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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.

2012 Journal Publications

Alfaro, JF, CX Gong, ME Monroe, JT Aldrich, TR Clauss, SO Purvine, Z Wang, DG Camp II, J Shabanowitz, P Stanley, GW Hart, DF Hunt, F Yang, and RD Smith. 2012. "Tandem Mass Spectrometry Identifies Many Mouse Brain O-GlcNAcylated Proteins Including EGF Domain-Specific O-GlcNAc Transferase Targets." PNAS, 109(19), 7280-7285.
PMCID: PMC3358849

Andreev, VP, VA Petyuk, HM Brewer, YV Karpievitch, F Xie, J Clarke, DG Camp II, RD Smith, AP Lieberman, RL Albin, Z Nawaz, J El Hokayem, AJ Myers. 2012. "Label-Free Quantitative LC-MS Proteomics of Alzheimer’s Disease and Normally Aged Human Brains." J Proteome Res., 11, 3053-3067.
PMCID: PMC3445701

Angel, TE, JM Jacobs, RP Smith, MS Pasternack, S Elias, MA Gritsenko, A Shukla, EC Gilmore, C McCarthy, DG Camp II, RD Smith, and HS Warren. 2012. “Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease.” J. Proteome Res., 11(10), 4814-4822.
PMCID: PMC3465517

Angel, TE, JM Jacobs, SS Spudich, MA Gritsenko, D Fuchs, T Liegler, H Zetterberg, DG Camp II, RW Price, and RD Smith. 2012. "The Cerebrospinal Fluid Proteome in HIV Infection: Change Associated with Disease Severity." Clinical Proteomics., 9(1), 3.
PMCID: PMC3353874

Angel, TE, UK Aryal, SM Hengel, ES Baker, RT Kelly, EW Robinson, and RD Smith. 2012. "Mass Spectrometry-Based Proteomics: Existing Capabilities and Future Direction." Chem. Soc. Rev., 41(10), 3912-3928.
PMCID: PMC3375054

Baker, ES, T Liu, VA Petyuk, KE Burnum-Johnson, YM Ibrahim, GA Anderson, and RD Smith. 2012. “Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications.” Genome Med, 4(8), 63.
Abstract on PubMed

Bordbar, A, ML Mo, ES Nakayasu, AC Schrimpe-Rutledge, YM Kim, TO Metz, MB Jones, BC Frank, RD Smith, SN Peterson, DR Hyduke, JN Adkins, and BO Palsson. 2012. "Model-Driven Multi-omic Data Analysis Elucidates Metabolic Immunomodulators of Macrophage Activation." Mol. Syst. Biol., 8, 558.
PMCID: PMC3397418

Brown, JN, M Ortiz, TE Angel, JM Jacobs, M Gritsenko, EY Chan, DE Purdy, RD Murnane, K Larsen, RE Palermo, AK Shukla, TR Clauss, MG Katze, JM McCune, and RD Smith. 2012. "Morphine Produces Immunosuppressive Effects in Nonhuman Primates at the Proteomic and Cellular Levels." Mol. Cell. Proteomics., 11(9), 605-618.
PMCID: PMC3434775

Brown, RN, JA Sanford, JH Park, BL Deatherage, BL Champion, RD Smith, F Heffron, and JN Adkins. 2012. "A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking Versus Standard Laboratory Conditions." Int J Proteomics., 123076.
PMCID: PMC3410353

Burnum, KE, Y Hirota, ES Baker, M Yoshie, YM Ibrahim, ME Monroe, GA Anderson, RD Smith, T Daikoku, and SK Dey. 2012. “Uterine Deletion of Trp53 Compromises Antioxidant Responses in the Mouse Decidua.” Endocrinology 153(9), 4568-4579.
PMCID: PMC3423619

Chauvigne-Hines, LM, LN Anderson, HM Weaver, JN Brown, PK Koech, CD Nicora, BA Hofstad, RD Smith, MJ Wilkins, SJ Callister, and AT Wright. 2012. “Suite of Activity-Based Probes for Cellulose-Degrading Enzymes.” J Am Chem Soc, 134(50), 20521-20532.
PMCID: PMC3538167

Chauvin, T, F Xie, T Liu, CD Nicora, F Yang, DG Camp, RD Smith, and KP Roberts. 2012. “A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome.” Biol Reprod, 87(6), 141.
Abstract on PubMed

Diamond, DL, A Krasnoselski, KE Burnum, ME Monroe, BJM Webb-Robertson, JE McDermott, MM Yeh, S Strom, S Proll, S Belisle, A Rasmussen, KA Walters, JM Jacobs, MA Gritsenko, DG Camp II, R Bhattacharya, JD Perkins, RL Carithers, IW Liou, AM Larson, KM Waters, RD Smith, and MG Katze. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Post-Transplantation." Hepatology, 56(1), 28-38.
PMCID: PMC3387320

Haag, JR, TS Ream, M Marasco, CD Nicora, AD Norbeck, and L Pasa-Tolic. 2012. "In Vitro Transcription Activities of Pol IV, Pol V, and RDR2 Reveal Coupling of Pol IV and RDR2 for dsRNA Syntheses in Plant RNA Silencing." Mol Cell, 45(5), 811-818.
PMCID: PMC3532817

