Publications
Journal Publications by year
Posters
ASMS posters that describe PNNL research supported by the BER project are available at http://ncrr.pnl.gov/posters/.
2007 Journal Publications
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 (2007).
Sharma S, DC Simpson, N Tolic, N Jaitly, A. M 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 (2007).
2006 Journal Publications
Callister SJ, RC Barry, JN Adkins, ET Johnson, WJ Qian, BJ 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.
Callister SJ, CD Nicora, X Zeng, JH Roh, MA Dominguez, CL Tavano, ME Monroe, S Kaplan, TJ 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.
Ding YH, 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 1764(7):1198-1206.
Elias DA, ME Monroe, RD Smith, J K 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.
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 5(4):714-725.
Ibrahim Y, 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.
Jaitly N, ME Monroe, VA Petyuk, TR 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, DA 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.
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 (2006).
Lipton MS, MF Romine, ME Monroe, DA Elias, L Pasa-Tolic, GA Anderson, DJ Anderson, JFredrickson, KK Hixson, C Masselon, H Mottaz, N Tolic, and RD Smith. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus radiodurans and Shewanella oneidensis." Methods of Biochemical Analysis 49:113-134.
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.
Smith RD. 2006. "Future Directions for Electrospray Ionization for Biological Analysis Using Mass Spectrometry." Biotechniques 41(2):147-148.
Smith RD, K Tang, and Y Shen. 2006. "Ultra-Sensitive and Quantitative Characterization of Proteomes." Molecular Biosystems 2(5):221-230 (2006).
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.
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 Metabolism as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry." Proteomics 6(15):4286-4299.
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.
2005 Journal Publications
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." Proteomics 5(12):3120-3130.
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 USA 102(6):2099-2104.
Havre SL, M Singhal, DA Payne, MS Lipton, and BJ Webb-Robertson. 2005. "Enabling Proteomics Discovery Through Visual Analysis: The Peptide Permutation and Protein Prediction Tool." IEEE Engineering in Medicine and Biology Magazine 24(3):50-57.
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 and RD Smith. 2005. "Proteomic Analyses Using High-Efficiency Separations and Accurate Mass Measurements." In Separation Methods in Proteomics, GB Smejkal and A Lazareu, Editors, CRC Taylor & Francis, New York. Chapter 20, pp. 263-385.
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.
Jacobs JM, M Monroe, WJ 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, D A Elias, YA Gorby, T Holzman, JA Klappenbach, KT Konstantinidis, ML Land, MS Lipton, LA McCue, M Monroe, L Pasa-Tolic, G Pinchuk, S Purvine, MH Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, FW Larimer, CE Lawrence, M Riley, FR Collart, JR Yates III, RD Smith, CS Giometti, KH Nealson, JK 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 their Performance for Proteomics Analyses." Analytical Chemistry 77(15):5028-5035.
Masselon C, L Pasa-Tolic, N Tolic, GA Anderson, B Bogdanov, AN Vilkov, Y Shen, R Zhao, WJ Qian, MS Lipton, DG Camp, and RD Smith. 2005. "Targeted Comparative Proteomics by Liquid Chromatography-Tandem Fourier Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 77(2):400-406 (2005).
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):1215-2122.
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.
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, H 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 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, 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.
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 Measurements." Analytical Chemistry 77(23):7763-7773.
Simpson DC and RD Smith. 2005. "Combining Capillary Electrophoresis with Mass Spectrometry for Applications in Proteomics." Electrophoresis 26(7-8):1291-1305.
Yang F, B Bogdanov, EF Strittmatter, AN Vilkov, M Gritsenko, L Shi, DA Elias, S Ni, M 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 oneidensis Cytochromes Using Mass Spectrometry." Journal of Proteome Research 4(3):846-854.
2004 Journal Publications
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.
Camp DG II and RD Smith. 2004. "The Use of Accurate Mass and Time Tags Based upon High-Throughput Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Global Proteomic Characterization." Chapter 8, pp. 183-224 in: Proteome Analysis: Interpreting the Genome, DW Speicher, Editor, Elsevier, Amsterdam, The Netherlands.
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.
Liu T, WJ Qian, EF Strittmatter, DG Camp, 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." In Capillary Electrophoresis of Proteins and Peptides, MA Strege and AL Lagu, Editors. Methods in Molecular Biology, Volume 276, Chapter 14, pp. 291-304.
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 WJ, 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.
Romine MF, DA Elias, ME Monroe, K 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 8(3):239-254.
Shen Y, N Tolic, C Masselon, L Pasa-Tolic, DG Camp II MS Lipton, GA Anderson, and RD Smith. 2004. "Nanoscale Proteomics." Analytical and Bioanalytical Chemistry 378(4):1037-1045.
Shen Y, N Tolic, CD Masselon, L Pasa-Tolic, DG Camp, 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.
Smith RD, YF Shen, and K Tang. 2004. "Ultrasensitive 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, 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.
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.
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.