Journal Publications by year
- 2007 Journal Publications
- 2006 Journal Publications
- 2005 Journal Publications
- 2004 Journal Publications
Posters
ASMS posters that describe PNNL research supported by the BER project are available at http://ncrr.pnl.gov/posters/.
MicroSPE-nanoLC-ESI-MS/MS using 10-µm-i.d. silica-based monolithic columns for proteomics, Q. Luo, J. S. Page, K. Tang, and R. D. Smith. Anal. Chem., 79 (2), 540-545 (2007).
Proteomic profiling of intact proteins using WAX-RPLC 2-D separations and FTICR mass spectrometry, S. Sharma, D. C. Simpson, N. Tolic, N. Jaitly, A. M. Mayampurath, R. D. Smith, and L. Pasa-Tolic. J. Proteome. Res., 6 (2), 602-610 (2007).
AMT tag approach to proteomic characterization of Deinococcus radiodurans and Shewanella oneidensis, M. S. Lipton, M. F. Romine, M. E. Monroe, D. A. Elias, L. Pasa-Tolic, G. A. Anderson, D. J. Anderson, J. Fredrickson, K. K. Hixson, C. Masselon, H. Mottaz, N. Tolic, and R. D. Smith. Methods Biochem. Anal., 49, 113-134 (2006).
Chemically etched open tubular and monolithic emitters for nanoelectrospray ionization mass spectrometry, R. T. Kelly, J. S. Page, Q. Luo, R. J. Moore, D. J. Orton, K. Tang, and R. D. Smith. Anal. Chem., 78 (22), 7796-7801 (2006).
Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes, S. J. Callister, C. D. Nicora, X. Zeng, J. H. Roh, M. A. Dominguez, C. L. Tavano, M. E. Monroe, S. Kaplan, T. J. Donohue, R. D. Smith, and M. S. Lipton. J. Microbiol. Methods, 67 (3), 424-436 (2006).
Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1, D. A. Elias, M. E. Monroe, R. D. Smith, J. K. Fredrickson, and M. S. Lipton. J. Microbiol. Methods, 66 (2), 223-233 (2006).
Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach, R. Fang, D. A. Elias, M. E. Monroe, Y. Shen, M. McIntosh, P. Wang, C. D. Goddard, S. J. Callister, R. J. Moore, Y. A. Gorby, J. N. Adkins, J. K. Fredrickson, M. S. Lipton, and R. D. Smith. Mol. Cell. Proteomics, 5 (4), 714-725 (2006).
Future directions for electrospray ionization for biological analysis using mass spectrometry, R. D. Smith. Biotechniques, 41 (2), 147-148 (2006).
Improving mass spectrometer sensitivity using a high-pressure electrodynamic ion funnel interface, Y. Ibrahim, K. Tang, A. V. Tolmachev, A. A. Shvartsburg, and R. D. Smith. J. Am. Soc. Mass Spectrom., 17 (9), 1299-1305 (2006).
An IMS-IMS analogue of MS-MS, S. L. Koeniger, S. I. Merenbloom, S. J. Valentine, M. F. Jarrold, H. R. Udseth, R. D. Smith, and D. E. Clemmer. Anal. Chem., 78 (12), 4161-4174 (2006).
LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris, W. Zhang, D. E. Culley, M. A. Gritsenko, R. J. Moore, L. Nie, J. C. Scholten, K. Petritis, E. F. Strittmatter, D. G. Camp, 2nd, R. D. Smith, and F. J. Brockman. Biochem. Biophys. Res. Commun., 349 (4), 1412-1419 (2006).
Mass measurement accuracy in analyses of highly complex mixtures based upon multidimensional recalibration, A. V. Tolmachev, M. E. Monroe, N. Jaitly, V. A. Petyuk, J. N. Adkins, and R. D. Smith. Anal. Chem., 78 (24), 8374-8385 (2006).
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics, S. J. Callister, R. C. Barry, J. N. Adkins, E. T. Johnson, W. J. Qian, B. J. Webb-Robertson, R. D. Smith, and M. S. Lipton. J. Proteome Res., 5 (2), 277-286 (2006).