Hengel, SM, E Floyd, ES Baker, R Zhao, S Wu, and L Pasa-Tolic. 2012. "Evaluation of SDS Depletion using an Affinity Spin Column and IMS-MS Detection.” Proteomics, 12(21). 3138-3142.
PMCID: PMC3553591

Lee, JH, SW Hyung, DG Mun, HJ Jung, H Kim, H Lee, SJ Kim, KS Park, RJ Moore, RD Smith, and SW Lee. 2012. "Fully Automated Multifunctional Ultrahigh Pressure Liquid Chromatography System for Advanced Proteome Analyses." J Proteome Res., 11(8), 4373-4381.
PMCID: PMC3412908

Liu, T, M Hossian, A Schepmoes, T Fillmore, L Sokoll, S Kronewitter, G Izmirlian, T Shi, W Shi, R Leach, I Thompson, D Chan, RD Smith, J Kagan, S Srivastana, K Rodland, DG Camp II. 2012. “Analysis of Serum Total and Free PSA using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests.” J Proteomic., 75(15), 4747-4557.
PMCID: PMC3410652

Malouli, D, ES Nakayasu, K Viswanathan, DG Camp II, WI Chang, PA Barry, RD Smith, and K Frűh. 2012. “Reevaluation of the Coding Potential and Proteomic Analysis of the BAC-Derived Rhesus Cytomegalovirus strain 68-1.” J. Virol, 86(17), 8959-8973.
PMCID: PMC3416160

Marginean, I, SR Kronewitter, RJ Moore, GW Slysz, ME Monroe, GA Anderson, K Tang, and RD Smith. 2012. “Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure.” Anal Chem, 84(21), 9208-9213.
PMCID: PMC3491124

Maxwell, E, Y Tan, H Hu, G Benson, K Aizikov, S Conely, GO Staples, GW Slysz, RD Smith, and J Zaia. 2012. “GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data.” PLoS One, 7(9), e45474.
PMCID: PMC3458864

McDermott, JE, DL Diamond, C Corley, AL Rasmussen, MG Katze, and KM Waters. 2012. “Topological Analysis of Protein Co-Abundance Networks Identifies Novel Host Targets Important for HCV Infection and Pathogenesis.” BMC Syst. Biol., 6, 28.
PMCID: PMC3383540

Rutledge, AC, MB Jones, S Chauhan, SO Purvine, J Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, S Peterson, VL Motin, and JN Adkins. 2012. “Comparative ‘Omics’ Driven Genome Annotation Refinement: Application Across Multiple Yersiniae including Plague Strains.” PLoS One, 7(3), e33903.
PMCID: PMC3313959

Sadler, NC, TE Angel, MP Lewis, LM Pederson, LM Chauvigne-Hines, SD Wiedner, EM Zink, RD Smith, and AT Wright. 2012. "Activity-Based Protein Profiling Reveals Mitochondrial OXidative Enzyme Impairment and Restoration in Diet-Induced Obese Mice." PLoS One, 7(10), e47996.
PMCID: PMC3480472

Shen, Y, N Tolić, SO Purvine, and RD Smith. 2012. “Improving CID, HCD, and ETD FT MS/MS Degradome-Peptidome Identifications using High Accuracy Mass Information.” J. Proteome Res., 11(2): 668-677.
PMCID: PMC3272082

Shi, T, D Su, T Liu, K Tang, DG Camp II, W-J Qian, and RD Smith. 2012. “Advancing the Sensitivity of Selected Reaction Monitoring-Based Targeted Quantitative Proteomics.” Proteomics-Special Issue, 12(8), 1074-1092.
PMCID: PMC3375056

Shi, T, J Zhou, MA Gritsenko, M Hossain, DG Camp II, RD Smith, and WJ Qian. 2012. “IgY14 and SuperMix Immunoaffinity Separations Coupled with Liquid Chromatography-Mass Spectrometry for Human Plasma Proteomic Biomarker Discovery.” Methods, 56(2), 246-253.
PMCID: PMC33261331

Shi, T, TL Fillmore, X Sun, R Zhao, AA Schepmoes, M Hossain, F Xie, S Wu, J-S Kim, N Jones, RJ Moore, L Paša-Tolić, J Kagan, KD Rodland, T Liu, K Tang, DG Camp II, RD Smith, and W-J Qian. 2012. “Antibody-Free, Targeted Mass Spectrometric Approach for Quantification of Proteins at Low Pictogram Per Milliliter Levels in Human Plasma/Serum.” PNAS, 109(38), 15395-15400.
PMCID: PMC3458402

Shvartsburg, AA and RD Smith. 2012. “Protein Analyses using Differential Ion Mobility Microchips with Mass Spectrometry.” Anal Chem, 84(17), 7297-7300.
PMCID: PMC3462738

Shvartsburg, AA, Y Zheng, RD Smith, and NL Kelleher. 2012. “Ion Mobility Separation of Variant Histone Tails Extending to the “Middle-Down” Range.” Anal. Chem., 84(10), 4271-4276.
PMCID: PMC3353003

Shvartsburg, AA, Y Zheng, RD Smith, and NL Kelleher. 2012. “Separation of Variant methylated Histone Tails by Differential Ion Mobility.” Anal. Chem., 84(15), 6317-6320.
PMCID: PMC3418378

Smith, RD. 2012. “Mass Spectrometry in Biomarker Applications: From Untargeted Discovery to Targeted Verification, and Implications for Platform Convergence and Clinical Application.” Clin. Chem., 58(3), 525-530.

