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Staff information

Richard

Richard Smith

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

Biography

As a Battelle Fellow and Chief Scientist within the Biological Sciences Division, Dr. Smith's research interests span development of advanced analytical methods and instrumentation, with particular emphasis on high-resolution separations and mass spectrometry, and their applications in biological and biomedical research. Over the last 20 years, much of Dr. Smith's research has centered on creating and applying new ultra-sensitive technologies to quantitatively probe entire proteomes expressed by cells, tissues, and organisms. In the last decade, these efforts have broadened to include development and application of highly sensitive, high-throughput technologies for measuring the "pan-ome" (also including the metabolome, lipidome, and glycome) to augment biological research. To enable much more effective pan-omics applications, he has recently been leading the development of novel Structures for Lossless Ion Manipulations (SLIM) and their use for very-high-throughput sample processing, reactions, separations, and other manipulations of ions in the gas phase, and particularly in conjunction with mass spectrometry.

Dr. Smith also is Director of Proteome Research at PNNL, Director of the NIH Research Resource for Integrative Biology, an adjunct faculty member in the chemistry departments at Washington State University and the University of Utah, and an affiliate faculty member in the Department of Chemistry at the University of Idaho and the Department of Molecular Microbiology & Immunology at Oregon Health & Science University. Dr. Smith completed his Ph.D. work in Physical Chemistry at the University of Utah.

Dr. Smith is the author/co-author of approximately 1000 peer-reviewed journal articles and is the recipient of 50 patents and 10 R&D 100 Awards.

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
  • Affiliate Professor, Department of Molecular Microbiology & Immunology, Oregon Health & Science University

Awards and Recognitions

  • American Society for Mass Spectrometry Distinguished Contribution in Mass Spectrometry Award (2013)
  • R&D Magazine 2010 Scientist of the Year
  • Ten R&D 100 Awards:
    • Combined Orthogonal Mobility & Mass Evaluation Technology (2013)
    • Ion Mobility Spectrometer on a Microchip (2010)
    • Ultrasensitive Electrospray Ionization Mass Spectrometry Source and Interface (2009)
    • Development of the FT-MS Proteome Express (2003)
    • Electrodynamic Ion Funnel (1999)
    • Rapid Microdialyzer (1998)
    • MICLEAN/MICARE Process (1998)
    • Rapid Expansion of Supercritical Fluid Solutions Process (1988)
    • Capillary Electrophoresis-Electrospray Ionization-MS (1988). Named among top 40 R&D 100 Awards of all time.
    • Development of Supercritical Fluid Chromatography-MS (1983)
  • Federal Laboratory Consortium Award for the Electrodynamic Ion Funnel (2004)
  • Elected Fellow, American Association for the Advancement of Science (2007)
  • Wiley Research Fellow, Environmental Molecular Sciences Laboratory
  • Eastern Analytical Symposium Award for Outstanding Achievements in the Fields of Analytical Chemistry (2010)
  • Elected to Washington State Academy of Sciences
  • Gordon Battelle Prize for Scientific Discovery
  • HUPO Discovery Award in Proteomic Sciences (2009)
  • Council of the Human Proteome Organization (HUPO) 2007-2016
  • Scientific American 50--shared with Dr. Desmond Smith, University of California at Los Angeles, for their work on understanding the human brain (2007)
  • 2003 ACS Award for Analytical Chemistry
  • American Oil Chemists Society Award
  • Battelle-Northwest Director's Award for Excellence
  • AWU-DOE Distinguished Lecturer
  • 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

