed

Auberry, KJ, GR Kiebel, ME Monroe, JN Adkins, GA Anderson, and RD Smith. 2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." J. Proteomics & Bioinformatics, 3(1), 1-4.
PMCID: PMC2888287 - Abstract on PubMed

Baker, ES, EA Livesay, DJ Orton, RJ Moore, WF Danielson, DC Prior, Y Ibrahim, BL Lamarche, A Mayampurath, AA Schepmoes, DF Hopkins, K. Tang, RD Smith and M Belov. 2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." J. Proteome Res., 9, 997-1006.
Abstract on PubMed

Brown JN, RD Estep, D Lopez-Ferrer, HM Brewer, TR Clauss, NP Manes, M O’Connor, H Li, JN Adkins, SW Wong, and RD Smith. 2010. "Characterization of Macaque Pulmonary Fluid Proteome during Monkeypox Infection: Dynamics of Host Response." Mol. Cell. Proteomics, 9, 2760-2771.
Abstract on PubMed

Brown JN, RE Palermo, CR Baskin, M Gritsenko, PJ Sabourin, JP Long, CL Sabourin, H Bielefeldt-Ohmann, A García-Sastre, R Albrecht, TM Tumpey, JM Jacobs, RD Smith, and MG Katze. 2010. "Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections." J. Virology, 84, 12058-12068.
Abstract on PubMed

Buchko GW, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, and JE McDermott. 2010. "A Multi-Pronged Search for a Common Structural Motif in the Secretion Signal of Salmonella Enterica Serovar Typhimurium Type III Effector Proteins." Molecular Biosystems, 6(12), 2448-2458.
Abstract on PubMed

Diamond, DL, AJ Syder, JM Jacobs, CM Sorensen, KA Walters, S Proll, JE McDermott, MA Gritsenko, Q Zhang, R Zhao, TO Metz, DG Camp II, KM Waters, RD Smith, CM Rice, and MG Katze. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics." PloS Pathogens, 6, 1, e1000719.
Abstract on PubMed

Gupta, N, KK Hixson, DE Culley, RD Smith, and PA Pevzner. 2010. "Analyzing Protease Specificity and Detecting in vivo Proteolytic Events using Tandem Mass Spectrometry." Proteomics, 10, 2833-2844.
Abstract on PubMed

Ham, BM, H Jayachandran, F Yang, N Jaitly, AD Polpitiya, ME Monroe, L Wang, R Zhao, SO Purvine, EA Livesay, DG Camp II, S Rossie, and RD Smith. 2010. "Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis." J. Proteome Res., 9, 945-953.
Abstract on PubMed

Jun, S-H, MS Chang, BC Kim, HJ An, D Lopez-Ferrer, R Zhao, RD Smith, S-W Lee, and J Kim. 2010. "Trypsin Coatings on Electrospun and Alcohol-Dispersed Polymer Nanofibers for Trypsin Digestion Column." Anal. Chem., 82, 7828-7834.
Abstract on PubMed

Jung, H-J, SO Purvine, H Kim, VA Petyuk, S-W Hyung, ME Monroe, D-G Mun, K-C Kim, J-M Park, S-J Kim, N Tolic, GW Slysz, RJ Moore, R Zhao, JN Adkins, GA Anderson, H Lee, DG Camp II, M-H Yu, RD Smith and S-W Lee. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Anal. Chem., 82, 8510-8518.

Karpievitch, YV, AD Polpitiya, GA Anderson, RD Smith, and AR Dabney. 2010. "Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects." Annals of Applied Statistics, 4, 1797-1823.

Kelly, RT, AV Tolmachev, JS Page, K Tang, and RD Smith. 2010. "The Ion Funnel: Theory, Implementations, and Applications." Mass Spectrom. Rev., 29, 294-312.
Abstract on PubMed

Kim, J, BC Kim, D Lopez-Ferrer, K Petritis, and R.D. Smith. 2010. "Nanobiocatalysis for Protein Digestion in Proteomic Analysis." Proteomics, 10, 687-699.
Abstract on PubMed

Kotz, KT, W Xiao, C Miller-Graziano, W-J Qian, AE Rosenbach, A Russom, EA Warner, LL Moldawer, A De, PE Bankey, BO Petritis, DG Camp II, J Goverman, SP Fagan, BH Brownstein, D Irimia, W Xu, J Wilhelmy, MN Mindrinos, RD Smith, RW Davis, RG Tompkins and M Toner, and the Inflammation and the Host Response to Injury Collaborative Research Program. 2010. "Clinical Microfluidics for Neutrophil Genomics and Proteomics." Nature Med., 16, 1042-1047.
Abstract on PubMed