PRISM: A data management system for high-throughput proteomics, G. R. Kiebel, K. J. Auberry, N. Jaitly, D. A. Clark, M. E. Monroe, E. S. Peterson, N. Tolic, G. A. Anderson, and R. D. Smith. Proteomics, 6 (6), 1783-1790 (2006).
The proteome of dissimilatory metal-reducing microorganism Geobacter sulfurreducens under various growth conditions, Y. H. Ding, K. K. Hixson, C. S. Giometti, A. Stanley, A. Esteve-Nunez, T. Khare, S. L. Tollaksen, W. Zhu, J. N. Adkins, M. S. Lipton, R. D. Smith, T. Mester, and D. R. Lovley. Biochim. Biophys. Acta, 1764 (7), 1198-1206 (2006).
Proteomic approaches to bacterial differentiation, A. D. Norbeck, S. J. Callister, M. E. Monroe, N. Jaitly, D. A. Elias, M. S. Lipton, and R. D. Smith. J. Microbiol. Methods, 67 (3), 473-486 (2006).
A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry, W. Zhang, M. A. Gritsenko, R. J. Moore, D. E. Culley, L. Nie, K. Petritis, E. F. Strittmatter, D. G. Camp, 2nd, R. D. Smith, and F. J. Brockman. Proteomics, 6 (15), 4286-4299 (2006).
Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline, N. Jaitly, M. E. Monroe, V. A. Petyuk, T. R. Clauss, J. N. Adkins, and R. D. Smith. Anal. Chem., 78 (21), 7397-7409 (2006).
Ultra-sensitive and quantitative characterization of proteomes, R. D. Smith, K. Tang, and Y. Shen. Mol. Biosyst., 2 (5), 221-230 (2006).
Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics, Y. Shen, and R. D. Smith. Expert Rev. Proteomics, 2 (3), 431-447 (2005).
Automated 20 Kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics, Y. Shen, R. Zhang, R. J. Moore, J. Kim, T. O. Metz, K. K. Hixson, R. Zhao, E. A. Livesay, H. R. Udseth, and R. D. Smith. Anal. Chem., 77 (10), 3090-3100 (2005).
Automatic gain control in mass spectrometry using a jet disrupter electrode in an electrodynamic ion funnel, J. S. Page, B. Bogdanov, A. N. Vilkov, D. C. Prior, M. A. Buschbach, K. Tang, and R. D. Smith. J. Am. Soc. Mass Spectrom., 16 (2), 244-253 (2005).
Characterization of purified c-type heme-containing peptides and identification of c-type heme-attachment sites in Shewanella oneidenis cytochromes using mass spectrometry, F. Yang, B. Bogdanov, E. F. Strittmatter, A. N. Vilkov, M. Gritsenko, L. Shi, D. A. Elias, S. Ni, M. Romine, L. Pasa-Tolic, M. S. Lipton, and R. D. Smith. J. Proteome Res., 4 (3), 846-854 (2005).
Combining capillary electrophoresis with mass spectrometry for applications in proteomics, D. C. Simpson, and R. D. Smith. Electrophoresis, 26 (7-8), 1291-1305 (2005).
Enabling proteomics discovery through visual analysis. The peptide permutation and protein prediction tool, S. L. Havre, M. Singhal, D. A. Payne, M. S. Lipton, and B. J. Webb-Robertson. IEEE Eng. Med. Biol. Mag., 24 (3), 50-57 (2005).
Evaluation of two-dimensional electrophoresis and liquid chromatography--tandem mass spectrometry for tissue-specific protein profiling of laser-microdissected plant samples, M. Schad, M. S. Lipton, P. Giavalisco, R. D. Smith, and J. Kehr. Electrophoresis, 26 (14), 2729-2738 (2005).
Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics, D. A. Elias, M. E. Monroe, M. J. Marshall, M. F. Romine, A. S. Belieav, J. K. Fredrickson, G. A. Anderson, R. D. Smith, and M. S. Lipton. Proteomics, 5 (12), 3120-3130 (2005).
Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations, E. Kolker, A. F. Picone, M. Y. Galperin, M. F. Romine, R. Higdon, K. S. Makarova, N. Kolker, G. A. Anderson, X. Qiu, K. J. Auberry, G. Babnigg, A. S. Beliaev, P. Edlefsen, D. A. Elias, Y. A. Gorby, T. Holzman, J. A. Klappenbach, K. T. Konstantinidis, M. L. Land, M. S. Lipton, L. A. McCue, M. Monroe, L. Pasa-Tolic, G. Pinchuk, S. Purvine, M. H. Serres, S. Tsapin, B. A. Zakrajsek, W. Zhu, J. Zhou, F. W. Larimer, C. E. Lawrence, M. Riley, F. R. Collart, J. R. Yates, 3rd, R. D. Smith, C. S. Giometti, K. H. Nealson, J. K. Fredrickson, and J. M. Tiedje. Proc. Natl. Acad. Sci., USA, 102 (6), 2099-2104 (2005).
Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans, A. K. Schmid, M. S. Lipton, H. Mottaz, M. E. Monroe, R. D. Smith, and M. E. Lidstrom. J. Proteome Res., 4 (3), 709-718 (2005).
Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurements, Y. Shen, E. F. Strittmatter, R. Zhang, T. O. Metz, R. J. Moore, F. Li, H. R. Udseth, R. D. Smith, K. K. Unger, D. Kumar, and D. Lubda. Anal. Chem., 77 (23), 7763-7773 (2005).
Preparation of 20-µm-i.d. silica-based monolithic columns and their performance for proteomics analyses, Q. Luo, Y. Shen, K. K. Hixson, R. Zhao, F. Yang, R. J. Moore, H. M. Mottaz, and R. D. Smith. Anal. Chem., 77 (15), 5028-5035 (2005).
Proteomic analyses using high-efficiency separations and accurate mass measurements, J. M. Jacobs, and R. D. Smith, Eds. Separation Methods in Proteomics, Marcel-Dekker Inc., New York (2005).
Proteomic analysis of Lyme disease: global protein comparison of three strains of Borrelia burgdorferi, J. M. Jacobs, X. Yang, B. J. Luft, J. J. Dunn, D. G. Camp, 2nd, and R. D. Smith. Proteomics, 5 (5), 1446-1453 (2005).
Proteomics by FTICR mass spectrometry: top down and bottom up, B. Bogdanov, and R. D. Smith. Mass Spectrom. Rev., 24 (2), 168-200 (2005).
Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns, Y. Huang, J. M. Triscari, G. C. Tseng, L. Pasa-Tolic, M. S. Lipton, R. D. Smith, and V. H. Wysocki. Anal. Chem, 77 (18), 5800-5813 (2005).
Targeted comparative proteomics by liquid chromatography-tandem Fourier ion cyclotron resonance mass spectrometry, C. Masselon, L. Pasa-Tolic, N. Tolic, G. A. Anderson, B. Bogdanov, A. N. Vilkov, Y. Shen, R. Zhao, W. J. Qian, M. S. Lipton, D. G. Camp, and R. D. Smith. Anal. Chem., 77 (2), 400-406 (2005).
Ultra-sensitive, high-throughput and quantitative proteomics measurements, J. M. Jacobs, M. Monroe, W. J. Qian, Y. Shen, G. A. Anderson, and R. D. Smith. Int. J. Mass Spectrom., 240 (3), 195-212 (2005).
The utility of accurate mass and LC elution time information in the analysis of complex proteomes, A. D. Norbeck, M. E. Monroe, J. N. Adkins, K. K. Anderson, D. S. Daly, and R. D. Smith. J. Am. Soc. Mass Spectrom., 16 (8), 1239-1249 (2005).