2014

  • Aryal UK, SJ Callister, BH McMahon, LA McCue, JN Brown, J Stockel, ML Liberton, S Mishra, X Zhang, CD Nicora, TE Angel, DW Koppenaal, RD Smith, HB Pakrasi, and LA Sherman. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13(7):3262-3276.  doi:10.1021/pr5000889
  • Fujimoto GM, ME Monroe, LM Rodriguez, C Wu, B MacLean, RD Smith, M MacCoss, and SH Payne. 2014. "Accounting for population variation in targeted proteomics." Journal of Proteome Research 13(1):321-323.  doi:10.1021/pr4011052
  • Marginean I, K Tang, RD Smith, and RT Kelly. 2014. "Picoelectrospray Ionization Mass Spectrometry Using Narrow-bore Chemically Etched Emitters." Journal of the American Society for Mass Spectrometry 25(1):30-36.  doi:10.1007/s13361-013-0749-z
  • Shvartsburg AA, YM Ibrahim, and RD Smith. 2014. "Differential Ion Mobility Separations in up to 100% Helium Using Microchips." Journal of the American Society for Mass Spectrometry 25(3):480-489.  doi:10.1007/s13361-013-0797-4
  • Slysz GW, LA Steinke, DM Ward, CG Klatt, TRW Clauss, SO Purvine, SH Payne, GA Anderson, RD Smith, and MS Lipton. 2014. "Automated data extraction from in situ protein stable isotope probing studies." Journal of Proteome Research 13(3):1200-1210.  doi:10.1021/pr400633j
  • Webb IK, TC Chen, WF Danielson, III, YM Ibrahim, K Tang, GA Anderson, and RD Smith. 2014. "Implementation of Dipolar Resonant Excitation Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS." Journal of the American Society for Mass Spectrometry 25(4):563-571.  doi:10.1007/s13361-013-0815-6
  • Wiedner SD, LN Anderson, NC Sadler, WB Chrisler, VK Kodali, RD Smith, and AT Wright. 2014. "Organelle-Specific Activity-Based Protein Profiling in Living Cells." Angewandte Chemie International Edition 53(11):2919-2922.  doi:10.1002/anie.201309135
  • Amidan BG, DJ Orton, BL Lamarche, ME Monroe, RJ Moore, AM Venzin, RD Smith, LH Sego, MF Tardiff, and SH Payne. 2014. "Signatures for Mass Spectrometry Data Quality." Journal of Proteome Research 13(4):2215-2222.  doi:10.1021/pr401143e
  • Baker ES, KE Burnum-Johnson, JM Jacobs, DL Diamond, RN Brown, YM Ibrahim, DJ Orton, PD Piehowski, DE Purdy, RJ Moore, WF Danielson, III, ME Monroe, KL Crowell, GW Slysz, MA Gritsenko, JD Sandoval, BL Lamarche, MM Matzke, BJM Webb-Robertson, BC Simons, BJ McMahon, R Bhattacharya, JD Perkins, RL Carithers, S Strom, S Self, MG Katze, GA Anderson, and RD Smith. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics 13(4):1119-1127.  doi:10.1074/mcp.M113.034595
  • Depuydt GG, F Xie, VA Petyuk, A Smolders, HM Brewer, DG Camp, II, RD Smith, and BP Braeckman. 2014. "LC-MS Proteomics Analysis of the Insulin/IGF-1 Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism." Journal of Proteome Research 13(4):1938-1956.  doi:10.1021/pr401081b
  • Depuydt GG, F Xie, VA Petyuk, A Smolders, HM Brewer, DG Camp, II, RD Smith, and BP Braeckman. 2014. "LC-MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism." Journal of Proteome Research 13(4):1938-1956.  doi:10.1021/pr401081b
  • Granholm V, S Kim, JC Navarro, E Sjolund, RD Smith, and L Kall. 2014. "Fast and accurate database searches with MS-GF+Percolator." Journal of Proteome Research 13(2):890-897.  doi:10.1021/pr400937n
  • Guo J, MJ Gaffrey, D Su, T Liu, DG Camp, II, RD Smith, and W Qian. 2014. "Resin-assisted enrichment of thios as a general strategy for proteomic profiling of cysteine-based reversible modifications." Nature Protocols 9(1):64-75.  doi:10.1038/nprot.2013.161
  • Ibrahim YM, VBS Garimella, AV Tolmachev, ES Baker, and RD Smith. 2014. "Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel-Trap." Analytical Chemistry 86(11):5295-5299.  doi:10.1021/ac404250z