Lewis, NE, KK Hixson, TM Conrad, P Charusanti, AD Polpitiya, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, RD Smith, and BO Palsson. 2010. "Omic Data from Evolved E. coli are Consistent with Computed Optimal Growth from Genome-scale Models." Mol. Syst. Biol., 6, 390.
Abstract on PubMed

Lourette, N, H Smallwood, S Wu, EW Robinson, TC Squier, RD Smith, and L Paša-Tolic. 2010. "A Top-Down LC-FTICR MS Based Strategy for Characterizing Oxidized Calmodulin in Activated Macrophages." J. Am. Soc. Mass Spectr., 21, 930-939.
Abstract on PubMed

Marginean, I, JS Page, AV Tolmachev, K Tang, and RD Smith. 2010. "Achieving 50% Ionization Efficiency in Subambient Pressure Ionization with Nanoelectrospray." Anal Chem., 82, 9344-9349.
Abstract on PubMed

Petyuk, VA, AM Mayampurath, ME Monroe, AD Polpitiya, SO Purvine, GA Anderson, DG Camp II, and RD Smith. 2010. "DtaRefinery: A Software Tool for Elimination of Systematic Errors from Parent Ion Mass Measurements in Tandem Mass Spectra Datasets." Mol. Cell. Proteomics, 9, 486-496.
Abstract on PubMed

Petyuk, VA, W-J Qian, RD Smith, and DJ Smith. 2010. “Mapping Protein Abundance Patterns in the Brain using Voxelation Combined with Liquid Chromatography and Mass Spectrometry.” Methods, 50(2), 77-84.
PMCID: PMC2818068 - Abstract on PubMed

Qian, W-J, BO Petritis, A Kaushal, CC Finnerty, MG Jeschke, ME Monroe, RJ Moore, AA Schepmoes, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DN Herndon, DG Camp II, RD Smith, and the Inflammation and the Host Response to Injury Large Scale Collaborative Research Program. 2010. "Plasma Proteome Response to Severe Burn Injury Revealed by 18O-Labeled ‘Universal’ Reference-based Quantitative Proteomics." J. Proteome Res., 9, 4779-4789.
Abstract on PubMed

Schutzer, SE, T Liu, B Natelson, TE Angel, AA Schepmoes, SO Purvine, KK Hixson, MS Lipton, DG Camp II, PK Coyle, RD Smith and J Bergquist. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid." PLoS One, 5(6), e10980.
Abstract on PubMed

Shah, AR, K Agarwal, ES Baker, M Singhal, AM Mayampurath, YM Ibrahim, LJ Kangas, ME Monroe, R Zhao, ME Belov, GA Anderson, and RD Smith. 2010. "Machine Learning Based Prediction for Peptide Drift Times in Ion Mobility Spectrometry." Bioinformatics, 26, 1601-1607.
Abstract on PubMed

Shen, Y, N Tolic, T Liu, R Zhao, BO Petritis, MA Gritsenko, DG Camp II, RJ Moore SO Purvine, FJ Esteva, and RD Smith. 2010. "Blood Peptidome-Degradome Profile of Breast Cancer." (2010) PLoS One, 5(10), e13133.
Abstract on PubMed

Shen, Y, N Tolic, SO Purvine, and RD Smith. 2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products using de novo-Protein Unique Sequence Tags Approach." J. Proteome Res., 9, 4053-4060.
Abstract on PubMed

Shen, Y, T Liu, N Tolic, BO Petritis, R Zhao, RJ Moore, SO Purvine, DG Camp II, and RD Smith. 2010. "Strategy for Degradomic-Peptidomic Analysis of Human Blood Plasma." J. Proteome Res., 9, 2339-2346.
Abstract on PubMed

Shvartsburg, AA, K Tang, and RD Smith. 2010. "Differential Ion Mobility Separations of Peptides with Resolving Power Exceeding 50." Anal. Chem., 82, 32-35.
Abstract on PubMed

Shvartsburg, AA, WF Danielson, and RD Smith. 2010. "High-Resolution Differential Ion Mobility Separations Using Helium-Rich Gases." Anal. Chem., 82, 2456-2462.
Abstract on PubMed

Shvartsburg, AA, DC Prior, K Tang, and RD Smith. 2010. "High-Resolution Differential Ion Mobility Separations Using Planar Analyzers at Elevated Dispersion Fields." Anal. Chem., 82, 7649-7655.
Abstract on PubMed

Shvartsburg, AA, DE Clemmer, and RD Smith. 2010. "Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry." Anal. Chem., 82, 8047-8051.
Abstract on PubMed

