Staff information

Richard Smith

Biological Sciences Division
Battelle Fellow
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352
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Biography

Dr. Smith's research has included the development and application of advanced analytical methods and instrumentation, with particular emphasis on high resolution separations and mass spectrometry, and their applications in biological and biomedical research. Much of his research over the last 25 years has focused on the development and application of new ultra-sensitive methods for quantitatively probing the entire array of proteins expressed by a cell, tissue or organism, i.e., their "proteomes." Current interests also include increasing the throughput and sensitivity of proteomics measurements to augment systems biology research and, for example, support biomarker discovery.

Dr. Smith is an adjunct faculty member of the Department of Chemistry, Washington State University, and the Department of Chemistry, University of Utah, and an affiliate faculty member of the Department of Chemistry, University of Idaho. He has presented more than 300 invited or plenary lectures at national and international scientific meetings. Dr. Smith is the author or coauthor of more than 700 peer reviewed publications and holds 33 patents. He is also the Director of the NIH Research Resource Center for Integrative Proteomics located at PNNL.

Research Interests

Development and application of advanced analytical methods and instrumentation, with particular emphasis on high resolution separations and mass spectrometry, and their applications in biological and biomedical research
Development and application of new ultra-sensitive methods for quantitatively probing the entire array of proteins expressed by a cell, tissue or organism, i.e., their “proteomes”
Increasing the throughput and sensitivity of proteomics and metabolomics measurements to augment systems biology research

Education and Credentials

B.S., Chemistry, Lowell Technological Institute, University of Massachusetts
Ph.D., Physical Chemistry, University of Utah

Affiliations and Professional Service

American Chemical Society
American Society for Mass Spectrometry
American Association for the Advancement of Science (Fellow)
Adjunct Professor, Department of Chemistry, Washington State University
Affiliate Professor, Department of Chemistry, University of Idaho
Adjunct Professor of Chemistry, University of Utah

Awards and Recognitions

HUPO Discovery Award in Proteomic Sciences
R&D 100 Award: Ultrasensitive Electrospray Ionization Mass Spectrometry Source and Interface
Editor-in-Chief, Journal of Proteomics & Bioinformatics
Council of the Human Proteome Organization (HUPO) 2007-2010
Scientific American 50--shared with Dr. Desmond Smith, University of California at Los Angeles, for their work on understanding the human brain
2003 ACS Award for Analytical Chemistry
R&D 100 Award: Development of Supercritical Fluid Chromatography-Mass Spectrometry
American Oil Chemists Society Award
R&D 100 Award: Rapid Expansion of Supercritical Fluid Solutions Process
R&D 100 Award: Capillary Electrophoresis-Electrospray Ionization-MS
Battelle-Northwest Director's Award for Excellence
AWU-DOE Distinguished Lecturer
R&D 100 Award: Rapid Microdialyzer
R&D 100 Award: MICLEAN/MICARE Process
R&D 100 Award: Electrodynamic Ion Funnel
R&D 100 Award: Capillary Electrophoresis-Electrospray Ionization-MS; among top 40 R&D 100 Awards of all time
Battelle Inventor of the Year
Pacific Northwest National Laboratory Mentor of the Year
DOE Energy 100 Award
ACS Award for Analytical Chemistry
ICI List of most cited chemists
Serves on nine scientific journal advisory boards

PNNL Publications

2009

Marginean I, RT Kelly, RJ Moore, DC Prior, BL Lamarche, K Tang, and RD Smith. 2009. "Selection of the Optimum Electrospray Voltage for Gradient Elution LC-MS Measurements." Journal of the American Society for Mass Spectrometry 20(4):682-688.
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 ." Analytical Chemistry 81(15):6489-6495. doi:10.1021/ac900892u
Shvartsburg AA, S Noskov, R Purves, and RD Smith. 2009. " Pendular Proteins in Gases and New Avenues for Characterization of Macromolecules by Ion Mobility Spectrometry ." Proceedings of the National Academy of Sciences of the United States of America 106(16):6495-6500. doi:doi: 10.1073/pnas.0812318106
Alquier T, ML Peyot, MG Latour, M Kebede, CM Sorensen, S Gesta, CR Kahn, RD Smith, TL Jetton, TO Metz, M Prentki, and VJ Poitout. 2009. "Deletion of GPR40 Impairs Glucose-Induced Insulin Secretion In Vivo in Mice Without Affecting Intracellular Fuel Metabolism in Islets ." Diabetes 58(11):2607-2615.
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. doi:10.1371/journal.pone.0004809
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 ." Journal of Proteome Research 8(3):1504-1514 .
Heibeck TH, SJ Ding, LK Opresko, R Zhao, AA Schepmoes, F Yang, AV Tolmachev, ME Monroe, DG Camp, II, RD Smith, HS Wiley, and W Qian. 2009. "An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells." Journal of Proteome Research 8(8):3852-3861.
Jaitly N, AM Mayampurath, KA 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:,
Karpievitch Y, JR Stanley, T Taverner, J Huang, JN Adkins, C Ansong, F Heffron, TO Metz, W Qian, H Yoon, RD Smith, and AR Dabney. 2009. "AA statistical framework for protein quantitation in bottom-up MS-based proteomics ." Bioinformatics 25(16):2028-2034. doi:10.1093/bioinformatics/btp362
Kelly RT, JS Page, I Marginean, K Tang, and RD Smith. 2009. "Dilution-Free Analysis from Picoliter Droplets by Nano-Electrospray Ionization Mass Spectrometry." Angewandte Chemie International Edition 48(37):6832-6835. doi:10.1002/anie.200902501
Kim BC, D Lopez-Ferrer, S Lee, H Ahn, S Nair, SH Kim, BS Kim, K Petritis, DG Camp, II, JW Grate, RD Smith, Y Koo, MB Gu, and J Kim. 2009. "Highly Stable Trypsin-Aggregate Coatings on Polymer Nanofibers for Repeated Protein Digestion." Proteomics 9(7):1893-1900.
Lopez-Ferrer D, KK Hixson, HS 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." Analytical Chemistry 81(15):6272-6277.
Mabrouki RB, RT Kelly, DC Prior, AA Shvartsburg, K Tang, and RD Smith. 2009. "Improving FAIMS Sensitivity using a Planar Geometry with Slit Interfaces." Journal of the American Society for Mass Spectrometry 20(9):1768-1774. doi:10.1016/j.jasms.2009.05.019
Qian W, T Liu, VA Petyuk, MA Gritsenko, BO Petritis, AD Polpitiya, A Kaushal, W Xiao, CC Finnerty, MG Jescheke, N Jaitly, ME Monroe, RJ Moore, LL Moldawer, RW Davis, RG Tompkins, DN Hemdon, DG Camp, II, and RD Smith. 2009. "Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled "Universal" Reference Sample ." Journal of Proteome Research 8(1):290-299.
Shi L, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TRW Clauss, F Heffron, RD Smith, and JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77(8):3227-3233. doi:10.1128/IAI.00063-09
Sowell SM, L Wilhelm, AD Norbeck, MS Lipton, CD Nicora, DF Barofsky, C carlson, RD Smith, and SJ Giovannoni. 2009. " Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3(1):93-105.
Tolmachev AV, EW Robinson, S Wu, L Pasa-Tolic, and RD Smith. 2009. "FT-ICR MS optimization for the analysis of intact proteins." International Journal of Mass Spectrometry 287(1-3 SP ISS):32-38. doi:10.1016/j.ijms.2008.10.010
Tolmachev AV, BH Clowers, ME Belov, and RD Smith. 2009. "Coulombic Effects on Ion Mobility Spectrometry ." Analytical Chemistry 81(12):4778-4787.
Weber TJ, LK Opresko, DM Waisman, GJ Newton, RD Quesenberry, N Bollinger, RJ Moore, and RD Smith. 2009. "Regulation of the Low Dose Radiation Paracrine-Specific Anchorage-Independent Growth Response by Annexin A2." Radiation Research 172(1):96-105. doi:10.1667/RR1220.1
Wu S, F Yang, R Zhao, N Tolic, EW Robinson, DG Camp, II, RD Smith, and L Pasa-Tolic. 2009. "An integrated workflow for characterizing intact phosphoproteins from complex mixtures." Analytical Chemistry 81(11):4210-4219. doi:10.1021/ac802487q
Wu S, NM Lourette, N Tolic, R Zhao, R 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." Journal of Proteome Research 8(3):1347-1357.
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, II, and RD Smith. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81(10):4137-4143. doi:10.1021/ac802605m
Zhao R, SJ Ding, Y Shen, DG Camp, II, EA Livesay, HR Udseth, and RD Smith. 2009. "Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput." Journal of Chromatography B 877(8-9):663-670.