  • Kronewitter SR, GW Slysz, I Marginean, CD Hagler, BL Lamarche, R Zhao, MY Harris, ME Monroe, CA Polyukh, KL Crowell, TL Fillmore, TS Carlson, DG Camp, II, RJ Moore, SH Payne, GA Anderson, and RD Smith. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86(13):6268-6276.  doi:10.1021/ac501492f
  • Malouli D, SG Hansen, ES Nakayasu, EE Marshall, CM Hughes, AB Ventura, RM Gilbride, MS Lewis, G Xu, CN Kreklywich, N Whizin, M Fischer, AW Legasse, K Viswanathan, D Siess, DG Camp, II, MK Axthelm, C Kahl, VR DeFilippis, RD Smith, DN Streblow, LJ Picker, and K Fruh. 2014. "Cytomegalovirus pp65 limits dissemination but is dispensable for persistence." Journal of Clinical Investigation 124(5):1928-1944.  doi:10.1172/JCI67420
  • Menachery V, AJ Eisfeld, A Schafer, L Josset, AC Sims, S Proll, S Fan, C Li, G Neumann, SC Tilton, JH Chang, L Gralinski, C Long, R Green, CM Williams, JM Weiss, MM Matzke, BJM Webb-Robertson, AA Schepmoes, AK Shukla, TO Metz, RD Smith, KM Waters, MG Katze, Y Kawaoka, and R Baric. 2014. "Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-Stimulated Gene Responses." mBio 5(3):Article No. e01174-14.  doi:10.1128/mBio.01174-14
  • Merkley ED, TO Metz, RD Smith, J Baynes, and N Frizell. 2014. "The Succinated Proteome." Mass Spectrometry Reviews 33(22):98-109.  doi:10.1002/mas.21382
  • Sadler NC, MR Melnicki, MH Serres, ED Merkley, WB Chrisler, EA Hill, MF Romine, S Kim, EM Zink, S Datta, RD Smith, AS Beliaev, A Konopka, and AT Wright. 2014. "Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium." ACS Chemical Biology 9(1):291-300.  doi:10.1021/cb400769v
  • Shi T, Y Gao, SI Quek, TL Fillmore, CD Nicora, D Su, R Zhao, KD Rodland, T Liu, RD Smith, DW Chan, DG Camp, II, AY Liu, and W Qian. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13(2):875-882.  doi:10.1021/pr400912c
  • Sigdel TK, N Salomonis, CD Nicora, S Ryu, J He, V Dinh, DJ Orton, RJ Moore, SC Hsieh, H Dai, M Thien-Vu, W Xiao, RD Smith, W Qian, DG Camp, II, and MM Sarwal. 2014. "The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics." Molecular & Cellular Proteomics. MCP 13(2):621-631.  doi:10.1074/mcp.M113.030577
  • Smith JS, TE Angel, C Chavkin, DJ Orton, RJ Moore, and RD Smith. 2014. "Characterization of individual mouse cerebrospinal fluid proteomes." Proteomics 14(9):1102-1106.  doi:10.1002/pmic.201300241
  • Su D, MJ Gaffrey, J Guo, KE Hatchell, RK Chu, TRW Clauss, JT Aldrich, S Wu, SO Purvine, DG Camp, II, RD Smith, BD Thrall, and W Qian. 2014. "Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling." Free Radical Biology & Medicine 67:460-470.  doi:10.1016/j.freeradbiomed.2013.12.004
  • Wu S, JN Brown, N Tolic, D Meng, X Liu, H Zhang, R Zhao, RJ Moore, PA Pevzner, RD Smith, and L Pasa-Tolic. 2014. "Quantitative Analysis of Human Salivary Gland-Derived Intact Proteome Using Top-Down Mass Spectrometry." Proteomics 14(10):1211-1222.  doi:10.1002/pmic.201300378
  • Zaborin A, J Defazio, M Kade, BLD Kaiser, N Belogortseva, DG Camp, II, RD Smith, JN Adkins, SM Kim, A Alverdy, D Goldfeld, M Firestone, J Collier, B Jabri, M Tirrell, O Zaborina, and JC Alverdy. 2014. "Phosphate-Containing Polyethylene Glycol Polymers Prevent Lethal Sepsis by Multidrug-Resistant Pathogens." Antimicrobial Agents and Chemotherapy 58(2):966.  doi:10.1128/AAC.02183-13
  • Zhang Q, MM Matzke, AA Schepmoes, RJ Moore, BJM Webb-Robertson, Z Hu, ME Monroe, W Qian, RD Smith, and WF Morgan. 2014. "High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model." PLoS One 9(3):Article No. e92332.  doi:10.1371/journal.pone.0092332