Shvartsburg, AA, AJ Creese, RD Smith, and HJ Cooper. 2010. "Separation of Peptide Isomers with Variant Modified Sites by High-Resolution Differential Ion Mobility Spectrometry." Anal. Chem., 82, 8327-8334.
Abstract on PubMed

Sigdel, TK, A Kaushal, M Gritsenko, AD Norbeck, W-J Qian, W Xiao, DG Camp II, RD Smith, and MM Sarwal. 2010. "Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection." Proteom. Clin. Appl., 10, 32-47.
Abstract on PubMed

Sun, X, RT Kelly, K Tang, and RD Smith. 2010. "Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry using Poly(dimethylsiloxane) Microchips with Monolithically Integrated Emitters." Analyst, 135, 2296 – 2302.
Abstract on PubMed

Tian, Z, R Zhao, N Tolic, RJ Moore, DL Stenoien, EW Robinson, RD Smith, and L Paša-Tolic. 2010. "Two-Dimensional Liquid Chromatography System for Online Top-Down Mass Spectrometry." Proteomics, 10, 3610-3620.
Abstract on PubMed

True, LD, H Zhang, M Ye, C-Y Huang, PS Nelson, PD von Haller, LW Tjoelker, J-S Kim, W-J Qian, RD Smith, WJ Ellis, ES Liebeskind, and AY Liu. 2010. "CD90/THY1 is Over-Expressed in Prostate Cancer-Associated Fibroblasts and Could Serve as a Cancer Biomarker." Mod. Pathol., 10, 1346-1356.
Abstract on PubMed

Turse JE, MJ Marshall, JK Fredrickson, MS Lipton, and SJ Callister. 2010. “An Empirical Strategy for Characterizing Bacterial Proteomes Across Species in the Absence of Genomic Sequences.” PLoS One, 5(11), e13968.
Abstract on PubMed

Yang, F, KM Waters, JH Miller, MA Gristenko, R Zhao, X Du, E Livesay, SO Purvine, ME Monroe, Y Wang, DG Camp II, RD Smith, and DL Stenoien. 2010. "Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation." PLoS One, 5(11), e14152.
Abstract on PubMed

Zhang, H, R Brown, W-J Qian, M Monroe, S Purvine, R Moore, M Gritsenko, L Shi, M Romine, J Fredrickson, L Paša-Tolic, RD Smith, and MS Lipton. 2010. "Quantitative Analysis of Cell Surface Membrane Proteins using Membrane-Impermeable Chemical Probe Coupled with 18O labeling." J. Proteome Res., 9, 2160-2169.
Abstract on PubMed

Zhang, X, ME Monroe, B Chen, MH Chin, TH Heibeck, AA Schepmoes, F Yang, BO Petritis, D.G. Camp II, JG Pounds, JM Jacobs, DJ Smith, DJ Bigelow, RD Smith, and W-J Qian. 2010. "Endogenous 3,4-Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: Links to Mitochondrially-Derived Oxidative Stress via Hydroxyl Radical." Mol. Cell. Proteomics, 9, 1199-1208.
Abstract on PubMed

Zhang, X, J Zhou, MH Chin, AA Schepmoes, VA Petyuk, KK Weitz, BO Petritis, ME Monroe, DG Camp II, SA Wood, WP Melega, DJ Bigelow, DJ Smith, W-J Qian, and RD Smith. 2010. "Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model." J. Proteome Res., 9, 1496-1509.
Abstract on PubMed

Zhou, J-Y, A Schepmoes, X Zhang, RJ Moore, M Monroe, J-H Lee, DG Camp II, RD Smith and W-J Qian. 2010. “Improved LC-MS/MS Spectral Counting Statistics by Recovering Low Scoring Spectra Matched to Confidently Identified Peptide Sequences.” J. Proteome Res., 9(11), 5698-5704.
PMCID: PMC2974764 - Abstract on PubMed


2010 Book Chapters

Adkins, JN, HM Brewer, TO Metz, CK Ansong, NP Manes, RD Smith, and F Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." Chap. 2 in Peptidomics: Methods and Protocols, vol. 615, ed. Mikhail Soloviev, 13-27.

Belov, ME, YM Ibrahim, and RD Smith. 2010. “Ion Accumulation Approaches for Increasing Sensitivity and Dynamic Range in the Analysis of Complex Samples.” In Practical Aspects of Trapped Ion Mass Spectrometry, Volume IV, Theory and Instrumentation (Ed. RE March and JFJ Todd) CRC Press, Chapter 7:401-432.

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