2008

Ansong C, SO Purvine, JN Adkins, MS Lipton, and RD Smith. 2008. "Proteogenomics: the needs and roles to be filled by proteomics in genome annotation." Briefings in Functional Genomics and Proteomics 7(1):50-62.
Baker ES, K Tang, B Danielson, III, DC Prior, and RD Smith. 2008. "Simultaneous Fragmentation of Multiple Ions Using IMS Drift Time Dependent Collision Energies." Journal of the American Society for Mass Spectrometry 19(3):411-419. doi:10.1016/j.jasms.2007.11.018
Jacobs JM, KM Waters, LE Kathmann, DG Camp, II, HS Wiley, RD Smith, and BD Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7(2):558-569. doi:10.1021/pr0704377
Kelly RT, K Tang, D Irimia, M Toner, and RD Smith. 2008. "Elastomeric Microchip Electrospray Emitter for Stable Cone-Jet Mode Operation in the Nanoflow Regime." Analytical Chemistry 80(10):3824-3831.
Manes NP, RD Estep, HM Mottaz, RJ Moore, TRW Clauss, ME Monroe, X Du, JN Adkins, S Wong, and RD Smith. 2008. "Comparative Proteomics of Human Monkeypox and Vaccinia Intracellular Mature and Extracellular Enveloped Virions." Journal of Proteome Research 3:960-8. doi:10.1021/pr070432+
Marginean I, RT Kelly, DC Prior, BL Lamarche, K Tang, and RD Smith. 2008. "Analytical Characterization of the Electrospray Ion Source in the Nanoflow Regime." Analytical Chemistry 80(17):6573-6579. doi:10.1021/ac800683s
Page JS, K Tang, RT Kelly, and RD Smith. 2008. "Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry ." Analytical Chemistry Vol. 80(5):1800-1805. doi:10.1021/ac702354b
Page JS, RT Kelly, DG Camp, II, and RD Smith. 2008. "Improving low-level plasma protein mass spectrometry-based detection for candidate biomarker discovery and validation." ICBC Newsletter 3(3):,
Pounds JG, JW Flora, JN Adkins, KM Lee, GSJB Rana, T Sengupta, RD Smith, and WJ McKinney. 2008. "Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry." Journal of Chromatography B 864(1-2):95-101.
Shen Y, KK Hixson, N Tolic, DG Camp, II, SO Purvine, RJ Moore, and RD Smith. 2008. "Mass Spectrometry Analysis of Proteome-wide Proteolytic Post-translational Degradation of Proteins." Analytical Chemistry 80(15):5819-5828. doi:10.1021/ac800077w
Shen Y, N Tolic, KK Hixson, SO Purvine, GA Anderson, and RD Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins ." Analytical Chemistry 80(20):7742-7754. doi:10.1021/ac801123p
Shvartsburg AA, and RD Smith. 2008. " Fundamentals of Traveling Wave Ion Mobility Spectrometry." Analytical Chemistry 80(24):9689-9699. doi:10.1021/ac8016295
Shvartsburg AA, and RD Smith. 2008. "Optimum Waveforms for Differential Ion Mobility Spectrometry (FAIMS)." Journal of the American Society for Mass Spectrometry 19(9):1286-1295.
Shvartsburg AA, K Tang, and RD Smith. 2008. "Two-Dimensional Ion Mobility Analyses of Proteins and Peptides." Chapter 26 in Mass Spectrometry of Proteins and Peptides: Methods and Protocols, Methods in Molecular Biology, vol. 492, ed. MS Lipton and L Pasa-Tolic, pp. 417-445. Humana Press, Totowa, NJ.
Zhang Q, AA Schepmoes, JW Brock, S Wu, RJ Moore, SO Purvine, J Baynes, RD Smith, and TO Metz. 2008. "Improved Methods for the Enrichment and Analysis of Glycated Peptides ." Analytical Chemistry 80(24):9822-9829. doi:10.1021/ac801704j
Zhang Q, JM Ames, RD Smith, J Baynes, and TO Metz. 2008. "A Perspective on the Maillard Reaction and the Analysis of Protein Glycation by Mass Spectrometry: Probing the Pathogenesis of Chronic Disease." Journal of Proteome Research 8(2):754-769. doi:DOI: 10.1021/pr800858h
Zhang Q, N Tang, AA Schepmoes, LS Phillips, RD Smith, and TO Metz. 2008. "Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membrane." Journal of Proteome Research 7(5):2025-2032. doi:10.1021/pr700763r
Zhang Q, VA Petyuk, AA Schepmoes, DJ Orton, ME Monroe, F Yang, RD Smith, and TO Metz. 2008. "Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry." Rapid Communications in Mass Spectrometry 22(19):3027-3034. doi:10.1002/rcm.3703
Ansong C, H Yoon, AD Norbeck, JK Gustin, JE McDermott, HM Mottaz, J Rue, JN Adkins, F Heffron, and RD Smith. 2008. "Proteomics Analysis of the Causative Agent of Typhoid Fever." Journal of Proteome Research 7(2):546-557. doi:10.1021/pr070434u
Belov ME, BH Clowers, DC Prior, WF Danielson, III, AV Liyu, BO Petritis, and RD Smith. 2008. "Dynamically Multiplexed Ion Mobility Time-of-Flight Mass Spectrometry ." Analytical Chemistry 80(15):5873-5883. doi:10.1021/ac8003665
Brewer HM, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, S Wong, RD Estep, F Heffron, L Pasa-Tolic, and RD Smith. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19(5):285-295.
Callister SJ, LA McCue, JE Turse, ME Monroe, KJ Auberry, RD Smith, JN Adkins, and MS Lipton. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3(2):e1542.
Chin MH, W Qian, H Wang, VA Petyuk, JS Bloom, DM Sforza, G Lacan, D Liu, AH Khan, RM Cantor, DJ Bigelow, WP Melega, DG Camp, II, RD Smith, and DJ Smith. 2008. "Mitochondrial dysfunction, oxidative stress and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease." Journal of Proteome Research 7(2):666-677. doi:10.1021/pr070546l
Clowers BH, ME Belov, DC Prior, WF Danielson, III, YM Ibrahim, and RD Smith. 2008. " Pseudorandom Sequence Modifications for Ion Mobility Orthogonal Time-of-Flight Mass Spectrometry." Analytical Chemistry 80(7):2464-2473. doi:10.1021/ac7022712
Clowers BH, YM Ibrahim, DC Prior, WF Danielson, ME Belov, and RD Smith. 2008. "Enhanced Ion Utilization Efficiency Using an Electrodynamic Ion Funnel Trap as an Injection Mechanism for Ion Mobility Spectrometry ." Analytical Chemistry 80(3):612-623. doi:10.1021/ac701648p
Ding J, CM Sorensen, N Jaitly, H Jiang, DJ Orton, ME Monroe, RJ Moore, RD Smith, and TO Metz. 2008. "Application of the accurate mass and time tag approach in studies of the human blood lipidome." Journal of Chromatography B 871(2):243-252. doi:10.1016/j.jchromb.2008.04.040
Ding YHR, KK Hixson, M Aklujkar, MS Lipton, RD Smith, DR Lovley, and T Mester. 2008. "Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor." Biochimica et Biophysica Acta--Proteins and Proteomics 1784(12):1935-1941. doi:10.1016/j.bbapap.2008.06.011
Du X, F Yang, NP Manes, DL Stenoien, ME Monroe, JN Adkins, DJ States, SO Purvine, DG Camp, II, and RD Smith. 2008. "Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications ." Journal of Proteome Research 7(6):2195-2203. doi:10.1021/pr070510t
Du X, SJ Callister, NP Manes, JN Adkins, RA Alexandridis, X Zeng, JH Roh, WE Smith, TJ Donohue, S Kaplan, RD Smith, and MS Lipton. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7(7):2595-2604. doi:10.1021/pr0704837
Dumortier J, DN Streblow, AV Moses, JM Jacobs, CN Kreklywich, DG Camp, II, RD Smith, SL Orloff, and J Nelson. 2008. "Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing." Journal of Virology 82(13):6524-6535. doi:doi:10.1128/JVI.00502-08
Gupta N, J Benhamida, V Bhargava, D Goodman, E Kain , I Kerman, N Nguyen , N Ollikainen, J Rodriguez, J Wang, MS Lipton, MF Romine, V Bafna, RD Smith, and PA Pevzner. 2008. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Research 18(7):1133-1142.
Ham BM, F Yang, H Jayachandran, N Jaitly, ME Monroe, MA Gritsenko, EA Livesay, R Zhao, SO Purvine, DJ Orton, JN Adkins, DG Camp, II, SS Rossie, and RD Smith. 2008. "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Journal of Proteome Research 7(6):2215-2221.
Ibrahim YM, ME Belov, AV Liyu, and RD Smith. 2008. "Automated Gain Control Ion Funnel Trap for Orthogonal Time-of-Flight Mass Spectrometry ." Analytical Chemistry 80(14):5367-5376. doi:10.1021/ac8003488
Kelly RT, JS Page, I Marginean, K Tang, and RD Smith. 2008. "Nanoelectrospray Emitter Arrays Providing Interemitter Electric Field Uniformity." Analytical Chemistry 80(14):5660-5665. doi:10.1021/ac800508q
Kelly RT, JS Page, R Zhao, W Qian, HM Mottaz, K Tang, and RD Smith. 2008. "Capillary-Based Multi Nanoelectrospray Emitters: Improvements in Ion Transmission Efficiency and Implementation with Capillary Reversed-Phase LC-ESI-MS." Analytical Chemistry 80(1):143-149. doi:10.1021/ac701647s
Kim J, R Zhang, EF Strittmatter, RD Smith, and R Zand. 2008. "Post-translational Modifications of Chicken Myelin Basic Protein Charge Components." Neurochemical Research 34(2):360-372. doi:10.1007/s11064-008-9788-4
Livesay EA, K Tang, BK Taylor, MA Buschbach, DF Hopkins, BL Lamarche, R Zhao, Y Shen, DJ Orton, RJ Moore, RT Kelly, HR Udseth, and RD Smith. 2008. "Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses." Analytical Chemistry 80(1):294-302. doi:10.1021/ac701727r
Lopez-Ferrer D, K Petritis, KK Hixson, TH Heibeck, RJ Moore, ME Belov, DG Camp, II, and RD Smith. 2008. "Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly." Journal of Proteome Research 7(8):3276-3281. doi:10.1021/pr7008077
Lopez-Ferrer D, TH Heibeck, K Petritis, KK Hixson, W Qian, ME Monroe, AM Mayampurath, RJ Moore, ME Belov, DG Camp, II, and RD Smith. 2008. "Rapid Sample Processing For LC-MS Based Quantitative Proteomics Using High Intensity Focused Ultrasounds." Journal of Proteome Research 7(9):3860-3867. doi:10.1021/pr800161x
Mathivanan S, M Ahmed, NG Ahn, H Alexandre, R Amanchy, PC Andrews, JS Bader, BM Balgley, M Bantscheff, K Bennett, E Bjorling, B Blagoev, R Bose , SK Brahmachari, AS Burlingame, XR Bustelo, G Cagney, GT Cantin, HL Cardasis, JE Celis, R Chaerkady, F Chu, PA Cole, CE Costello, RJ Cotter , D Crockett, JP DeLany , AM De Marzo, LV DeSouza, EW Deutsch, E Dransfield , G Drewes , A Droit , M Dunn, K Elenitoba-Johnson, RM Ewing, J Van Eyk , V Faca , J Falkner , X Fang, C Fenselau , D Figeys , P Gagne , C Gelfi , K Gevaert , J Gimble , F Gnad , R Goel, P Gromov , SM Hanash, WS Hancock, HC Harsha , G Hart , H Faith , F He , P Hebbar , K Helsens , H Hermeking , W Hide , K Hjerno, DF Hochstrasser, O Hofmann, DM Horn , RH Hruban , N Ibarrola , P James , ON Jensen , PH Jensen, P Jung , K Kandasamy, I Kheterpal , R Kikuno , U Korf, R Korner, B Kuster, MS Kwon , HJ Lee , YJ Lee , M Lefevre , M Lehvaslaiho, P Lescuyer, F Levander, MS Lim, C Lobke, J Loo, M Mann, L Martens , J Martinez-Heredia, ME McComb, J McRedmond , A Mehrle, R Menon, CA Miller, H Mischak, SS Mohan, R Mohmood , H Molina , MF Moran , JD Morgan, R Moritz , M Morzel, DC Muddiman, A Nalli , JD Navarro, TA Neubert , O Ohara , R Oliva, G Omenn, M Oyama , YK Paik, K Pennington , R Pepperkok, B Periaswamy, EF Petricoin, GG Poirier, TSK Prasad, SO Purvine, BA Rahiman , P Ramachandran, YL Ramachandra , RH Rice, J Rick , RH Ronnholm , J Salonen , JC Sanchez , T Sayd , B Seshi, K Shankari, SJ Sheng , V Shetty , K Shivakumar, RJ Simpson, R Sirdeshmukh, KWM Siu , JC Smith, RD Smith, DJ States, S Sugano, M Sullivan , G Superti - Furga, M Takatalo , V Thongboonkerd , JC Trinidad , M Uhlen , J Vandekerckhove, J Vasilescu , TD Veenstra, JM Vidal - Taboada, M Vihinen, R Wait , X Wang, S Wiemann, B Wu , T Xu, JR Yates, J Zhong, M Zhou, Y Zhu, P Zurbig, and A Pandey. 2008. "Human Proteinpedia enables sharing of human protein data." Nature Biotechnology 26(2):164-167.
Mayampurath AM, N Jaitly, SO Purvine, ME Monroe, KJ Auberry, JN Adkins, and RD Smith. 2008. "DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra." Bioinformatics 24(7):1021-1023. doi:10.1093/bioinformatics/btn063
Metz TO, W Qian, JM Jacobs, MA Gritsenko, RJ Moore, AD Polpitiya, ME Monroe, DG Camp, II, PW mueller, and RD Smith. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset ." Journal of Proteome Research 7(2):698-707. doi:10.1021/pr700606w
Metz TO, JS Page, ES Baker, K Tang, J Ding, Y Shen, and RD Smith. 2008. "High Resolution Separations and Improved Ion Production and Transmission in Metabolomics." Trends in Analytical Chemistry. TrAC 27(3):205-214. doi:10.1016/j.trac.2007.11.003
Monroe ME, JL Shaw, DS Daly, JN Adkins, and RD Smith. 2008. "MASIC: a software program for fast quantitation and flexible visualization of chromatographic profiles from detected LC-MS(/MS) features." Computational Biology and Chemistry 32(3):215-217. doi:10.1016/j.compbiolchem.2008.02.006
Pertz OC, Y Wang, F Yang, W Wang, J gay, MA Gritsenko, TRW Clauss, DJ Anderson, T Liu, KJ Auberry, DG Camp, II, RD Smith, and RL Klemke. 2008. ""Spatial Mapping of the Neurite and Soma Proteomes Reveals a Functional Cdc42/Rac Regulatory Network"." Proceedings of the National Academy of Sciences of the United States of America 105(6):1931-1936. doi:10.1073/pnas.0706545105
Petyuk VA, W Qian, C Hinault, MA Gritsenko, M Singhal, ME Monroe, DG Camp, II, RN Kulkarni, and RD Smith. 2008. "Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues." Journal of Proteome Research 7(8):3114-3126. doi:10.1021/pr800205b
Petyuk VA, N Jaitly, RJ Moore, J Ding, TO Metz, K Tang, ME Monroe, AV Tolmachev, JN Adkins, ME Belov, AR Dabney, W Qian, DG Camp, II, and RD Smith. 2008. "Elimination of Systematic Mass Measurement Errors in Liquid Chromatography-Mass Spectrometry Based Proteomics using Regression Models and a priori Partial Knowledge of the Sample Content ." Analytical Chemistry 80(3):693-706. doi:10.1021/ac701863d
Polpitiya AD, W Qian, N Jaitly, VA Petyuk, JN Adkins, DG Camp, II, GA Anderson, and RD Smith. 2008. " DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24(13):1556-1558. doi:10.1093/bioinformatics/btn217
Qian W, DT Kaleta, BA Ogata, H Jiang, T Liu, X Zhang, HM Mottaz, SM Varnum, DG Camp, II, huang, X Fang, W Zhang, and RD Smith. 2008. "Enhanced Detection of Low Abundant Human Plasma Proteins using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy." Molecular & Cellular Proteomics. MCP 7(10):1963-1973. doi:10.1074/mcp.M800008-MCP200
Robinson EW, AA Shvartsburg, K Tang, and RD Smith. 2008. "Control of Ion Distortion in Field Asymmetric Waveform Ion Mobility Spectrometry via Variation of Dispersion Field and Gas Temperature ." Analytical Chemistry 80(19):7508-7515. doi:10.1021/ac800655d
Rodland KD, JN Adkins, C Ansong, SM Chowdhury, NP Manes, L Shi, H Yoon, RD Smith, and F Heffron. 2008. "Use of high-throughput mass spectrometry to elucidate host pathogen interactions in Salmonella." Future Microbiology 3(6):625-634.
Shen Y, N Tolic, KK Hixson, SO Purvine, L Pasa-Tolic, W Qian, JN Adkins, RJ Moore, and RD Smith. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80(6):1871-82. doi:10.1021/ac702328x
Sowell SM, AD Norbeck, MS Lipton, CD Nicora, SJ Callister, RD Smith, DF Barofsky, and SJ Giovannoni. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74(13):4091-4100. doi:10.1128/AEM.00599-08
Tolmachev AV, ME Monroe, SO Purvine, RJ Moore, N Jaitly, JN Adkins, GA Anderson, and RD Smith. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments ." Analytical Chemistry 80(22):8514-8525. doi:10.1021/ac801376g
Tolmachev AV, EW Robinson, S Wu, H Kang, NM Lourette, L Pasa-Tolic, and RD Smith. 2008. " Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS." Journal of the American Society for Mass Spectrometry 19(4):586 - 597. doi:10.1016/j.jasms.2008.01.006
Wegener KM, EA Welsh, LE Thornton, NS Keren, JM Jacobs, KK Hixson, ME Monroe, DG Camp, II, RD Smith, and HB Pakrasi. 2008. "High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex." Journal of Biological Chemistry 283(41):27829-27837. doi:10.1074/jbc.M803918200
Welsh EA, ML Liberton, J Stockel, T Loh, TR Elvitigala, C Wang, A Wollam, RS Fulton, SW Clifton, JM Jacobs, R Aurora, BK Ghosh, LA Sherman, RD Smith, RK Wilson, and HB Pakrasi. 2008. "The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle." Proceedings of the National Academy of Sciences of the United States of America 105(39):15094-15099. doi:10.1073/pnas.0805418105
Yu RC, O Resnekov, AP Abola , SS Andrews, KR Benjamin , J Bruck , IE Burbulis , A Colman-Lener, D Endy, A Gordon , M Holl, L Lok , CG Pesce, E Serra , RD Smith, TM Thomson , AE Tsong, and R Brent. 2008. "The Alpha Project: a model system for systems biology research." IET Systems Biology 2(5):222-233. doi:10.1049/iet-syb:20080127