2013

  • Anderson LN, DE Culley, BA Hofstad, LM Chauvigne-Hines, EM Zink, SO Purvine, RD Smith, SJ Callister, JM Magnuson, and AT Wright. 2013. "Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30." Molecular Biosystems 9(12):2992-3000.  doi:10.1039/c3mb70333a
  • Ansong C, C Ortega, SH Payne, DH Haft, LM Chauvigne-Hines, MP Lewis, AR Ollodart, SO Purvine, AK Shukla, S Fortuin, RD Smith, JN Adkins, C Grundner, and AT Wright. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20(1):123-133.  doi:10.1016/j.chembiol.2012.11.008
  • Ansong C, S Wu, D Meng, X Liu, HM Brewer, BLD Kaiser, ES Nakayasu, JR Cort, PA Pevzner, RD Smith, F Heffron, JN Adkins, and L Pasa-Tolic. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions." Proceedings of the National Academy of Sciences of the United States of America 110(25):10153-10158.  doi:10.1073/pnas.1221210110
  • Aryal UK, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, and L Sherman. 2013. "Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions Resulting in Enhanced H-2 Production." Applied and Environmental Microbiology 79(4):1070-1077.  doi:10.1128/AEM.02864-12
  • Kim YM, B Schmidt, AS Kidwai, MB Jones, BL Deatherage, HM Brewer, HD Mitchell, BO Palsson, JE McDermott, F Heffron, RD Smith, SN Peterson, C Ansong, DR Hyduke, TO Metz, and JN Adkins. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9(6):1522-1534.  doi:10.1039/C3MB25598K
  • Piehowski PD, VA Petyuk, DJ Orton, F Xie, RJ Moore, M Ramirez Restrepo, A Engel, AP Lieberman, RL Albin, DG Camp, II, RD Smith, and AJ Myers. 2013. "Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis." Journal of Proteome Research 12(5):2128-2137.  doi:10.1021/pr301146m
  • Piehowski PD, VA Petyuk, JD Sandoval, KE Burnum, GR Kiebel, ME Monroe, GA Anderson, DG Camp, II, and RD Smith. 2013. "STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results." Proteomics 13(5):766-770.  doi:10.1002/pmic.201200096
  • Shvartsburg AA, and RD Smith. 2013. "High-Resolution Differential Ion Mobility Spectrometry of a Protein." Analytical Chemistry 85(1):10-13.  doi:10.1021/ac3029129
  • Shvartsburg AA, and RD Smith. 2013. "Separation of Protein Conformers by Differential Ion Mobility in Hydrogen-Rich Gases." Analytical Chemistry 85(14):6967-6973.  doi:10.1021/ac4015963
  • Shvartsburg AA, GA Anderson, and RD Smith. 2013. "Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS." Mass Spectrometry Society of Japan. Journal 2:Article No. S0011.  doi:10.5702/massspectrometry.S0011
  • Sun X, K Tang, RD Smith, and RT Kelly. 2013. "Controlled Dispensing and Mixing of Pico- to Nanoliter Volumes Using On-Demand Droplet-Based Microfluidics." Microfluidics and Nanofluidics 15(1):117-126.  doi:10.1007/s10404-012-1133-1
  • Wiedner SD, C Ansong, BJM Webb-Robertson, LM Pederson, S Fortuin, BA Hofstad, AK Shukla, EA Panisko, RD Smith, and AT Wright. 2013. "Disparate Proteome Responses of Pathogenic and Non-pathogenic Aspergilli to Human Serum Measured by Activity-Based Protein Profiling (ABPP)." Molecular & Cellular Proteomics. MCP 12(7):1791-1805.  doi:10.1074/mcp.M112.026534
  • Ansong C, AC Rutledge, HD Mitchell, S Chauhan, MB Jones, YM Kim, K Mcateer, BL Deatherage, JL DuBois, HM Brewer, BC Frank, JE McDermott, TO Metz, SN Peterson, RD Smith, VL Motin, and JN Adkins. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9(1):44-54.  doi:10.1039/C2MB25287B