Variable low-mass filtering using an electrodynamic ion funnel, J. S. Page, A. V. Tolmachev, K. Tang, and R. D. Smith. J. Mass Spectrom., 40 (9), 1215-2122 (2005).
Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry, E. F. Strittmatter, L. J. Kangas, K. Petritis, H. M. Mottaz, G. A. Anderson, Y. Shen, J. M. Jacobs, D. G. Camp, and R. D. Smith. J. Proteome Res., 3 (4), 760-769 (2004).
An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics, M. E. Belov, G. A. Anderson, M. A. Wingerd, H. R. Udseth, K. Tang, D. C. Prior, K. R. Swanson, M. A. Buschbach, E. F. Strittmatter, R. J. Moore, and R. D. Smith. J. Am. Soc. Mass Spectrom., 15 (2), 212-232 (2004).
Capillary isoelectric focusing--mass spectrometry of proteins and protein complexes, S. Martinovic, L. Pasa-Tolic, and R. D. Smith. Methods Mol. Biol., 276, 291-304 (2004).
Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry, K. Tang, J. S. Page, and R. D. Smith. J. Am. Soc. Mass Spectrom., 15, 1416-1423 (2004).
Collisional activation of ions in RF ion traps and ion guides: the effective ion temperature treatment, A. V. Tolmachev, A. N. Vilkov, B. Bogdanov, L. Pasa-Tolic, C. D. Masselon, and R. D. Smith. J. Am. Soc. Mass Spectrom., 15 (11), 1616-1628 (2004).
Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots, Y. Huang, J. M. Triscari, L. Pasa-Tolic, G. A. Anderson, M. S. Lipton, R. D. Smith, and V. H. Wysocki. J. Am. Chem. Soc., 126 (10), 3034-3035 (2004).
FTICR mass spectrometry for qualitative and quantitative bioanalyses, J. S. Page, C. D. Masselon, and R. D. Smith. Curr. Opin. Biotechnol., 15 (1), 3-11 (2004).
High-throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology, T. Liu, W. J. Qian, E. F. Strittmatter, D. G. Camp, G. A. Anderson, B. D. Thrall, and R. D. Smith. Anal. Chem., 76 (18), 5345-5353 (2004).
High-throughput proteomics using Fourier transform ion cyclotron resonance mass spectrometry, W. J. Qian, D. G. Camp, 2nd, and R. D. Smith. Expert Rev. Proteomics, 1 (1), 87-95 (2004).
Nanoscale proteomics, Y. Shen, N. Tolic, C. Masselon, L. Pasa-Tolic, D. G. Camp, 2nd, M. S. Lipton, G. A. Anderson, and R. D. Smith. Anal. Bioanal. Chem., 378 (4), 1037-1045 (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, A. N. Vilkov, B. Bogdanov, L. Pasa-Tolic, D. C. Prior, G. A. Anderson, C. D. Masselon, R. J. Moore, and R. D. Smith. Rapid Commun. Mass Spectrom., 18 (22), 2682-2690 (2004).
Ultra-sensitive proteomics using high-efficiency on-line microSPE-nanoLC-nanoESI MS and MS/MS, Y. Shen, N. Tolic, C. D. Masselon, L. Pasa-Tolic, D. G. Camp, K. K. Hixson, R. Zhao, G. A. Anderson, and R. D. Smith. Anal. Chem., 76, 144-154 (2004).
Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes, R. D. Smith, Y. F. Shen, and K. Tang. Acc. Chem. Res., 37 (4), 269-278 (2004).
The use of accurate mass and time tags based upon high-throughput Fourier transform ion cyclotron resonance mass spectrometry for global proteomic characterization, D. G. Camp, 2nd, and R. D. Smith, Eds. Proteome Analysis: Interpreting the Genome, Elsevier B.V., Amsterdam, The Netherlands (2004).
Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis, M. F. Romine, D. A. Elias, M. E. Monroe, K. Auberry, R. Fang, J. K. Fredrickson, G. A. Anderson, R. D. Smith, and M. S. Lipton. OMICS, 8 (3), 239-254 (2004).