2007

Belov ME, MA Buschbach, DC Prior, K Tang, and RD Smith. 2007. "Multiplexed Ion Mobility Spectrometry - Orthogonal Time-Of-Flight Mass Spectrometry ." Analytical Chemistry 79(6):2451-2462. doi:10.1021/ac0617316
Kang H, L Pasa-Tolic, and RD Smith. 2007. "Targeted Tandem Mass Spectrometry for High-Throughput Comparative Proteomics Employing NanoLC-FTICR MS with External Ion Dissociation." Journal of the American Society for Mass Spectrometry 18(7):1332-1343. doi:doi:10.1016/j.jasms.2007.04.011
Marginean N, RT Kelly, JS Page, K Tang, and RD Smith. 2007. "Electrospray characteristic curves: in pursuit of improved performance in the nano-flow regime." Analytical Chemistry 79(21):8030-8036. doi:10.1021/ac070800t
Page JS, K Tang, and RD Smith. 2007. "An electrodynamic ion funnel interface for greater sensitivity and higher throughput with linear ion trap mass spectrometers." International Journal of Mass Spectrometry 265(2-3):244-250. doi:10.1016/j.ijms.2007.02.032
Page JS, RT Kelly, K Tang, and RD Smith. 2007. "Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface." Journal of the American Society for Mass Spectrometry 18(9):1582-1590. doi:10.1016/j.jasms.2007.05.018
Sharma S, DC Simpson, N Tolic, N Jaitly, AM Mayampurath, RD Smith, and L Pasa-Tolic. 2007. "Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry." Journal of Proteome Research 6(2):602-610. doi:10.1021/pr060354a
Shvartsburg AA, and RD Smith. 2007. "Scaling of the Resolving Power and Sensitivity for Planar FAIMS and Mobility-Based Discrimination in Flow- and Field- Driven Analyzers." Journal of the American Society for Mass Spectrometry 18(9):1672-1681. doi:10.1016/j.jasms.2007.06.013
Zhang Q, A Frolov, N Tang, R Hoffman, T van der Goor, TO Metz, and RD Smith. 2007. "Application of Electron Transfer Dissociation Mass Spectrometry in Analyses of Non-enzymatically Glycated Peptides." Rapid Communications in Mass Spectrometry 21(5):661-666. doi:10.1002/rcm.2884
Zhang Q, N Tang, JW Brock, HM Mottaz, JM Ames, J Baynes, RD Smith, and TO Metz. 2007. "Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry." Journal of Proteome Research 6(6):2323-2330. doi:doi:10.1021/pr070112q
Baker ES, BH Clowers, F Li, K Tang, AV Tolmachev, DC Prior, ME Belov, and RD Smith. 2007. "Ion Mobility Spectrometry - Mass Spectrometry Performance Using Electrodynamic Ion Funnels and Elevated Drift Gas Pressures." Journal of the American Society for Mass Spectrometry 18(7):1176-1187. doi:doi:10.1016/j.jasms.2007.03.031
Chan EY, W Qian, DL Diamond, T Liu, MA Gritsenko, ME Monroe, DG Camp, II, RD Smith, and MG Katze. 2007. "Quantitative analysis of human immunodeficiency virus type 1-infected CD4(+) cell proteome: Dysregulated cell cycle progression and nuclear transport coincide with robust virus production." Journal of Virology 81(14):7571-7583.
Chin MH, AB Geng, AH Khan, W Qian, VA Petyuk, J Boline, S Levy, AW Toga, RD Smith, RM Leahy, and DJ Smith. 2007. "A genome-scale map of expression for a mouse brain section obtained using voxelation." Physiological Genomics 30(3):313-321.
Diamond DL, JM Jacobs, B Paeper, S Proll, MA Gritsenko, RL Carithers, Jr., AM Larson , MM Yeh, DG Camp, II, RD Smith, and MG Katze. 2007. "Proteomic Profiling of Human Liver Biopsies: Hepatitis C Virus-Induced Fibrosis and Mitochondrial Dysfunction." Hepatology 46(3):649-657. doi:10.1002/hep.21751
Ding J, CM Sorensen, Q Zhang, H Jiang, N Jaitly, EA Livesay, Y Shen, RD Smith, and TO Metz. 2007. "Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling." Analytical Chemistry 79(16):6081-6093. doi:10.1021/ac070064t
Ding SJ, W Qian, and RD Smith. 2007. "Quantitative Proteomic Approaches for Studying Phosphotyrosine Signaling." Expert Review of Proteomics 4(1):13-23. doi:doi:10.1586/14789450.4.1.13
Gupta N, S Tanner, N Jaitly, JN Adkins, MS Lipton, R Edwards, MF Romine, A Osterman, V Bafna, RD Smith, and PA Pevzner. 2007. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Research 17(9):1362-1377. doi:0.1101/gr.6427907
Ibrahim YM, ME Belov, AV Tolmachev, DC Prior, and RD Smith. 2007. "Ion Funnel Trap Interface for Orthogonal Time-of-Flight Mass Spectrometry ." Analytical Chemistry 79(20):7845-7852. doi:10.1021/ac071091m
Kelly RT, JS Page, K Tang, and RD Smith. 2007. "Array of Chemically Etched Fused Silica Emitters for Improving the Sensitivity and Quantitation of Electrospray Ionization Mass Spectrometry." Analytical Chemistry 79(11):4192-4198. doi:10.1021/ac062417e
Kim J, K Petritis, Y Shen, DG Camp, II, RJ Moore, and RD Smith. 2007. "Phosphopeptide elution times in reversed-phase liquid chromatography." Journal of Chromatography A 1172(1):9-18. doi:doi:10.1016/j.chroma.2007.09.032
Liu T, ME Belov, N Jaitly, W Qian, and RD Smith. 2007. "Accurate Mass Measurements in Proteomics." Chemical Reviews 107(8):3621-3653. doi:10.1021/cr068288j
Luo Q, JS Page, K Tang, and RD Smith. 2007. "MicroSPE-nanoLC-ESI-MS/MS using 10-µm-i.d. silica-based monolithic columns for proteomics." Analytical Chemistry 79(2):540-545.
Manes NP, JK Gustin, J Rue, HM Mottaz, SO Purvine, AD Norbeck, ME Monroe, JS Zimmer, TO Metz, JN Adkins, RD Smith, and F Heffron. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6(4):717-727. doi:10.1074/mcp.M600282-MCP200
Metz TO, Q Zhang, JS Page, Y Shen, SJ Callister, JM Jacobs, and RD Smith. 2007. "The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery." Biomarkers in Medicine 1(1):159-185. doi:doi: 10.2217/17520363.1.1.159
Monroe ME, N Tolic, N Jaitly, JL Shaw, JN Adkins, and RD Smith. 2007. "VIPER: an advanced software package to support high-throughput LC-MS peptide identification." Bioinformatics 23(15- August 2007):2021-2023. doi:10.1093/bioinformatics/btm281
Petyuk VA, W Qian, MH Chin, HH Wang, EA Livesay, ME Monroe, JN Adkins, N Jaitly, DJ Anderson, DG Camp, II, DJ Smith, and RD Smith. 2007. "Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry." Genome Research 17(3):328-336. doi:doi:10.1101/gr.5799207
Shvartsburg AA, F Li, K Tang, and RD Smith. 2007. "Distortion of Ion Structures by Field Asymmetric Waveform Ion Mobility Spectrometry." Analytical Chemistry 79(4):1523-1528. doi:10.1021/ac061306c
Shvartsburg AA, SV Mashkevich, ES Baker, and RD Smith. 2007. "Optimization of Algorithms for Ion Mobility Calculations." Journal of Physical Chemistry A 111(10):2002-2010. doi:10.1021/jp066953m
Smallwood HS, NM Lourette, CB Boschek, DJ Bigelow, RD Smith, L Pasa-Tolic, and TC Squier. 2007. "Identification of a Denitrase Activity Against Calmodulin in Activated Macrophages Using High-Field Liquid Chromatography - FTICR Mass Spectrometry." Biochemistry 46(37):10498-10505.
Wang Y, SJ Ding, W Wang, F Yang, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2007. "Methods for Pseudopodia Purification and Proteomic Analysis." Sciences STKE Signal Transduction Knowledge Environment 2007(400):p14. doi:DOI: 10.1126/stke.4002007pl4
Wang Y, SJ Ding, W Wang, JM Jacobs, W Qian, RJ Moore, F Yang, DG Camp, II, RD Smith, and RL Klemke. 2007. "Profiling Signaling Polarity in Chemotactic Cells." Proceedings of the National Academy of Sciences of the United States of America 104(20):8328-8333. doi:10.1073/pnas.0701103104
Whiteaker JR, H Zhang, JK Eng, R Fang, BD Piening, LC Feng, TD lorentzen, RM Schoenherr, JF Keane, T Holzman, M Fitzgibbon, CW Lin, H Zhang, K Cooke, T Liu, DG Camp, II, LN Anderson, J Watts, RD Smith, M McIntosh, and AG Paulovich. 2007. "Head-to-Head Comparison of Serum Fractionation Techniques." Journal of Proteome Research 6(2):828-836. doi:10.1021/pr0604920
Yang F, DG Camp, II, MA Gritsenko, Q Luo, RT Kelly, TRW Clauss, WR Brinkley, RD Smith, and DL Stenoien. 2007. " Identification of a novel mitotic phosphorylation motif associated with protein localization to the mitotic apparatus." Journal of Cell Science 120(22):4060-70. doi:10.1242/jcs.014795
Yang F, N Jaitly, H Jayachandran, Q Lou, ME Monroe, X Du, MA Gritsenko, R Zhang, DJ Anderson, SO Purvine, JN Adkins, RJ Moore, HM Mottaz, SJ Ding, MS Lipton, DG Camp, II, HR Udseth, RD Smith, and SS Rossie. 2007. "Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Journal of Proteome Research 6(11):4489-4497. doi:10.1021/pr070068e
Zhang Q, W Qian, TV Knyushko, TRW Clauss, SO Purvine, RJ Moore, CA Sacksteder, MH Chin, DJ Smith, DG Camp, II, DJ Bigelow, and RD Smith. 2007. "A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples." Journal of Proteome Research 6(6):2257-2268. doi:10.1021/pr0606934