  • Aylward FO, KE Burnum-Johnson, SG Tringe, C Teiling, D Tremmel, J Moeller, JJ Scott, KW Barry, PD Piehowski, CD Nicora, S Malfatti, ME Monroe, SO Purvine, LA Goodwin, RD Smith, G Weinstock, N Gerardo, G Suen, MS Lipton, and CR Currie. 2013. "Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens." Applied and Environmental Microbiology 79(12):3770-3778.  doi:10.1128/AEM.03833-12
  • Conlon BP, ES Nakayasu, LE Fleck, MD LaFleur, VM Isabella, K Coleman, SN Leonard, RD Smith, JN Adkins, and K Lewis. 2013. "Activated ClpP kills persisters and eradicates a chronic biofilm infection." Nature 503(7476):365-370.  doi:10.1038/nature12790
  • Crowell KL, ES Baker, SH Payne, YM Ibrahim, ME Monroe, GW Slysz, BL Lamarche, VA Petyuk, PD Piehowski, WF Danielson, III, GA Anderson, and RD Smith. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry 354-355:312-317.  doi:10.1016/j.ijms.2013.06.028
  • Crowell KL, GW Slysz, ES Baker, BL Lamarche, ME Monroe, YM Ibrahim, SH Payne, GA Anderson, and RD Smith. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29(21):2804-2805 .  doi:10.1093/bioinformatics/btt465
  • Dai Z, UK Aryal, AK Shukla, W Qian, RD Smith, JK Magnuson, WS Adney, GT Beckham, R Brunecky, ME Himmel, SR Decker, X Ju, X Zhang, and SE Baker. 2013. "Impact of alg3 gene deletion on growth, development, pigment production, protein secretion, and functions of recombinant Trichoderma reesei cellobiohydrolases in Aspergillus niger." Fungal Genetics and Biology : FG & B 61:120-132.  doi:10.1016/j.fgb.2013.09.004
  • Depuydt GG, F Xie, VA Petyuk, N Shanmugam, A Smolders, I Dhondt, HM Brewer, DG Camp, II, RD Smith, and BP Braeckman. 2013. "Reduced insulin/Insulin-like Growth Factor-1signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans." Molecular and Cellular Proteomics 12(12):3624-3639.  doi:10.1074/mcp.M113.027383
  • Ellis M, M Gillette, SA Carr, AG Paulovich, RD Smith, KD Rodland, R Townsend, C Kinsinger, M Mesri, H Rodriguez, and D Liebler. 2013. "Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium ." Cancer Discovery 3(10):1108-1112.  doi:10.1158/2159-8290.CD-13-0219
  • Finnerty CC, MG Jeschke, W Qian, A Kaushal, W Xiao, T Liu, MA Gritsenko, RJ Moore, DG Camp, II, LL Moldawer, C Elson, D Schoenfeld, R Gamelli, N Gibran, M Klein, B Arnoldo, D Remick, RD Smith, RW Davis, RG Tompkins, and DN Herndon. 2013. "DETERMINATION OF BURN PATIENT OUTCOME BY LARGE-SCALE QUANTITATIVE DISCOVERY PROTEOMICS." Critical Care Medicine 41(6):1421-1434.  doi:10.1097/CCM.0b013e31827c072e
  • Gibbs DL, A Baratt, R Baric, Y Kawaoka, RD Smith, ES Orwoll, MG Katze, and SK Mcweeney. 2013. "Protein Co-Expression Network Analysis (ProCoNA)." Journal of Clinical Bioinformatics 3:Article No. 11.  doi:10.1186/2043-9113-3-11
  • Gralinski L, A Bankhead, S Jeng, V Menachery, S Proll, S Belisle, MM Matzke, BJM Webb-Robertson, ML Luna, AK Shukla, MT Ferris, M Bolles, JH Chang, LD Aicher, KM Waters, RD Smith, TO Metz, GL Law, MG Katze, SK Mcweeney, and R Baric. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 4(4):Article No. e00271-13.  doi:10.1128/mBio.00271-13
  • Kaiser BLD, J Li, JA Sanford, YM Kim, SR Kronewitter, MB Jones, C Peterson, SN Peterson, BC Frank, SO Purvine, JN Brown, TO Metz, RD Smith, F Heffron, and JN Adkins. 2013. "A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection." PLoS One 8(6):Article No. e67155.  doi:10.1371/journal.pone.0067155
