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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.

2009 Journal Publications

Ansong C, H Yoon, S Porwollik, H Mottaz-Brewer, BO Petritis, N Jaitly, JN Adkins, M McClelland, F Heffron, and RD Smith. 2009. "Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation." PLoS ONE 4(3), e4809.
Abstract on PubMed

Chowdhury SM, X Du, N Tolic, S Wu, RJ Moore, MU Mayer, RD Smith, and JN Adkins. 2009. "Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry." Anal Chem 81(13), 5524-5532.
Abstract on PubMed

Chowdhury SM, L Shi, H Yoon, C Ansong, LM Rommereim, AD Norbeck, KJ Auberry, RJ Moore, JN Adkins, F Heffron, and RD Smith. 2009. "A Method for Investigating Protein-Protein Interactions Related to Salmonella Typhimurium Pathogenesis." J Proteome Res 8, 1505-1514.
Abstract on PubMed

Cuschieri, J, S Sakr, E Bulger, M Knoll, S Arbabi, RV Maier. 2009. “Oxidant Alterations in CD16 Expression are Cytoskeletal Induced.” Shock, 32(6), 572-577.
Abstract - PMCID: PMC2783368

Heibeck TH, SJ Ding, LK Opresko, R Zhao, AA Schepmoes, F Yang, AV Tolmachev, ME Monroe, DG Camp, 2nd, RD Smith, HS Wiley, and WJ Qian. 2009. "An extensive survey of tyrosine phosphorylation revealing new sites in human mammary epithelial cells." J Proteome Res 8(8), 3852-3861.
Abstract on PubMed

Jaitly N, A Mayampurath, K Littlefield, JN Adkins, GA Anderson, and RD Smith. 2009. "Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data." BMC Bioinformatics 10, 87.
Abstract on PubMed

Karpievitch YV, T Taverner, JN Adkins, SJ Callister, GA Anderson, RD Smith, and AR Dabney. 2009. "Normalization of Peak Intensities in Bottom-Up MS-Based Proteomics Using Singular Value Decomposition." Bioinformatics 25, 2573-2580.
Abstract on PubMed

Kelly, RT, JS Page, I Marginean, K Tang, and RD Smith. 2009. “Dilution-Free Analysis from Picoliter Droplets by Nano-ESI MS.” Angewandte Chemie, 48, 6832-6835.
Abstract - PMCID: PMC2957286

Kim BC, D Lopez-Ferrer, SM Lee, HK Ahn, S Nair, SH Kim, BS Kim, K Petritis, DG Camp, JW Grate, RD Smith, YM Koo, MB Gu, and J Kim. 2009. "Highly stable trypsin-aggregate coatings on polymer nanofibers for repeated protein digestion." Proteomics 9(7), 1893-900.
Abstract on PubMed

Lopez-Ferrer D, KK Hixson, H Smallwood, TC Squier, K Petritis, and RD Smith. 2009. "Evaluation of a High-Intensity Focused Ultrasound-Immobilized Trypsin Digestion and (18)O-Labeling Method for Quantitative Proteomics." Anal Chem 81, 6272.
Abstract on PubMed

Mabrouki R, RT Kelly, DC Prior, AA Shvartsburg, K Tang, and RD Smith. 2009. "Improving FAIMS Sensitivity Using a Planar Geometry with Slit Interfaces." J Am Soc Mass Spectrom 20, 1768-1774.
Abstract on PubMed

Marginean I, JS Page, RT Kelly, K Tang, and RD Smith. 2009. "Effect of pressure on electrospray characteristics." Appl Phys Lett 95(18), 184103.
Abstract on PubMed

Page JS, I Marginean, ES Baker, RT Kelly, K Tang, and RD Smith. 2009. "Biases in ion transmission through an electrospray ionization-mass spectrometry capillary inlet." J Am Soc Mass Spectrom 20(12), 2265-2272.
Abstract on PubMed

Park, CC, VA Petyuk, WJ Qian, RD Smith, and DJ Smith. 2009. “Dual Spatial Maps of Transcript and Protein Abundance in the Mouse Brain.” Expert Rev. Proteomics, 6(3), 243-249.
Abstract - PMCID: PMC2744401

Petritis BO, WJ Qian, DG Camp, 2nd, and RD Smith. 2009. "A simple procedure for effective quenching of trypsin activity and prevention of 18O-labeling back-exchange." J Proteome Res 8(5), 2157-2163.
Abstract on PubMed

Prasad S, K Tang, D Manura, D Papanastasiou, and RD Smith. 2009. "Simulation of ion motion in FAIMS through combined use of SIMION and modified SDS." Anal Chem 81(21), 8749-8757.
Abstract on PubMed

Qian WJ, T Liu, VA Petyuk, MA Gritsenko, BO Petritis, AD Polpitiya, A Kaushal, W Xiao, CC Finnerty, MG Jeschke, N Jaitly, ME Monroe, RJ Moore, LL Moldawer, RW Davis, RG Tompkins, DN Herndon, DG Camp, RD Smith, and IHRI L. 2009. "Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled "Universal" Reference Sample." J Proteome Res 8(1), 290-299.
Abstract on PubMed