2006

Jacobs JM, and RD Smith. 2006. "Proteomic Analyses using High-Efficiency Separations and Accurate Mass Measurements." Chapter 20 in Separations in Proteomics , ed. Smejkal, GB and A Lazareu, pp. 363-385. CRC Taylor and Francis Group, New York, NY.
Norbeck AD, SJ Callister, ME Monroe, N Jaitly, DA Elias, MS Lipton, and RD Smith. 2006. "Proteomic approaches to bacterial differentiation ." Journal of Microbiological Methods 67(3):473-486. doi:10.1016/j.mimet.2006.04.024
Norbeck AD, SJ Callister, ME Monroe, N Jaitly, DA Elias, MS Lipton, and RD Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods 67(3):473-486.
Page JS, AV Tolmachev, K Tang, and RD Smith. 2006. "Theoretical and experimental evaluation of the low m/z transmission of an electrodynamic ion funnel." Journal of the American Society for Mass Spectrometry 17(4):586-592.
Qian W, JM Jacobs, T Liu, DG Camp, II, and RD Smith. 2006. "Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications." Molecular & Cellular Proteomics. MCP 5(10):1727-1744. doi:10.1074/mcp.M600162-MCP200
Shvartsburg AA, SV Mashkevich, and RD Smith. 2006. "Feasibility of Higher-Order Differential Ion Mobility Separations Using New Asymmetric Waveforms ." Journal of Physical Chemistry A 110(8):2663-2673. doi:10.1021/jp055349t
Shvartsburg AA, T Bryskiewicz, R Purves, K Tang, R Guevremont, and RD Smith. 2006. "Field Asymmetric Waveform Ion Mobility Spectrometry Studies of Proteins: Dipole Alignment in Ion Mobility Spectrometry?" Journal of Physical Chemistry B 110(43):21966-21980. doi:10.1021/jp062573p
Smith RD. 2006. "Future directions for electrospray ionization for biological analysis using mass spectrometry." BioTechniques 41(2):147-148.
Adkins JN, HM Mottaz, AD Norbeck, JK Gustin, J Rue, TRW Clauss, SO Purvine, KD Rodland, F Heffron, and RD Smith. 2006. "Analysis of the Salmonella typhimurium Proteome through Environmental Response toward Infectious Conditions." Molecular & Cellular Proteomics. MCP 5(8):1450-1461. doi:10.1074/mcp.M600139-MCP200
Baas T, CR Baskin, DL Diamond, A Garcia-Sastre, H Bielefeldt-Ohmann, TM Tumpey, MJ Thomas, VS Carter, TH Teal, N Van Hoven, S Proll, JM Jacobs, Z Caldwell, MA Gritsenko, R Hukkanen, DG Camp, II, RD Smith, and MG Katze. 2006. "Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics." Journal of Virology 80(21):10813 (16 pages). doi:10.1128/JVI.00851-06
Callister SJ, CD Nicora, X Zeng, JH Roh, M Dominguez, C Tavano, ME Monroe, S Kaplan, T Donohue, RD Smith, and MS Lipton. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes." Journal of Microbiological Methods 67(3):424-436. doi:10.1016/j.mimet.2006.04.021
Callister SJ, M Dominguez, CD Nicora, X Zeng, C Tavano, S Kaplan, T Donohue, RD Smith, and MS Lipton. 2006. "Application of the Accurate Mass and Time Tag Approach to the Proteome Analysis of Sub-cellular Fractions Obtained from Rhodobacter sphaeroides 2.4.1 Aerobic and Photosynthetic Cell Cultures." Journal of Proteome Research 5(8):1940-1947.
Callister SJ, RC Barry, JN Adkins, ET Johnson, W Qian, BJM Webb-Robertson, RD Smith, and MS Lipton. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5(2):277-286. doi:10.1021/pr050300l
Diamond DL, S Proll, JM Jacobs, EY Chan, DG Camp, II, RD Smith, and MG Katze. 2006. "HepatoProteomics: Applying Proteomic Technologies to the Study of Liver Function and Disease." Hepatology 44(2):299-308.
Ding YHR, KK Hixson, CS Giometti, A Stanley, A Esteve-Nunez, T Khare, SL Tollaksen, W Zhu, JN Adkins, MS Lipton, RD Smith, T Mester, and DR Lovley. 2006. "The Proteome of Dissimilatory Metal-reducing Microorganism Geobacter Sulfurreducens under Various Growth Conditions." Biochimica et Biophysica Acta--Proteins and Proteomics 1764(7):1198-1206. doi:10.1016/j.bbapap.2006.04.017
Elias DA, ME Monroe, RD Smith, JK Fredrickson, and MS Lipton. 2006. "Confirmation of the Expression of a Large Set of Conserved Hypothetical Proteins in Shewanella oneidensis MR-1." Journal of Microbiological Methods 66(2):223-233.
Elshafey A, N Tolic, MM Young, KL Sale, RD Smith, and V Kery. 2006. ""Zero-length" Cross-linking in Solid State as an Approach for Analysis of Protein -Protein Interactions." Protein Science 15(3):429-440.
Fang R, DA Elias, ME Monroe, Y Shen, M McIntosh, P Wang, CD Goddard, SJ Callister, RJ Moore, YA Gorby, JN Adkins, JK Fredrickson, MS Lipton, and RD Smith. 2006. "Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 5(4):714-725. doi:10.1074/mcp.M500301-MCP200
Hixson KK, JN Adkins, SE Baker, RJ Moore, RD Smith, SL McCutchen-Maloney, and MS Lipton. 2006. "Biomarker Candidate Identification in Yersinia Pestis Using Organism-Wide Semiquantitative Proteomics ." Journal of Proteome Research 5(11):3008-3017.
Ibrahim YM, K Tang, AV Tolmachev, AA Shvartsburg, and RD Smith. 2006. "Improving Mass Spectrometer Sensitivity Using a High-Pressure Electrodynamic Ion Funnel Interface." Journal of the American Society for Mass Spectrometry 17(9):1299-1305. doi:10.1016/j.jasms.2006.06.005
Jaitly N, ME Monroe, VA Petyuk, TRW Clauss, JN Adkins, and RD Smith. 2006. "Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline." Analytical Chemistry 78(21):7397-7409.
Kelly RT, JS Page, Q Luo, RJ Moore, DJ Orton, K Tang, and RD Smith. 2006. "Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry." Analytical Chemistry 78(22):7796-7801.
Kiebel GR, KJ Auberry, N Jaitly, D Clark, ME Monroe, ES Peterson, N Tolic, GA Anderson, and RD Smith. 2006. "PRISM: A Data Management System for High-Throughput Proteomics ." Proteomics 6(6):1783-1790. doi:10.1002/pmic.200500500
Koeniger SL, SI Merenbloom, SJ Valentine, MF Jarrold, HR Udseth, RD Smith, and DE Clemmer. 2006. "An IMS-IMS Analogue of MS-MS." Analytical Chemistry 78(12):4161-4174.
Lipton MS, MF Romine, ME Monroe, DA Elias, L Pasa-Tolic, GA Anderson, DJ Anderson, JK Fredrickson, KK Hixson, CD Masselon, HM Mottaz, N Tolic, and RD Smith. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis ." In Microbial Proteomics, Methods of Biochemical Analysis, vol. 49, ed. I. Humphery-Smith and M. Hecker, pp. 113-134. John Wiley & Sons, Inc., Hoboken, NJ.
Liu T, W Qian, HM Mottaz, MA Gritsenko, AD Norbeck, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry ." Molecular & Cellular Proteomics. MCP 5(11):2167-2174.
Liu T, W Qian, MA Gritsenko, W Xiao, LL Moldawer, A Kaushal, ME Monroe, SM Varnum, RJ Moore, SO Purvine, RV Maier, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome ." Molecular & Cellular Proteomics. MCP 5(10):1899-1913. doi:10.1074/mcp.M600068-MCP200
Luo Q, K Tang, F Yang, A Elias, Y Shen, RJ Moore, R Zhao, KK Hixson, SS Rossie, and RD Smith. 2006. "More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry ." Journal of Proteome Research 5(5):1091-1097.
Metz TO, JM Jacobs, MA Gritsenko, G Fontes, W Qian, DG Camp, II, VJ Poitout, and RD Smith. 2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5(12):3345-3354. doi: 10.1021/pr060322n
Patwardhan AJ, EF Strittmatter, DG Camp, II, RD Smith, and M Pallavicini. 2006. "Quantitative Proteome Analysis of Breast Cancer Cell Lines using 18O-Labeling and an Accurate Mass and Time Tag Strategy." Proteomics 6(9):2903-2915. doi:10.1002/pmic200500582
Petritis K, LJ Kangas, B Yan, ME Monroe, EF Strittmatter, W Qian, JN Adkins, RJ Moore, Y Xu, MS Lipton, DG Camp, II, and RD Smith. 2006. "Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information." Analytical Chemistry 78(14):5026-5039. doi:10.1021/ac060143p
Sacksteder CA, W Qian, TV Knyushko, HH Wang, MH Chin, G Lacan, WP Melega, DG Camp, II, RD Smith, DJ Smith, TC Squier, and DJ Bigelow. 2006. "Endogenously Nitrated Proteins in Mouse Brain: Links To Neurodegenerative Disease ." Biochemistry 45(26):8009-8022. doi:10.1021/bi060474w
Shi L, JN Adkins, JR Coleman, AA Schepmoes, A Dohnalkova, HM Mottaz, AD Norbeck, SO Purvine, NP Manes, HS Smallwood, HH Wang, J Forbes, P Gros, S Uzzau, KD Rodland, F Heffron, RD Smith, and TC Squier. 2006. "Proteomic Analysis of Salmonella enterica Serovar Typhimurium Isolated from RAW 264.7 Macrophages: identification of a novel protein that contributes to the replication of serovar Typhimurium inside macrophages." Journal of Biological Chemistry 281:29131-29140. doi:10.1074/jbc.M604640200
Shvartsburg AA, F Li, K Tang, and RD Smith. 2006. "Characterizing the Structures and Folding of Free Proteins Using 2-D Gas-Phase Separations: Observation of Multiple Unfolded Conformers." Analytical Chemistry 78(10):3304-3315. doi:10.1021/ac060283z
Shvartsburg AA, F Li, K Tang, and RD Smith. 2006. "High-Resolution Field Asymmetric Waveform Ion Mobility Spectrometry Using New Planar Geometry Analyzers." Analytical Chemistry 78(11):3706-3714. doi:10.1021/ac052020v
Simson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Brewer, AN Vilkov, GA Anderson, MS Lipton, and RD Smith. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling ." Electrophoresis 27(13):2722-2733. doi:10.1002/elps.200600037
Smith RD, K Tang, and Y Shen. 2006. "Ultra-sensitive and quantitative characterization of proteomes." Molecular Biosystems 2(5):221-230. doi:10.1039/b601468b
Streblow DN, SM Varnum, RD Smith, and J Nelson. 2006. "A Proteomics Analysis of Human Cytomegalovirus Particles." Chapter 5 in Cytomegaloviruses: Molecular Biology and Immunology, ed. Matthias J. Reddehase, pp. 91-110. Caister Academic Press, Hethersett, United Kingdom.
Tolmachev AV, ME Monroe, N Jaitly, VA Petyuk, JN Adkins, and RD Smith. 2006. "Mass Measurement Accuracy In Analyses Of Highly Complex Mixtures Based Upon Multidimensional Recalibration." Analytical Chemistry 78(24):8374-8385. doi:10.1021/ac0606251
Valentine SJ, MD Plasencia, X Liu, M Krishnan, S Naylor, HR Udseth, RD Smith, and DE Clemmer. 2006. "Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry." Journal of Proteome Research 5(11):2977-2984. doi:10.1021/pr060232i
Wang HH, W Qian, MH Chin, VA Petyuk, RC Barry, T Liu, MA Gritsenko, HM Mottaz, RJ Moore, DG Camp, II, AH Khan, D Smith, and RD Smith. 2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5(2):361-369.
Yang F, DL Stenoien, EF Strittmatter, J Wang, L Ding, MS Lipton, ME Monroe, CD Nicora, MA Gritsenko, K Tang, R Fang, JN Adkins, DG Camp, II, DJ Chen, and RD Smith. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation ." Journal of Proteome Research 5(5):1252-1260.
Zhang W, DE Culley, MA Gritsenko, RJ Moore, L Nie, JC Scholten, K Petritis, EF Strittmatter, DG Camp, II, RD Smith, and FJ Brockman. 2006. "LC-MS/MS Based Proteomic Analysis and Functional Inference of Hypothetical Proteins in Desulfovibrio Vulgaris." Biochemical and Biophysical Research Communications 349(4):1412-1419. doi:10.1016/j.bbrc.2006.09.019
Zhang W, MA Gritsenko, RJ Moore, DE Culley, L Nie, K Petritis, EF Strittmatter, DG Camp, II, RD Smith, and FJ Brockman. 2006. "A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry." Proteomics 6(15):4286-4299. doi:10.1002/pmic.200500930
Zimmer JS, ME Monroe, W Qian, and RD Smith. 2006. "Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach ." Mass Spectrometry Reviews 25(3):450-482.