  • Kim JS, ME Monroe, DG Camp, II, RD Smith, and W Qian. 2013. "In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics." Journal of Proteome Research 12(2):910-916.  doi:10.1021/pr300955f
  • Kim JS, Z Dai, UK Aryal, RJ Moore, DG Camp, II, SE Baker, RD Smith, and W Qian. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing." Analytical Chemistry 85(14):6826-6832.  doi:10.1021/ac401000q
  • Lamarche BL, KL Crowell, N Jaitly, VA Petyuk, AR Shah, AD Polpitiya, JD Sandoval, GR Kiebel, ME Monroe, SJ Callister, TO Metz, GA Anderson, and RD Smith. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14:Article No. 49.  doi:10.1186/1471-2105-14-49
  • Latif H, JA Lerman, VA Portnoy, Y Tarasova, H Nagarajan, AC Rutledge, RD Smith, JN Adkins, DH Lee, Y Qiu, and K Zengler. 2013. "The Genome Organization of Thermotoga maritima Reflects Its Lifestyle." PLoS Genetics 9(4):Article No. e1003485.  doi:10.1371/journal.pgen.1003485
  • Matzke MM, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, and BJM Webb-Robertson. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13(3-4):493-503.  doi:10.1002/pmic.201200269
  • Merkley ED, ES Baker, KL Crowell, DJ Orton, T Taverner, C Ansong, YM Ibrahim, MC Burnet, JR Cort, GA Anderson, RD Smith, and JN Adkins. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking ." Journal of the American Society for Mass Spectrometry 24(3):444-449.  doi:10.1007/s13361-012-0565-x
  • Mitchell HD, AJ Eisfeld, A Sims, JE McDermott, MM Matzke, BJM Webb-Robertson, SC Tilton, N Tchitchek, L Josset, C Li, AL Ellis, JH Chang, RA Heegel, ML Luna, AA Schepmoes, AK Shukla, TO Metz, G Neumann, A Benecke, RD Smith, R Baric, Y Kawaoka, MG Katze, and KM Waters. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8(7):e69374.  doi:10.1371/journal.pone.0069374
  • Nakayasu ES, C Ansong, JN Brown, F Yang, D Lopez-Ferrer, W Qian, RD Smith, and JN Adkins. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry 24(8):1214-1223.  doi:10.1007/s13361-013-0619-8
  • Nakayasu ES, R Tempel, XA Cambronne, VA Petyuk, MB Jones, MA Gritsenko, ME Monroe, F Yang, RD Smith, JN Adkins, and F Heffron. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Molecular and Cellular Proteomics 12(11):3297-3309.  doi:10.1074/mcp.M113.029850
  • Nakayasu ES, RN Brown, C Ansong, MA Sydor, S Imtiaz, C Mihai, RL Sontag, KK Hixson, ME Monroe, T Sobreira, G Orr, VA Petyuk, F Yang, RD Smith, and JN Adkins. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12(8):2136-2147.  doi:10.1074/mcp.M112.026138
  • Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ." Proteomics 13(18-19):2776-2785.  doi:10.1002/pmic.201300003
  • Niemann G, RN Brown, IT Mushamiri, NT Nguyen, R Taiwo, A Stufkens, RD Smith, JN Adkins, JE McDermott, and F Heffron. 2013. "RNA Type III Secretion Signals that require Hfq." Journal of Bacteriology 195(10):2119-2125.  doi:10.1128/JB.00024-13
  • Pincus DE, C Ryan, RD Smith, R Brent, and O Resnekov. 2013. "Assigning quantitative function to post---translational modifications reveals multiple sites of phosphorylation that tune yeast pheromone signaling output." PLoS One 8(3):Article No. e56544.  doi:10.1371/journal.pone.0056544
