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