2005

Jacobs JM, X Yang, BJ Luft, JJ Dunn, DG Camp, II, and RD Smith. 2005. "Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia burgdorferi." Proteomics 5(5):1446-1453.
Norbeck AD, ME Monroe, JN Adkins, KK Anderson, DS Daly, and RD Smith. 2005. "The utility of accurate mass and LC elution time information in the analysis of complex proteomes." Journal of the American Society for Mass Spectrometry 16(8):1239-1249.
Page JS, AV Tolmachev, K Tang, and RD Smith. 2005. "Variable low-mass filtering using an electrodynamic ion funnel." Journal of Mass Spectrometry 40(9):1215-1222. doi:10.1002/jms.900
Page JS, B Bogdanov, AN Vilkov, DC Prior, MA Buschbach, K Tang, and RD Smith. 2005. "Automatic Gain Control in Mass Spectrometry using a Jet Disrupter Electrode in an Electrodynamic Ion Funnel." Journal of the American Society for Mass Spectrometry 16(2):244-253.
Qian W, JM Jacobs, DG Camp, II, ME Monroe, RJ Moore, MA Gritsenko, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, and RD Smith. 2005. "Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry." Proteomics 5(2):572-584. doi:10.1002/pmic.200400942
Qian W, JM Jacobs, DG Camp, II, ME Monroe, RJ Moore, MA Gritsenko, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, and RD Smith. 2005. "Comparative Proteome Analyses of Human Plasma Following in vivo Lipopolysaccharide Administration Using Multidimensional Separations Coupled with Tandem Mass Spectrometry." Proteomics 5(2):572-584.
Qian W, ME Monroe, T Liu, JM Jacobs, GA Anderson, Y Shen, RJ Moore, DJ Anderson, R Zhang, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 4(5):700-709.
Qian W, T Liu, ME Monroe, EF Strittmatter, JM Jacobs, LJ Kangas, K Petritis, DG Camp, II, and RD Smith. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research 4(1):53-62.
Shen Y, and RD Smith. 2005. "Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics." Expert Review of Proteomics 2(3):431-447.
Shen Y, EF Strittmatter, R Zhang, TO Metz, RJ Moore, F Li, HR Udseth, RD Smith, KK Unger, D Kumar, and D Lubda. 2005. "Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurments." Analytical Chemistry 77(23):7763-7773. doi: 10.1021/ac051257o
Shen Y, R Zhang, RJ Moore, J Kim, TO Metz, KK Hixson, R Zhao, EA Livesay, HR Udseth, and RD Smith. 2005. "Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics ." Analytical Chemistry 77(10):3090-3100.
Shvartsburg AA, K Tang, and RD Smith. 2005. "FAIMS Operation for Realistic Gas Flow Profile and Asymmetric Waveforms Including Electronic Noise and Ripple." Journal of the American Society for Mass Spectrometry 16(9):1447-1455. doi:10.1016/j.jasms.2005.04.003
Shvartsburg AA, K Tang, and RD Smith. 2005. "Optimization of the Design and Operation of FAIMS Analyzers." Journal of the American Society for Mass Spectrometry 16(1):2-12.
Adkins JN, ME Monroe, KJ Auberry, Y Shen, JM Jacobs, DG Camp, II, F Vitzthum, KD Rodland, RC Zangar, RD Smith, and JG Pounds. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy." Proteomics 5(13):3454-3466. doi:10.1002/pmic.200401333
Aebersold R, LN Anderson, RM Caprioli, B Druker, LD Hartwell, and RD Smith. 2005. "Perspective: A Program to Improve Protein Biomarker Discovery for Cancer." Journal of Proteome Research 4(4):1104-1109.
Bogdanov B, and RD Smith. 2005. "Proteomics by FTICR Mass Spectrometry: Top Down and Bottom Up." Mass Spectrometry Reviews 24(2):168-200.
Elias DA, ME Monroe, MJ Marshall, MF Romine, AS Beliaev, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics 5(12):3120-3130. doi:10.1002/pmic.200401140
Huang Y, JM Triscari, GC Tseng, L Pasa-Tolic, MS Lipton, RD Smith, and VH Wysocki. 2005. "Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns." Analytical Chemistry 77(18):5800-5813.
Jacobs JM, DL Diamond, EY Chan, MA Gritsenko, W Qian, M Stastna, T Baas, DG Camp, II, RL Carithers, Jr., RD Smith, and MG Katze. 2005. "Proteome Analysis of Liver Cells Expressing a Full- Length Hepatitis C Virus (HCV) Replicon and Biopsy Specimens of Posttransplantation Liver from HCV-Infected Patients." Journal of Virology 79(12):7558-7569.
Jacobs JM, JN Adkins, W Qian, T Liu, Y Shen, DG Camp, II, and RD Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4(4):1073-1085. doi:10.1021/pr0500657
Jacobs JM, ME Monroe, W Qian, Y Shen, GA Anderson, and RD Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240(3):195-212.
Kolker E, AF Picone, MY Galperin, MF Romine, R Higdon, KS Makarova, N Kolker, GA Anderson, X Qiu, KJ Auberry, G Babnigg, AS Beliaev, P Edlefsen, DA Elias, YA Gorby, T Holzman, J Klappenbach, K Konstantinidis, ML Land, MS Lipton, LA McCue, ME Monroe, L Pasa-Tolic, GE Pinchuk, SO Purvine, M Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, F Larimer, C Lawrence, M Riley, FR Collart, JR Yates, III, RD Smith, CS Giometti, K Nealson, JK Fredrickson, and JM Tiedje. 2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102(6):2099-2104.
Liu T, W Qian, MA Gritsenko, DG Camp, II, ME Monroe, RJ Moore, and RD Smith. 2005. "Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry." Journal of Proteome Research 4(6):2070-2080.
Liu T, W Qian, WNU Chen, JM Jacobs, RJ Moore, DJ Anderson, MA Gritsenko, ME Monroe, BD Thrall, DG Camp, II, and RD Smith. 2005. "Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome." Proteomics 5(5):1263-1273.
Luo Q, Y Shen, KK Hixson, R Zhao, F Yang, RJ Moore, HM Mottaz, and RD Smith. 2005. "Preparation of 20-µm-i.d. Silica-based Monolithic Columns and Application for Proteomic Analysis." Analytical Chemistry 77(15):5028-5035.
Masselon CD, L Pasa-Tolic, N Tolic, GA Anderson, B Bogdanov, AN Vilkov, Y Shen, R Zhao, W Qian, MS Lipton, DG Camp, II, and RD Smith. 2005. "Targeted Comparative Proteomics by Liquid Chromatography - Tandem Fourier ion cyclotron resonance Mass Spectrometry." Analytical Chemistry 77(2):400-406.
Patwardhan AJ, EF Strittmatter, DG Camp, II, RD Smith, and M Pallavicini. 2005. "Comparison of Normal and Breast Cancer Cell lines using Proteome, Genome and Interactome data." Journal of Proteome Research 4(6):1952-1960.
Schad M, MS Lipton, P Giavalisco, RD Smith, and J Kehr. 2005. "Evaluation of two-dimensional electrophoresis and liquid chromatography - tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples." Electrophoresis 26(14):2729-2738.
Schmid AK, MS Lipton, HM Mottaz, ME Monroe, RD Smith, and ME Lidstrom. 2005. "Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans." Journal of Proteome Research 4(3):709-718.
Shen Y, J Kim, EF Strittmatter, JM Jacobs, DG Camp, II, R Fang, N Tolic, RJ Moore, and RD Smith. 2005. "Characterization of the human blood plasma proteome." Proteomics 5(15):4034-4045.
Simpson DC, and RD Smith. 2005. "Combining Capillary Electrophoresis with Mass Spectrometry for Applications in Proteomics." Electrophoresis 26(7-8):1291-1305.
Tang K, F Li, AA Shvartsburg, EF Strittmatter, and RD Smith. 2005. "Two-Dimensional Gas-Phase Separations Coupled to Mass Spectrometry for Analysis of Complex Mixtures." Analytical Chemistry 77(19):6381-6388.
Tang K, AA Shvartsburg, HN Lee, DC Prior, MA Buschbach, F Li, AV Tolmachev, GA Anderson, and RD Smith. 2005. "High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces ." Analytical Chemistry 77(10):3330-3339. doi:10.1021/ac048315a
Wang HH, W Qian, HM Mottaz, TRW Clauss, DJ Anderson, RJ Moore, DG Camp, II, AH Khan, DM Sforza, M Pallavicini, DJ Smith, and RD Smith. 2005. "Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method." Journal of Proteome Research 4(6):2397-2403. doi:10.1021/pr050160f
Yang F, B Bogdanov, EF Strittmatter, AN Vilkov, MA Gritsenko, L Shi, DA Elias, S Ni, MF Romine, L Pasa-Tolic, MS Lipton, and RD Smith. 2005. "Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry." Journal of Proteome Research 4(3):846-854. doi:10.1021/pr0497475
Zhang H, EC Yi, X Li, P Mallick, KS Kelly-Spratt, CD Masselon, DG Camp, II, RD Smith, C Kemp, and R Aebersold. 2005. "High Throughput Quantitative Analysis of Serum Proteins using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry." Molecular & Cellular Proteomics. MCP 4(2):144-155.
Zhang H, EC Yi, X Li, P Mallick, KS Kelly-Spratt, CD Masselon, DG Camp, II, RD Smith, CJ Kemp, and R Aebersold. 2005. "High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry ." Molecular & Cellular Proteomics. MCP 4:144-155.