  • Price RW, J Peterson, D Fuchs, TE Angel, H Zetterberg, L Hagberg, SS Spudich, RD Smith, JM Jacobs, JN Brown, and M Gisslen. 2013. "Approach to Cerebrospinal Fluid (CSF) Biomarker Discovery and Evaluation in HIV Infection." Journal of Neuroimmune Pharmacology 8(5):1147-1158.  doi:10.1007/s11481-013-9491-3
  • Schutzer SE, TE Angel, T Liu, AA Schepmoes, F Xie, JP Bergquist, L Vecsei, D Zadori, DG Camp, II, BK Holland, RD Smith, and PK Coyle. 2013. "Gray Matter Is Targeted in First-Attack Multiple Sclerosis." PLoS One 8(9):E6617.  doi:10.1371/journal.pone.0066117
  • Shi T, TL Fillmore, Y Gao, R Zhao, J He, AA Schepmoes, CD Nicora, C Wu, JL Chambers, RJ Moore, J Kagan, S Srivastava, AY Liu, KD Rodland, T Liu, DG Camp, II, RD Smith, and W Qian. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85(19):9196-9203.  doi:10.1021/ac402105s
  • Shi T, X Sun, Y Gao, TL Fillmore, AA Schepmoes, R Zhao, J He, RJ Moore, J Kagan, KD Rodland, T Liu, AY Liu, RD Smith, K Tang, DG Camp, II, and W Qian. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12(7):3353-3361.  doi:10.1021/pr400178v
  • Shvartsburg AA, TA Seim, WF Danielson, III, RV Norheim, RJ Moore, GA Anderson, and RD Smith. 2013. "High-Definition Differential Ion Mobility Spectrometry with Resolving Power up to 500." Journal of the American Society for Mass Spectrometry 24(1):109-114.  doi:10.1007/s13361-012-0517-5
  • Sims AC, SC Tilton, V Menachery, L Gralinski, A Schafer, MM Matzke, BJM Webb-Robertson, JH Chang, ML Luna, C Long, AK Shukla, A Bankhead, S Burkett, G Zornester, CK Tseng, TO Metz, R Pickles, SK Mcweeney, RD Smith, MG Katze, KM Waters, and R Baric. 2013. "Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells." Journal of Virology 87(7):3885-902.  doi:10.1128/JVI.02520-12
  • Su D, AK Shukla, B Chen, JS Kim, ES Nakayasu, Y Qu, UK Aryal, KK Weitz, TRW Clauss, ME Monroe, DG Camp, II, DJ Bigelow, RD Smith, RN Kulkarni, and W Qian. 2013. "Quantitative Site-specific Reactivity Profiling of S-Nitrosylation in Mouse Skeletal Muscle Using Cysteinyl Peptide Enrichment Coupled with Mass Spectrometry." Free Radical Biology & Medicine 57:68-78.  doi:10.1016/j.freeradbiomed.2012.12.010
  • Tchitchek N, AJ Eisfeld, J Tisoncik-Go, L Josset, L Gralinski, C Becavin, SC Tilton, BJM Webb-Robertson, MT Ferris, AL Totura, C Li, G Neumann, TO Metz, RD Smith, KM Waters, R Baric, Y Kawaoka, and MG Katze. 2013. "Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice." BMC Systems Biology 7:Article No. 69.  doi:10.1186/1752-0509-7-69
  • Wang CC, CS Lee, RD Smith, and K Tang. 2013. "Capillary Isotachophoresis-Nanoelectrospray Ionization-Selected Reaction Monitoring MS via a Novel Sheathless Interface for High Sensitivity Sample Quantification." Analytical Chemistry 85(15):7308-7315.  doi:10.1021/ac401202c
  • Zhang Q, TL Fillmore, AA Schepmoes, TRW Clauss, MA Gritsenko, PW Mueller, M Rewers, MA Atkinson, RD Smith, and TO Metz. 2013. "Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes." The Journal of Experimental Medicine 210(1):191-203.  doi:10.1084/jem.20111843
  • Zhou J, RK Krovvidi, Y Gao, H Gao, BO Petritis, A De, C Miller-Graziano, PE Bankey, VA Petyuk, CD Nicora, TRW Clauss, RJ Moore, T Shi, JN Brown, A Kaushal, W Xiao, RW Davis, RV Maier, RG Tompkins, W Qian, DG Camp, II, and RD Smith. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7(7-8):571-583.  doi:10.1002/prca.201200109