Ream TS, JR Haag, AT Wierzbicki, CD Nicora, AD Norbeck, JK Zhu, G Hagen, TJ Guilfoyle, L Pasa-Tolic, and CS Pikaard. 2009. "Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II." Mol Cell 33(2), 192-203.
Abstract on PubMed

Schepmoes, AA, Q Zhang, BO Petritis, W-J Qian, and RD Smith. 2009. “N-Terminal Enrichment: Developing a Protocol to Detect Specific Proteolytic Fragments.” J Biol Tech, 20(5), 263-268.
Abstract - PMCID: PMC2777345

Shi L, C Ansong, H Smallwood, L Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium." J Proteomics Bioinform 2, 388-397.
Abstract on PubMed

Shi L, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TR Clauss, F Heffron, RD Smith, and JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Salmonella Infection." Infect Immun 77, 3227-3233.
Abstract on PubMed

Shvartsburg AA, RD Smith, A Wilks, A Koehl, D Ruiz-Alonso, and B Boyle. 2009. "Ultrafast Differential Ion Mobility Spectrometry at Extreme Electric Fields in Multichannel Microchips." Anal Chem 81, 8048-8053.
Abstract on PubMed

Shvartsburg AA, K Tang, RD Smith, M Holden, M Rush, A Thompson, and D Toutoungi. 2009. "Ultrafast differential ion mobility spectrometry at extreme electric fields coupled to mass spectrometry." Anal Chem 81(19), 8048-8053.
Abstract on PubMed

Shvartsburg, AA, SY Noskov, RW Purves, and RD Smith. 2009. “Pendular Proteins in Gases and New Avenues for Characterization of Macromolecules by Ion Mobility Spectrometry.” Proc Natl Acad Sci USA, 106(16), 6495-6500.
Abstract - PMCID: PMC2672539

Tolmachev AA, EW Robinson, S Wu, L Pasa-Tolic, and RD Smith. 2009. "FT-ICR MS optimization for the analysis of intact proteins." Intern. J. Mass Spectrom. 287, 32-38.
Abstract - PMCID: PMC2869097

Tolmachev AV, BH Clowers, ME Belov, and RD Smith. 2009. "Coulombic effects in ion mobility spectrometry." Anal Chem 81(12), 4778-4787.
Abstract on PubMed

Umar, A, H Kang, AM Timmermans, MP Look, ME Meijer-van Gelder, MA den Bakker, N Jaitly, JW Martens, TM Luider, JA Foekens, and L Paša-Tolić. 2009. “Identification of a Putative Protein Profile Associated with Tamoxifen Therapy Resistance in Breast Cancer.” Mol Cell Proteomics, 8(6), 1278-1294. PMCID: PMC2690491
Abstract on PubMed

Wu S, NM Lourette, N Tolic, R Zhao, EW Robinson, AV Tolmachev, RD Smith, and L Pasa-Tolic. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." J Proteome Res 8(3), 1347-1357.
Abstract on PubMed

Wu S, F Yang, R Zhao, N Tolic, EW Robinson, DG Camp, 2nd, RD Smith, and L Pasa-Tolic. 2009. "Integrated workflow for characterizing intact phosphoproteins from complex mixtures." Anal Chem 81(11), 4210-4219.
Abstract on PubMed

Yang F, S Wu, DL Stenoien, R Zhao, ME Monroe, MA Gritsenko, SO Purvine, AD Polpitiya, N Tolic, Q Zhang, AD Norbeck, DJ Orton, RJ Moore, K Tang, GA Anderson, L Pasa-Tolic, DG Camp, 2nd, and RD Smith. 2009. "Combined pulsed-Q dissociation and electron transfer dissociation for identification and quantification of iTRAQ-labeled phosphopeptides." Anal Chem 81(10), 4137-4143.
Abstract on PubMed

Zhao R, SJ Ding, Y Shen, DG Camp II, EA Livesay, H Udseth, and RD Smith. 2009. "Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput." J Chromatogr B Analyt Technol Biomed Life Sci 877, 663-670.
Abstract on PubMed

Zhou JY, BO Petritis, K Petritis, AD Norbeck, KK Weitz, RJ Moore, DG Camp, RN Kulkarni, RD Smith, and WJ Qian. 2009. "Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome." J Proteome Res 8(11), 5387-5395.
Abstract on PubMed

2009 Book Chapters

Shen YF, JS Page, and RD Smith. 2009. "Advanced Capillary Liquid Chromatography-Mass Spectrometry for Proteomics." Advances in Chromatography 47, 31-58.

Shvartsburg AA, K Tang and RD Smith. 2009. "Two-dimensional ion mobility analyses of proteins and peptides." In Methods in Molecular Biology: Mass Spectrometry of Proteins and Peptides (Ed. M. S. Lipton and L. Pasa-Tolic) Humana Press, Chapter 26, pp. 417-445
Abstract on PubMed

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