2004

Camp DG, II, and RD Smith. 2004. "The Use of Accurate Mass Tags based upon High-Throughput Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Global Proteomic Characterization." Chapter 8 in Proteome Analysis: Interpreting the Genome, ed. David W Speicher, pp. 183-224. Elsevier, Amsterdam, Netherlands.
Jacobs JM, HM Mottaz, LR Yu, DJ Anderson, RJ Moore, WNU Chen, KJ Auberry, EF Strittmatter, ME Monroe, BD Thrall, DG Camp, II, and RD Smith. 2004. "Multidimensional Proteome Analysis of Human Mammary Epithelial Cells." Journal of Proteome Research 3(1):68-75.
Page JS, CD Masselon, and RD Smith. 2004. "FTICR Mass Spectrometry for Qualitative and Quantitative Bioanalyses." Current Opinion in Biotechnology 15(1):3-11.
Qian W, DG Camp, II, and RD Smith. 2004. "High Throughput Proteomics Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Expert Review of Proteomics 1(1):87-95.
Shen Y, N Tolic, CD Masselon, L Pasa-Tolic, DG Camp, II, GA Anderson, RD Smith, and MS Lipton. 2004. "Nanoscale Proteomics." Analytical and Bioanalytical Chemistry 378(4):1037-1045.
Shen Y, N Tolic, CD Masselon, L Pasa-Tolic, DG Camp, II, KK Hixson, R Zhao, GA Anderson, and RD Smith. 2004. "Ultrasensitive Proteomics using High-Efficiency on-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS." Analytical Chemistry 76(1):144-154.
Shvartsburg AA, K Tang, and RD Smith. 2004. "Modeling the Resolution and Sensitivity of FAIMS analyses." Journal of the American Society for Mass Spectrometry 15(10):1487-98.
Shvartsburg AA, K Tang, and RD Smith. 2004. "Understanding and Designing Field Asymmetric Waveform Ion Mobility Spectrometry Separations in Gas Mixtures." Analytical Chemistry 76(24):7366-7374. doi:10.1021/ac049299k
Tolmachev AV, AN Vilkov, B Bogdanov, L Pasa-Tolic, CD Masselon, and RD Smith. 2004. "Collisional Activation of Ions in RF Ion Traps and Ion Guides: The Effective Ion Temperature Treatment." Journal of the American Society for Mass Spectrometry 15(11):1616-1628.
Belov ME, GA Anderson, MA Wingerd, HR Udseth, K Tang, DC Prior, KR Swanson, MA Buschbach, EF Strittmatter, RJ Moore, and RD Smith. 2004. "An Automated High Performance Capillary Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for High-Throughput Proteomics." Journal of the American Society for Mass Spectrometry 15(2):212-232.
Blonder J, MB Goshe, W Xiao, DG Camp, II, MA Wingerd, RW Davis, and RD Smith. 2004. "Global Analysis of the Membrane Subproteome of Pseudomonas aeruginosa using Liquid Chromatography-Tandem Mass Spectrometry." Journal of Proteome Research 3(3):434-444.
Gorshkov MV, CD Masselon, EN Nikolaev, HR Udseth, L Pasa-Tolic, and RD Smith. 2004. "Consideration for Electron Capture Dissociation Efficiency in FTICR Mass Spectrometry." International Journal of Mass Spectrometry 234(1-3):131-136.
Huang Y, JM Triscari, L Pasa-Tolic, GA Anderson, MS Lipton, RD Smith, and VH Wysocki. 2004. "Dissociation Behavior of Doubly-Charged Tryptic Peptides: Correlation of Gas-Phase Cleavage Abundance with Ramachandran Plots." Journal of the American Chemical Society 126(10):3034-3035.
Kim J, DG Camp, II, and RD Smith. 2004. "Improved detection of multi-phosphorylated peptides in the presence of phosphoric acid in liquid chromatography/mass spectrometry." Journal of Mass Spectrometry 39(2):206-215.
Liu T, W Qian, EF Strittmatter, DG Camp, II, GA Anderson, BD Thrall, and RD Smith. 2004. "High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Analytical Chemistry 76(18):5345-5353.
Martinovic S, L Pasa-Tolic, and RD Smith. 2004. "Capillary Isoelectric Focusing-Mass Spectrometry of Proteins and Protein Complexes." Chapter 14 in Capillary Electrophoresis of Proteins and Peptides: Methods in Molecular Biology, vol. 276, ed. MA Strege and AL Lagu, pp. 291-304. Human Press, Totowa, NJ.
Pasa-Tolic L, CD Masselon, RC Barry, Y Shen, and RD Smith. 2004. "Proteomic Analyses using an Accurate Mass and Time Tag Strategy." BioTechniques 37(4):621-636.
Pedrioli PG, JK Eng, R Hubley, M Vogelzang, EW Deutsch, B Raught, B Pratt, E Nilsson, RH Angeletti, R Apweiler, K Cheung, CE Costello, H Hermjakob, S Huang, RK Julian, Jr., E Kapp, ME McComb, SG Oliver, G Omenn, NW Paton, R Simpson, RD Smith, CF Taylor, W Zhu, and R Aebersold. 2004. "A common open representation of mass spectrometry data and its application to proteomics research." Nature Biotechnology 22(11):1459-1466.
Prokisch H, CM Scharfe, DG Camp, II, W Xiao, L David, C Andreoli, ME Monroe, RJ Moore, MA Gritsenko, C Kozany, KK Hixson, HM Mottaz, H Zischka, M Ueffing, ZS Herman, RW Davis, T Meitinger, P Oefner, RD Smith, and LM Steinmetz. 2004. "Integrative Analysis of the Mitochondrial Proteome in Yeast." PloS Biology 2(6):0795-0804.
Romine MF, DA Elias, ME Monroe, KJ Auberry, R Fang, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2004. "Validation of Shewanella oneidensis MR-1 Small Proteins by AMT Tag-based Proteome Analysis." OMICS. A Journal of Integrative Biology 8(3):239-254.
Shen Y, JM Jacobs, DG Camp, II, R Fang, RJ Moore, RD Smith, W Xiao, RW Davis, and RG Tompkins. 2004. "Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome." Analytical Chemistry 76(4):1134-1144.
Smith RD, Y Shen, and K Tang. 2004. "Ultra-sensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes." Accounts of Chemical Research 37(4):269-278.
Strittmatter EF, LJ Kangas, K Petritis, HM Mottaz, GA Anderson, Y Shen, JM Jacobs, DG Camp, II, and RD Smith. 2004. "Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry." Journal of Proteome Research 3(4):760-769.
Tang K, JS Page, and RD Smith. 2004. "Charge Competition and the Linear Dynamic Range of Detection in Electrospray Ionization Mass Spectrometry." Journal of the American Society for Mass Spectrometry 15(10):1416-1423.
Varnum SM, DN Streblow, ME Monroe, P Smith, KJ Auberry, L Pasa-Tolic, D Wang, DG Camp, II, KD Rodland, HS Wiley, W Britt, T Shenk, RD Smith, and J Nelson. 2004. "Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome ." Journal of Virology 78(20):10960-10966.
Vilkov AN, B Bogdanov, L Pasa-Tolic, DC Prior, GA Anderson, CD Masselon, RJ Moore, and RD Smith. 2004. "Tailored Noise Waveform/ Collision-Induced Dissociation of Ions Stored in a Linear Ion Trap Combined with Liquid Chromatography/Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Rapid Communications in Mass Spectrometry 18(22):2682-2690.
Wunschel DS, CD Masselon, B Feng, and RD Smith. 2004. "Proofreading activity of Pfu thermostable DNA polymerase on a 6-O-Methylguanine Containing Template Monitored by ESI-FTICR Mass Spectrometry." Chembiochem 5(7):1012-1015.
Zangar RC, SM Varnum, CY Covington, and RD Smith. 2004. "A rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and ELISA microarrays." Disease Markers 20(3):135-148.

2003

Petritis K, LJ Kangas, PL Ferguson, GA Anderson, L Pasa-Tolic, MS Lipton, KJ Auberry, E Strittmatter, Y Shen, R Zhao, and RD Smith. 2003. "Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses." Analytical Chemistry 75(5):1039-1048.
Qian W, MB Goshe, DG Camp, II, LR Yu, K Tang, and RD Smith. 2003. "Phosphoprotein Isotope-Coded Solid-Phase Tag Approach for Enrichment and Quantitative Analysis of Phosphopeptides from Complex Mixtures." Analytical Chemistry 75(20):5441-5450.
Shen Y, RJ Moore, R Zhao, J Blonder, DL Auberry, CD Masselon, L Pasa-Tolic, KK Hixson, KJ Auberry, and RD Smith. 2003. "High-Efficiency On-Line Solid-Phase Extraction Coupling to 15-150 um I.D. Column Liquid Chromatography for Proteomic Analysis." Analytical Chemistry 75(14):3596-3605.
Tolmachev AV, AN Vilkov, L Pasa-Tolic, HR Udseth, and RD Smith. 2003. "Suppression of the Lower Charge State Ions in the External Accumulation RF Multipole with a Reduced Trapping DC Potential." Journal of the American Society for Mass Spectrometry 14(11):1229-1235.
Tolmachev AV, HR Udseth, and RD Smith. 2003. "Modeling the ion density distribution in collisional cooling RF multipole ion guides." International Journal of Mass Spectrometry 222(1-3):155-174.
Belov ME, R Zhang, EF Strittmatter, DC Prior, K Tang, and RD Smith. 2003. "Automated Gain Control and Internal Calibration With External Ion Accumulation Capillary liquid chromatography-electrospray ionization-fourier transform ion cyclotron resonance." Analytical Chemistry 75(16):4195-4205.
Belov ME, VS Rakov, EN Nikolaev, MB Goshe, GA Anderson, and RD Smith. 2003. "Initial Implementation of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control." Rapid Communications in Mass Spectrometry 17(7):627-636.
Chen WNU, LR Yu, E Strittmatter, BD Thrall, DG Camp, II, and RD Smith. 2003. "Detection of in situ labeled cell surface proteins by mass spectrometry: application to the membrane subproteome of human mammary epithelial cells." Proteomics 3(8):1647-1651.
Ferguson PL, and RD Smith. 2003. "Proteome Analysis by Mass Spectrometry." In Annual Review in Biophysics and Biomolecular Structure, vol. 32, ed. Robert M. Stroud, pp. 399-424. Annual Reviews, Palo Alto, CA.
Goshe MB, and RD Smith. 2003. "Stable Isotope-Coded Proteomic Mass Spectrometry." Current Opinion in Biotechnology 14(1):101-109.
Goshe MB, J Blonder, and RD Smith. 2003. "Affinity Labeling of Highly Hydrophobic Integral Membrane Proteins for Proteome-Wide Analysis." Journal of Proteome Research 2(2):153-161.
Masselon CD, L Pasa-Tolic, SW Lee, L Li, GA Anderson, R Harkewicz, and RD Smith. 2003. "Identification of Tryptic Peptides from Large Databases using Multiplexed Tandem Mass Spectrometry: Simulations and Experimental Results." Proteomics 3(7):1279-1286.
Mohan D, L Pasa-Tolic, CD Masselon, N Tolic, B Bogdanov, KK Hixson, RD Smith, and CS Lee. 2003. "Integration of Electrokinetic-Based Multidimensional Separations/Concentration Platform with electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry for Proteome Analysis of Shewanella Oneidensis." Analytical Chemistry 75(17):4432-4440.
Strittmatter EF, N Rodriguez, and RD Smith. 2003. "High Mass Measurement Accuracy Determination for Proteomics using Multivariate Regression Fitting: Application to Electrospray Ionization Time-Of-Flight Mass Spectrometry." Analytical Chemistry 75(3):460-468.
Strittmatter EF, PL Ferguson, K Tang, and RD Smith. 2003. "Proteome Analyses Using Accurate Mass and Elution Time Peptide Tags with Capillary LC Time-of-Flight Mass Spectrometry." Journal of the American Society for Mass Spectrometry 14(9):980-991.
Varnum SM, CC Covington, RL Woodbury, K Petritis, LJ Kangas, MS Abdullah, JG Pounds, RD Smith, and RC Zangar. 2003. "Proteomic Characterization of Nipple Aspirate Fluid: Identification of Potential Biomarkers of Breast Cancer ." Breast Cancer Research and Treatment 80(1):87-97.
Varnum SM, CC Covington, RL Woodbury, K Petritis, LJ Kangas, MS Abdullah, JG Pounds, RD Smith, and RC Zangar. 2003. "Proteomic Characterization of Nipple Aspirate Fluid: Identification of Potential Biomarkers of Breast Cancer." Breast Cancer Research and Treatment 80(1):87-97.
Varnum SM, CC Covington, RL Woodbury, K Petritis, LJ Kangas, MS Abdullah, JG Pounds, RD Smith, and RC Zangar. 2003. "Proteomic characterization of nipple aspirate fluid: Identification of potential biomarkers of breast cancer." Breast Cancer Research and Treatment 80(1):87-97. doi:10.1023/A:1024479106887
Yang XI, S Martinovic, RD Smith, and B Gong. 2003. "Duplex Foldamers from Assembly Induced Folding." Journal of the American Chemical Society 125(33):9932-9933.
Zeng H, X Yang, AL Brown, S Martinovic, RD Smith, and B Gong. 2003. "An extremely stable, self-complementary hydrogen-bonded duplex ." Chemical Communications 13:1556-1557.