Su, D, AK Shukla, B Chen, JS Kim, E Nakayasu, Y Qu, U Aryal, K Weitz, TR Clauss, ME Monroe, DG Camp II, DJ Bigelow, RD Smith, RN Kulkarni, and WJ Qian. 2012. "Quantitative Site-Specific Reactivity Profiling of S-nitrosylation in Mouse Skeletal Muscle using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radic Biol Med, 57C, 68-78.
PubMed Abstract

Taverner, T, YV Karpievitch, AD Polpitiya, JN Brown, AR Dabney, GA Anderson, and RD Smith. 2012. “DanteR: An Extensible R-based Tool for Quantitative Analysis of –Omics Data.” Bioinformatics, 28(18), 2404-2406.
PMCID: PMC3436848

Tolmachev, A, E Robinson, S Wu, RD Smith, J Futrell, and L Paša-Tolić. 2012. “Angular Averaged Profiling of the Radial Electric Field in Compensated FTICR Cells.” J Am. Soc. Mass Spectr., 23(7), 1169-1172.
PMCID: PMC3375389

Varnum, SM, BJ Webb-Roberston, JG Pounds, RJ Moore, RD Smith, CW Frevert, SJ Skerrett, and D Wunschel. 2012. “Proteomic Analysis of Bronchoalveolar Lavage Fluid Proteins from Mice Infected with Francisella tularensis ssp. novicida.” J. Proteome Res., 11(7), 3690-3703.
PMCID: PMC3423085

Wang, C, CS Lee, RD Smith, and K Tang. 2012. "Ultrasensitive Sample Quantitation via Selected Reaction Monitoring using CITP/CZE-ESI-triple Quadrupole MS." Anal Chem, 84(23), 10395-10403.
PMCID: PMC3547498

Wang, L, UK Aryal, Z Dai, AC Mason, ME Monroe, Z Tian, J Zhou, D Su, KK Weitz, T Liu, DG Camp II, RD Smith, SE Baker, and W-J Qian. 2012. “Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of aspergillus niger using Hydrazide Chemistry and Mass Spectrometry.” J. Proteome Res., 11(1), 143-156.
Abstract

Wang, X, G Anderson, RD Smith, and AR Dabney. 2012. “A Hybrid Approach to Protein Differential Expression in Mass Spectrometry – Based Proteomics.” Bioinformatics, 28(12), 1586-1591.
PMCID: PMC3371829

Waters, KM, T Liu, RD Quesenberry, AR Willse, S Bandyopadhyay, LE Kathmann, TJ Weber, RD Smith, HS Wiley, BD Thrall. 2012. “Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data.” PLoS One, 7(3), e34515.
PMCID: PMC3315547

Wiedner, SD, KE Burnum, LM Pederson, LN Anderson, S Fortuin, LM Chauvigne-Hines, AK Shukla, C Ansong, EA Panisko, RD Smith, and AT Wright. 2012. “Multiplexed Activity-Based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum.” J Biol Chem, 287(40), 33447-33459.
PMCID: PMC3460446

Xie, F, RD Smith and Y Shen. 2012. “Advanced Proteomic Liquid Chromatography.” Journal of Chromatography A, 1261, 78-90.

Yang, F, KM Waters, BJ Webb-Robertson, MB Sowa, C von Neubeck, JT Aldrich, LM Markillie, RM Wirgau, MA Gritsenko, R Zhao, DG Camp II, RD Smith, and DL Stenoien. 2012. “Quantitative Phosphoproteomics Identifies Filaggrin and Other Targets of Ionizing Radiation in a Human Skin Model.” Exp. Dermatol., 21(5), 352-357.
PMCID: PMC3387810

Yang, F, Y Shen, DG Camp II, and RD Smith. 2012. “High-pH Reversed-Phase Chromatography with Fraction Concatenation for 2D Proteomic Analysis.” Proteomics 9(2), 129-134.
PMCID: PMC3337716

Zhang, Q, TL Fillmore, AA Schepmoes, TR Clauss, MA Gritsenko, PW Mueller, M Rewers, MA Atkinson, RD Smith, and TO Metz. 2012. "Serum Proteomics Reveals Systemic Dysregulation of Innate Immunity in Type 1 Diabetes." J Exp Med, 201(1), 191-203.
PMCID: PMC3549705

Zhou, J, G Dann, T Shi, L Wang, X Gao, D Su, C Nicora, A Shukla, R Moore, T Liu, DG Camp II, RD Smith, and W-J Qian. 2012. “Simple Sodium dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS Based Proteomic Applications.” Anal. Chem., 84(6), 2862-2867.
PMCID: PMC3310275

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