2002

Belov ME, GA Anderson, and RD Smith. 2002. "Higher-Resolution Data-Dependent Selective External Ion Accumulation for Capillary LC-FTICR." International Journal of Mass Spectrometry 218(3):265-279.
Belov ME, GA Anderson, and RD Smith. 2002. "Higher-Resolution Data-Dependent Selective External ION Accumulation for Capillary LC-FTICR." International Journal of Mass Spectrometry 218(3):265-279.
Ramelot TA, JR Cort, A Yee, F Liu, MB Goshe, AM Edwards, RD Smith, CH Arrowsmith, TE Dever, and MA Kennedy. 2002. "Myxoma Virus Immunomodulatory Protein M156R is a Structural Mimic of Eukaryotic Translation Initiation Factor eIF2[alpha]." Journal of Molecular Biology 322(5):943-954.
Shen Y, and RD Smith. 2002. "Proteomics Based on High-Efficiency Capillary Separations." Electrophoresis 23:3106-3124.
Shen Y, R Zhao, SJ Berger, GA Anderson, N Rodriguez, and RD Smith. 2002. "High-Efficiency Nanoscale Liquid Chromatography Coupled On-Line with Mass Spectrometry using Nanoelectrospray Ionization for Proteomics." Analytical Chemistry 74:4235-4249.
Smith RD. 2002. "Advanced Mass Spectrometric Methods for the Rapid and Quantitative Characterization of Proteomes." Journal of Structural and Functional Genomics 3(2):143-150.
Smith RD. 2002. "Trends in mass spectrometry instrumentation for proteomics." Trends in Biotechnology 20(12):S3-S7.
Tolmachev AV, CD Masselon, GA Anderson, HR Udseth, and RD Smith. 2002. "Frequency Shifts Due to the Interference of Resolved Peaks in Magnitude-Mode Fourier-Transform Ion Cyclotron Resonance Mass Spectra." Journal of the American Society for Mass Spectrometry 13(4):387-401.
Adkins JN, SM Varnum, KJ Auberry, RJ Moore, N Angell, RD Smith, DL Springer, and JG Pounds. 2002. "Toward a Human Blood Serum Proteome: Analysis by Multidimensional Separation Coupled with Mass Spectrometry." Molecular & Cellular Proteomics. MCP 1(12):947-955.
Berger SJ, SW Lee, GA Anderson, L Pasa-Tolic, N Tolic, Y Shen, R Zhao, and RD Smith. 2002. "High-Throughput Global Peptide Proteomic Analysis by Combining Stable Isotope Amino Acid Labeling and Data-Dependent Multiplexed-MS/MS." Analytical Chemistry 74(19):4994-5000.
Blonder J, MB Goshe, RJ Moore, L Pasa-Tolic, CD Masselon, MS Lipton, and RD Smith. 2002. "Enrichment of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry." Journal of Proteome Research 1(4):351-360.
Borisov OV, MB Goshe, TP Conrads, VS Rakov, TD Veenstra, and RD Smith. 2002. "Low-Energy Collision-Induced Dissociation Fragmentation Analysis of Cysteinyl-Modified Peptides." Analytical Chemistry 74:2284-2292.
Buchanan MV, F Larimer, HS Wiley, SJ Kennel, TC Squier, JM Ramsey, KD Rodland, GB Hurst, RD Smith, Y Xu, DA Dixon, MJ Doktycz, SD Colson, R Gesteland, CS Giometti, ME Young, and RM Giddings. 2002. "Genomes to Life "Center for Molecular and Cellular Systems": A research program for identification and characterization of protein complexes." OMICS. A Journal of Integrative Biology 6(4):287-303.
Chen J, CS Lee, Y Shen, RD Smith, and EH Baehrecke. 2002. "Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation." Electrophoresis 23:3143-3148.
Gong B, H Zeng, J Zhu, L Yuan, Y Han, S Cheng, M Furukawa, RD Parra, AY Kovalevsky, JL Mills, E Skrzypczak-Jankun, S Martinovic, RD Smith, C Zheng, T Szyperski, and XC Zeng. 2002. "Creating nanocavities of tunable sizes: Hollow helices." Proceedings of the National Academy of Sciences of the United States of America 99(18):11583-88.
Goshe M, TD Veenstra, EA Panisko, TP Conrads, NH Angell, and RD Smith. 2002. "Phosphoprotein Isotope-coded Affinity Tags: Application to the Enrichment and Identification of Low-Abundance Phosphoproteins." Analytical Chemistry 74(3):607-616.
Harkewicz R, ME Belov, GA Anderson, L Pasa-Tolic, CD Masselon, DC Prior, HR Udseth, and RD Smith. 2002. "ESI-FTICR Mass Spectrometry Employing Data-Dependent External Ion Selection and Accumulation." Journal of the American Society for Mass Spectrometry 13(2):144-154.
Hixson KK, N Rodriguez, DG Camp, II, EF Strittmatter, MS Lipton, and RD Smith. 2002. "Evaluation of Enzymatic Digestion and Liquid Chromatography-Mass Spectrometry Peptide Mapping of the Integral Membrane Protein Bacteriorhodopsin." Electrophoresis 23(18):3224-3232.
Lee SW, SJ Berger, S Martinovic, L Pasa-Tolic, GA Anderson, Y Shen, R Zhao, and RD Smith. 2002. "Direct Mass Spectrometric Analysis of Intact Proteins of the Yeast Large Ribosomal Subunit using Capillary LC/FTICR." Proceedings of the National Academy of Sciences of the United States of America 99(9):5942-5947.
Lin Y, K Tang, and RD Smith. 2002. "Laser-Machined Microdevices for Mass Spectrometry." Chapter 6 in Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research, ed. J. Silberring and R. Ekman, pp. 171-192. John Wiley & Sons, Wiley Interscience, NY.
Lipton MS, L Pasa-Tolic, GA Anderson, DJ Anderson, DL Auberry, JR Battista, MJ Daly, JK Fredrickson, KK Hixson, HM Kostandarithes, CD Masselon, LM Markillie, RJ Moore, MF Romine, Y Shen, EF Strittmatter, N Tolic, HR Udseth, A Venkateswaran, KK Wong, R Zhao, and RD Smith. 2002. "Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags." Proceedings of the National Academy of Sciences of the United States of America 99(17):11049-11054.
Luo H, MS Lipton, and RD Smith. 2002. "Charge Effects for Differentiation of Oligodeoxynucleotide Isomers Containing 8-oxo-dG Residues." Journal of the American Society for Mass Spectrometry 13:195-199.
Martinovic S, TD Veenstra, GA Anderson, L Pasa-Tolic, and RD Smith. 2002. "Selective Incorporation Acids for Identification Proteome-wide Level." Journal of Mass Spectrometry 37(1):99-107.
Masselon CD, AV Tolmachev, GA Anderson, R Harkewicz, and RD Smith. 2002. "Mass Measurement Errors Caused by "Local" Frequency Perturbations in FTICR Mass Spectrometry"." Journal of the American Society for Mass Spectrometry 13:99-106.
Pasa-Tolic L, MS Lipton, CD Masselon, GA Anderson, Y Shen, N Tolic, and RD Smith. 2002. "Gene expression profiling using advanced mass spectrometric approaches." Journal of Mass Spectrometry 37(12):1185-1198.
Pasa-Tolic L, R Harkewicz, GA Anderson, N Tolic, Y Shen, R Zhao, BD Thrall, CD Masselon, and RD Smith. 2002. "Increased Proteome Coverage for Quantitative Peptide Abundance Measurements Based upon High Performance Separations and DREAMS FTICR Mass Spectrometry." Journal of the American Society for Mass Spectrometry 13(8):954-963.
Ramelot TA, JR Cort, A Yee, F Liu, MB Goshe, AM Edwards, RD Smith, CH Arrowsmith, TE Dever, and MA Kennedy. 2002. "Myxoma Virus Immunomodulatory Protein M156R is a Structural Mimic of Eukaryotic Translation Initiation Factor eIF2 alpha." Journal of Molecular Biology 322(5):943-954.
Smith RD, GA Anderson, MS Lipton, CD Masselon, L Pasa-Tolic, Y Shen, and HR Udseth. 2002. "The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics." OMICS. A Journal of Integrative Biology 6(1):61-90.
Smith RD, GA Anderson, MS Lipton, L Pasa-Tolic, Y Shen, TP Conrads, TD Veenstra, and HR Udseth. 2002. "An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements." Proteomics 2:513-523.
Smith RD, GA Anderson, TP Conrads, CD Masselon, MS Lipton, L Pasa-Tolic, and TD Veenstra. 2002. "Advanced Mass Spectrometric Approaches for Rapid and Quantitative Proteomics." Chapter 8 in Applied Electrospray Mass Spectrometry, ed. BN Pramanik,, AK Ganguly & ML Gross, pp. 307-360. Marcel Dekker, New York, NY.
Tang K, AV Tolmachev, EN Nikolaev, R Zhang, ME Belov, HR Udseth, and RD Smith. 2002. "Independent Control of Ion Transmission in a Jet Disrupter Dual-Channel Ion Funnel Electrospray Ionization MS Interface." Analytical Chemistry 74(20):5431-5437.
Yu LR, MD Johnson, TP Conrads, RD Smith, RS Morrison, and TD Veenstra. 2002. "Proteome Analysis of Camptothecin-Treated Cortical Neurons using Isotope-Coded Affinity Tags." Electrophoresis 23:1591-1598.

2001

Belov ME, EN Nikolaev, GA Anderson, HR Udseth, TP Conrads, TD Veenstra, CD Masselon, MV Gorshkov, and RD Smith. 2001. "Design and Performance of an ESI Interface for Selective External Ion Accumulation Coupled to a Fourier Transform Ion Cyclotron Mass Spectrometer." Analytical Chemistry 73(2):253-261.
Belov ME, EN Nikolaev, GA Anderson, KJ Auberry, R Harkewicz, and RD Smith. 2001. "Electrospray Ionization - Fourier Transform Ion Cyclotron Mass Spectrometry Using Ion Preselection and External Accumulation for Ultrahigh Sensitivity." Journal of the American Society for Mass Spectrometry 12(1):38-48.
Belov ME, EN Nikolaev, K Alving, and RD Smith. 2001. "A new technique for unbiased external ion accumulation in a quadrupole two-dimensional ion trap for electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry." Rapid Communications in Mass Spectrometry 15(14):1172-1180.
Belov ME, EN Nikolaev, R Harkewicz, CD Masselon, K Alving, and RD Smith. 2001. "Ion Discrimination During Ion Accumulation in a Quadrupole Interface External to a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer." International Journal of Mass Spectrometry 208(1-3):205-225.
Belov ME, MV Gorshkov, HR Udseth, and RD Smith. 2001. "Controlled Ion Fragmentation in a 2D Quadrupole Ion trap for External Ion Accumulation in ESI FTICR Mass Spectrometry." Journal of the American Society for Mass Spectrometry 12(12):1312-1319.
Belov ME, MV Gorshkov, K Alving, and RD Smith. 2001. "Optimal Pressure Conditions for Unbiased External Ion Accumulation in a Two-Dimensional Radio Frequency Quadrupole for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Rapid Communications in Mass Spectrometry 15(21):1988-1996.
Koppenaal DW, PD Ellis, and RD Smith. 2001. Annual Report 2000 Macromolecular Structure and Dynamics. PNNL-13626, Pacific Northwest National Laboratory, Richland, WA.
Shen Y, N Tolic, R Zhao, L Pasa-Tolic, L Li, SJ Berger, R Harkewicz, GA Anderson, ME Belov, and RD Smith. 2001. "High-Throughput Proteomics Using High Efficiency Multiple-Capillary Liquid Chromatography With On-Line High-Performance ESI FTICR Mass Spectrometry." Analytical Chemistry 73(13):3011-3021.
Shen Y, R Zhao, ME Belov, TP Conrads, GA Anderson, K Tang, L Pasa-Tolic, TD Veenstra, MS Lipton, HR Udseth, and RD Smith. 2001. "Packed Capillary Reversed-Phase Liquid Chromatography with High Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics ." Analytical Chemistry 73(8):1766-1775.
Shen Y, SJ Berger, and RD Smith. 2001. "High-Efficiency Capillary Isoelectric Focusing of Protein Complexes from Escherichia coli Cytosolic Extracts." Journal of Chromatography A 914(1-2):257-264.
Tang K, and RD Smith. 2001. "Physical/Chemical Separations in the Break-up of Highly Charged Droplets from Electrosprays." Journal of the American Society for Mass Spectrometry 12(3):343-347.
Tang K, and RD Smith. 2001. "Sensitivity Enhancement of Electrospray Ionization MS for Aqueous Solutions in the Corona-Assisted Cone-Jet Mode." International Journal of Mass Spectrometry and Ion Processes 162(1-3):69-76.
Tang K, Y Lin, DW Matson, TM Kim, and RD Smith. 2001. "Generation of Multiple Electrosprays Using Microfabricated Emitter Arrays for Improved Mass Spectrometric Sensitivity." Analytical Chemistry 73(8):1658-1663.
Belov ME, GA Anderson, NH Angell, Y Shen, N Tolic, HR Udseth, and RD Smith. 2001. "Dynamic Range Expansion Applied to Mass Spectrometry (DREAMS) Based on Data-Dependent Selective Ion Ejection in Capillary Liquid Chromatography Fourier Transform Ion Cyclotron Resonance for Enhanced Proteome Characterization." Analytical Chemistry 73(21):5052-5060.
Conrads TP, K Alving, TD Veenstra, ME Belov, GA Anderson, DJ Anderson, MS Lipton, L Pasa-Tolic, HR Udseth, WB Chrisler, BD Thrall, and RD Smith. 2001. "Quantitative Analysis of Bacterial and Mammalian Proteomes using a Combination of Cysteine Affinity Tags and 15N-Metabolic Labeling." Analytical Chemistry 73(9):2132-2139.
Gorshkov MV, CD Masselon, GA Anderson, HR Udseth, and RD Smith. 2001. "Dynamically Assisted Gated Trapping for Fourier Transform Ion Cyclotron Mass Spectrometry." Rapid Communications in Mass Spectrometry 15(17):1558-1561.
Gorshkov MV, CD Masselon, GA Anderson, HR Udseth, R Harkewicz, and RD Smith. 2001. "A Dynamic Ion Cooling Technique for FTICR Mass Spectrometry." Journal of the American Society for Mass Spectrometry 12(11):1169-1173.
Goshe MB, TP Conrads, EA Panisko, NH Angell, TD Veenstra, and RD Smith. 2001. "Phosphoprotein Isotope-coded Affinity Tag (PhIAT) Approach for Isolating and Quantitating Phosphopeptides in Proteome-wide Analyses." Analytical Chemistry 73(11):2578-2586.
Iakoucheva LM, AL Kimzey, CD Masselon, JE Bruce, EC Garner, CJ Brown, AK Dunker, RD Smith, and EJ Ackerman. 2001. "Identification of intrinsic order and disorder in the DNA repair protein XPA." Protein Science 10(3):560-571.
Iakoucheva LM, AL Kimzey, CD Masselon, RD Smith, AK Dunker, and EJ Ackerman. 2001. "Aberrant mobility phenomena of the DNA repair protein XPA ." Protein Science 10(7):1353-1362.
Kane RS, PT Glink, RG Chapman, JC Mcdonald, PK Jensen, H Gao, L Pasa-Tolic, RD Smith, and GM Whitesides. 2001. "Basicity of the Amino Groups of the Aminoglycoside Amikacin Using Capillary Electrophoresis and coupled CE-MS-MS techniques." Analytical Chemistry 73(16):4028-4036.
Kim TM, K Tang, HR Udseth, and RD Smith. 2001. "A Multi-capillary Inlet Jet Disruption Electrodynamic Ion Funnel Interface for Improved Sensitivity Using Atmospheric Pressure Ion Sources." Analytical Chemistry 73(17):4162-4170.
Li L, CD Masselon, GA Anderson, L Pasa-Tolic, SW Lee, Y Shen, R Zhao, MS Lipton, TP Conrads, N Tolic, and RD Smith. 2001. "High-Throughput Peptide Identification from Protein Digests Using Data-Dependent Multiplexed Tandem FTICR Mass Spectrometry Coupled with Capillary Liquid Chromatography." Analytical Chemistry 73(14):3312-3322.
Smith RD, L Pasa-Tolic, MS Lipton, PK Jensen, GA Anderson, Y Shen, TP Conrads, HR Udseth, R Harkewicz, ME Belov, CD Masselon, and TD Veenstra. 2001. "Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry." Electrophoresis 22:1652-1668.

2000

Tolmachev AV, HR Udseth, and RD Smith. 2000. "Charge Capacity Limitations of Radio Frequency Ion Guides in Their Use for Improved Ion Accumulation and Trapping in Mass Spectrometry." Analytical Chemistry 72(5):970-978.
Belov ME, MV Gorshkov, HR Udseth, GA Anderson, and RD Smith. 2000. "Zeptomole-Sensitivity Electrospray Ionization - Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Proteins." Analytical Chemistry 72(10):2271-2279.
Belov ME, MV Gorshkov, HR Udseth, GA Anderson, AV Tolmachev, DC Prior, R Harkewicz, and RD Smith. 2000. "Initial Implementation of an Electrodynamic Ion Funnel with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Journal of the American Society for Mass Spectrometry 11(1):19-23.
Lin Y, DW Matson, DE Kurath, JY Wen, F Xiang, WD Bennett, PM Martin, and RD Smith. 2000. "Microfluidic Devices on Polymer Substrates for Bioanalytical Applications." In 3rd International Conference on Microreaction Technology; Microreaction Technology: Industrial Prospects IMRET 3, April 1999. , pp. 451-460. Springer, New York, NY.
Shen Y, and RD Smith. 2000. "High-Resolution Capillary Isoelectric Focusing of Proteins Using Highly Hydrophilic-Substituted Cellulose-Coated Capillaries." Journal of Microcolumn Separations 12(3):135-141.
Shen Y, SJ Berger, GA Anderson, and RD Smith. 2000. "High-Efficiency Capillary Isoelectric Focusing of Peptides." Analytical Chemistry 72(9):2154-2159.
Smith RD. 2000. "Evolution of ESI-Mass Spectrometry and Fourier Transform Ion Cyclotron Resonance for Proteomics and Other Biological Applications." International Journal of Mass Spectrometry 200:509-544.
Smith RD. 2000. "Probing Proteomes-Seeing the Whole Picture?" Nature Biotechnology 18(10):1041-1042.
Tolmachev AV, HR Udseth, and RD Smith. 2000. "Radial Stratification of Ions as a Function of Mass to Charge Ratio in Collisional Cooling Radio Frequency Multipoles Used as Ion Guides or Ion Traps." Rapid Communications in Mass Spectrometry 14(20):1907-1913.
Tolmachev AV, TM Kim, HR Udseth, RD Smith, TH Bailey, and JH Futrell. 2000. "Simulation-Based Optimization of the Electrodynamic Ion Funnel for High Sensitivity Electrospray Ionization-Mass Spectrometry." International Journal of Mass Spectrometry 203(1-3):31-47.
Bruce JE, GA Anderson, CY Lin, MV Gorshkov, AL Rockwood, and RD Smith. 2000. "A Novel High Performance Fourier Transform Ion Cyclotron Resonance Cell for Improved Biopolymer Characterization ." Journal of Mass Spectrometry 35(1):85-94.
Bruce JE, GA Anderson, MD Brands, L Pasa-Tolic, and RD Smith. 2000. "Obtaining More Accurate Fourier Transform Ion Cyclotron Resonance Mass Measurements Without Internal Standards Using Multiply Charged Ions." Journal of the American Society for Mass Spectrometry 11(5):416-421.
Conrads TP, GA Anderson, TD Veenstra, L Pasa-Tolic, and RD Smith. 2000. "Utility of Accurate Mass Tags for Proteome-Wide Protein Identification." Analytical Chemistry 72(14):3349-3354.
Feng B, and RD Smith. 2000. "A Simple Nanoelectrospray Arrangement with Controllable Flowrate for Mass Analysis of Submicroliter Protein Samples." Journal of the American Society for Mass Spectrometry 11(1):94-99.
Gao H, Y Shen, TD Veenstra, R Harkewicz, GA Anderson, JE Bruce, L Pasa-Tolic, and RD Smith. 2000. "Two Dimensional Electrophoretic/Chromatographic Separations Combined with Electrospray Ionization FTICR Mass Spectrometry for High Throughput Proteome Analysis." Journal of Microcolumn Separations 12(7):383-390.
Goodlet DR, JE Bruce, GA Anderson, B Rist, L Pasa-Tolic, ON Fiehn, RD Smith, and R Aebersold. 2000. "Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching." Analytical Chemistry 72(6):1112-1118.
Jensen PK, L Pasa-Tolic, KK Peden, S Martinovic, MS Lipton, GA Anderson, N Tolic, KK Wong, and RD Smith. 2000. "Mass Spectrometric Detection for Capillary Isoelectric Focusing Separations of Complex Protein Mixtures." Electrophoresis 21(7):1372-1380.
Kim TM, AV Tolmachev, R Harkewicz, DC Prior, GA Anderson, HR Udseth, RD Smith, TH Bailey, VS Rakov, and JH Futrell. 2000. "Design and Implementation of a New Electrodynamic Ion Funnel." Analytical Chemistry 72:2247-2255.
Kim TM, HR Udseth, and RD Smith. 2000. "Improved Ion Transmission from Atmospheric Pressure to High Vacuum using a Multi-Capillary Inlet and Electrodynamic Ion Funnel Interface." Analytical Chemistry 72(20):5014-5019.
Krahmer MT, JJ Walters, KF Fox, A Fox, KE Creek, L Pirisi, DS Wunschel, RD Smith, DL Tabb, and JR Yates. 2000. "MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR Products." Analytical Chemistry 72(17):4033-4040.
Maier C, X Yan, ME Harder, MI Schimerlik, L Pasa-Tolic, and RD Smith. 2000. "Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometric Analysis of the Recombinant Human Macrophage Colony Stimulating Factor Beta and Derivatives." Journal of the American Society for Mass Spectrometry 11(3):237-243.
Martinovic S, L Pasa-Tolic, CD Masselon, PK Jensen, CL Stone, and RD Smith. 2000. "Characterization of Human Alcohol Dehydrogenase Isoenzymes by Capillary Isoelectric Focusing-Mass Spectrometry." Electrophoresis 21(12):2368-2375.
Martinovic S, SJ Berger, L Pasa-Tolic, and RD Smith. 2000. "Separation and Detection of Intact Noncovalent Protein Complexes from Mixtures by On-Line Capillary Isoelectric Focusing-Mass Spectrometry." Analytical Chemistry 72(21):5356-5360.
Masselon CD, GA Anderson, R Harkewicz, JE Bruce, L Pasa-Tolic, and RD Smith. 2000. "Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures." Analytical Chemistry 72(8):1918-1924.
Veenstra TD, S Martinovic, GA Anderson, L Pasa-Tolic, and RD Smith. 2000. "Proteome Analysis using Selective Incorporation of Isotopically Labeled Amino Acids." Journal of the American Society for Mass Spectrometry 11(1):78-82.
Wen JY, Y Lin, F Xiang, DW Matson, HR Udseth, and RD Smith. 2000. "Microfabricated Isoelectric Focusing Devices for Direct Electrospray Ionization-Mass Spectrometry." Electrophoresis 21(1):191-197.
Wunschel DS, L Pasa-Tolic, B Feng, and RD Smith. 2000. "Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Analysis of Large Polymerases Chain Reaction Products." Journal of the American Society for Mass Spectrometry 11(4):333-337.
Xiang F, GA Anderson, TD Veenstra, MS Lipton, and RD Smith. 2000. "Characterization of Microorganisms and Biomarker Development from Global ESI-MS/MS Analyses of Cell Lysates." Analytical Chemistry 72(11):2475-2481.
Zhang CX, F Xiang, L Pasa-Tolic, GA Anderson, TD Veenstra, and RD Smith. 2000. "Stepwise Mobilization of Focused Proteins in Capillary Isoelectric Focusing Mass Spectrometry." Analytical Chemistry 72(7):1462-1468.

1999

Lin Y, JY Wen, X Fan, DW Matson, and RD Smith. 1999. "Laser Micromachined Isoelectric Focusing Device on Polymer Substrate for Electrospray Mass Spectrometry." In Proceedings of SPIE. Microfluidic Devices and Systems II: September 20-21, 1999, Santa Clara, California, vol. 3877, ed. C.H. Ahn and A.B. Frazier, pp. 28-35. SPIE , Bellingham, WA.
Pasa-Tolic L, PK Jensen, GA Anderson, MS Lipton, KK Peden, S Martinovic, N Tolic, JE Bruce, and RD Smith. 1999. "High Throughput Proteome-Wide Precision Measurements of Protein Expression using Mass Spectrometry." Journal of the American Chemical Society 121(34):7949-7950.
Shen Y, F Xiang, TD Veenstra, NK Fung, and RD Smith. 1999. "High-Resolution Capillary Isoelectric Focusing of Complex Protein Mixtures from Lysates of Microogranisms." Analytical Chemistry 71:5348-5353.
Tang K, and RD Smith. 1999. "Theoretical Prediction of Charged Droplet Evaporation and Fission in Electrospray Ionization." International Journal of Mass Spectrometry 185/186/187:97-105.
Bruce JE, GA Anderson, JY Wen, R Harkewicz, and RD Smith. 1999. "High Mass Measurement Accuracy 100% Sequence Coverage of Enzymatically Digested Bovine Serum Albumin from a Single ESI-FTICR Mass Spectrum." Analytical Chemistry 71(14):2595-2599.
Feng B, DS Wunschel, CD Masselon, L Pasa-Tolic, and RD Smith. 1999. "Retrieval of DNA using Soft-Landing after Mass Analysis by ESI-FTICR for Enzymatic Manipulation." Journal of the American Chemical Society 121(38):8961-8962.
Gao J, Q Wu, J Carbeck, QP Lei, RD Smith, and GM Whitesides. 1999. "Probing the Energetics of Dissociation of Carbonic Anhydrase-Ligand Complexes in the Gas Phase." Biophysical Journal 76(6):3253-3260.
Gorshkov MV, L Pasa-Tolic, and RD Smith. 1999. "Pressure Limited Sustained Off-Resonance Irradiation for Collision-Activated Dissociation in Fourier Transform Mass Spectrometry." Journal of the American Society for Mass Spectrometry 10:15-18.
Jensen PK, L Pasa-Tolic, GA Anderson, JA Horner, MS Lipton, JE Bruce, and RD Smith. 1999. "Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 71(11):2076-2084.
Li L, RW Garden, PD Floyd, TP Moroz, JM Gleeson, JV Sweedler, L Pasa-Tolic, and RD Smith. 1999. "Egg-Laying Hormone Peptides in the Aplysiidae Family." Journal of Experimental Biology 202:2961-2973.
Shaffer SA, AV Tolmachev, DC Prior, GA Anderson, HR Udseth, and RD Smith. 1999. "Characterization of an Improved Electrodynamic Ion Funnel Interface for Electrospray Ionization Mass Spectrometry." Analytical Chemistry 71(15):2957-2964.
Xiang F, Y Lin, JY Wen, DW Matson, and RD Smith. 1999. "An Integrated Microfabricated Device for Dual Microdialysis and On-line ESI Ion Trap Mass Spectrometry for the Analysis of Complex Biological Samples." Analytical Chemistry 71(8):1485-1490.
Xu N, L Pasa-Tolic, RD Smith, S Ni, and BD Thrall. 1999. "Electrospray Ionization-Mass Spectrometry Study of the Interaction of Cisplatin-Adducted Oligonucleotides with Human XPA Minimal Binding Domain Protein." Analytical Biochemistry 272(1):26-33.

1998

Lin Y, N Xu, JY Wen, DW Matson, and RD Smith. 1998. "Micro fabricated Dual-Microdialysis and Capillary, Isoelectric Focusing Devices for Cleanup and Separations/Mass Spectrometric Analysis of Biomolecules." In Micro Total Analysis Systems '98; proceedings of the (mu)TAS '98 Workshop, held in Banff, Canada, 13-16 October 1998, ed. D.J. Harrison and A.V. den Berg, pp. 343-346. Kluwer Academic Publishers, Boston, MA.
Shaffer SA, DC Prior, GA Anderson, HR Udseth, and RD Smith. 1998. "An Ion Funnel Interface for Improved Ion Focusing and Sensitivity Using Electrospray Ionization Mass Spectometry." Analytical Chemistry 70(19):4111-4119.
Yang L, CS Lee, SA Hofstadler, and RD Smith. 1998. "Characterization of Microdialysis Acidification for Capillary Isoelectric Focusing Microelectrospray Ionization Mass Spectrometry." Analytical Chemistry 70(23):4945-4950.