2012

  • Baker ES, T Liu, VA Petyuk, KE Burnum-Johnson, YM Ibrahim, GA Anderson, and RD Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4:Article No. 63.  doi:10.1186/gm364
  • Gao X, Q Zhang, D Meng, G Isaac, R Zhao, TL Fillmore, RK Chu, J Zhou, K Tang, Z Hu, RJ Moore, RD Smith, MG Katze, and TO Metz. 2012. "A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling." Analytical and Bioanalytical Chemistry 402(9):2923-2933. 
  • Marginean I, SR Kronewitter, RJ Moore, GW Slysz, ME Monroe, GA Anderson, K Tang, and RD Smith. 2012. "Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure." Analytical Chemistry 84(21):9208-9213.  doi:10.1021/ac301961u
  • Shen Y, N Tolic, SO Purvine, and RD Smith. 2012. "Improving Collision Induced Dissociation (CID), High Energy Collision Dissociation (HCD), and Electron Transfer Dissociation (ETD) Fourier Transform MS/MS Degradome-Peptidome Identifications Using High Accuracy Mass Information." Journal of Proteome Research 11(2):668-677. 
  • Shvartsburg AA, and RD Smith. 2012. "Protein Analyses Using Differential Ion Mobility Microchips with Mass Spectrometry." Analytical Chemistry 84(17):7297-7300.  doi:10.1021/ac3018636
  • Shvartsburg AA, Y Zheng, RD Smith, and N Kelleher. 2012. "Ion Mobility Separation of Variant Histone Tails Extending to the "Middle-down" Range ." Analytical Chemistry 84(10):4271-4276.  doi:10.1021/ac300612y
  • Shvartsburg AA, Y Zheng, RD Smith, and N Kelleher. 2012. "Separation of Variant Methylated Histone Tails by Differential Ion Mobility." Analytical Chemistry 84(15):6317-6320.  doi:10.1021/ac301541r
  • Smith RD. 2012. "Mass spectrometry in biomarker applications: from untargeted discovery to targeted verification, and implications for platform convergence and clinical application." Clinical Chemistry 58(3):528-530.  doi:10.1373/clinchem.2011.180596
  • Sun X, K Tang, RD Smith, and RT Kelly. 2012. "Robust Extraction Interface for Coupling Droplet-Based and Continuous Flow Microfluidics." Chapter 7 in Advances in Microfluidics, ed. R Kelly, pp. 155-170.  InTech, Rijeka, Croatia (Local Name: Hrvatska). 
  • Taverner T, Y Karpievitch, AD Polpitiya, JN Brown, AR Dabney, GA Anderson, and RD Smith. 2012. "DanteR: an extensible R-based tool for quantitative analysis of -omics data." Bioinformatics 28(18):2404-2406.  doi:10.1093/bioinformatics/bts449
  • Tian Z, N Tolic, R Zhao, RJ Moore, SM Hengel, EW Robinson, DL Stenoien, S Wu, RD Smith, and L Pasa-Tolic. 2012. "Enhanced top-down characterization of histone post-translational modifications ." Genome Biology 13(10):R86.  doi:10.1186/gb-2012-13-10-r86
  • Wiedner SD, KE Burnum, LM Pederson, LN Anderson, S Fortuin, LM Chauvigne-Hines, AK Shukla, C Ansong, EA Panisko, RD Smith, and AT Wright. 2012. "Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum." Journal of Biological Chemistry 287(40):33447-33459.  doi:10.1074/jbc.M112.394106
  • Brown RN, JA Sanford, JH Park, BL Deatherage, BL Champion, RD Smith, F Heffron, and JN Adkins. 2012. "A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions." International Journal of Proteomics 2012:Article ID 123076.  doi:10.1155/2012/123076
  • Alfaro JF, CX Gong, ME Monroe, JT Aldrich, TRW Clauss, SO Purvine, Z Wang, DG Camp, II, J Shabanowitz, P Stanley, GW Hart, DF Hunt, F Yang, and RD Smith. 2012. "Tandem Mass Spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets." Proceedings of the National Academy of Sciences of the United States of America 109(19):7280-7285.  doi:10.1073/pnas.1200425109
  • Andreev VP, VA Petyuk, HM Brewer, Y Karpievitch, F Xie, J Clarke, DG Camp, II, RD Smith, AP Lieberman, RL Albin, Z Nawaz, JE Hokayem, and AJ Myers. 2012. "Label-Free Quantitative LC-MS Proteomics of Alzheimer's Disease and Normally Aged Human Brains." Journal of Proteome Research 11(6):3053-3067.  doi:10.1021/pr3001546
  • Angel TE, JM Jacobs, RP Smith, MS Pasternack, S Elias, MA Gritsenko, AK Shukla, EC Gilmore, C McCarthy, DG Camp, II, and RD Smith. 2012. "Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease." Journal of Proteome Research 11(10):4814-4822.  doi:10.1021/pr300577p
  • Angel TE, JM Jacobs, SS Spudich, MA Gritsenko, D Fuchs, T Liegler, H Zetterberg, DG Camp, II, RW Price, and RD Smith. 2012. "The cerebrospinal fluid proteome in HIV infection: change associated with disease severity." Clinical Proteomics 9:Article No. 3.  doi:10.1186/1559-0275-9-3
  • Angel TE, UK Aryal, SM Hengel, ES Baker, RT Kelly, EW Robinson, and RD Smith. 2012. "Mass spectrometry-based proteomics: existing capabilities and future directions." Chemical Society Reviews 41(10):3912-3928.  doi:10.1039/C2CS15331A
  • Aryal UK, J Stockel, EA Welsh, MA Gritsenko, CD Nicora, DW Koppenaal, RD Smith, HB Pakrasi, and JM Jacobs. 2012. "Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light." Journal of Proteome Research 11(2):609-619.  doi:10.1021/pr200959x
  • Aylward FO, KE Burnum, JJ Scott, G Suen, SG Tringe, SM Adams, KW Barry, CD Nicora, PD Piehowski, SO Purvine, GJ Starrett, LA Goodwin, RD Smith, MS Lipton, and CR Currie. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6(9):1688-1701.  doi:10.1038/ismej.2012.10
  • Bordbar A, ML Mo, ES Nakayasu, AC Rutledge, YM Kim, TO Metz, MB Jones, BC Frank, RD Smith, SN Peterson, DR Hyduke, JN Adkins, and BO Palsson. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8:Article No. 558.  doi:10.1038/msb.2012.21
  • Brown JN, GM Ortiz, TE Angel, JM Jacobs, MA Gritsenko, EY Chan, DE Purdy, RD Murnane, K Larsen, RE Palermo, AK Shukla, TRW Clauss, MG Katze, JM McCune, and RD Smith. 2012. "Morphine Produces Immunosuppressive Effects in Non-human Primates at the Proteomic and Cellular Levels." Molecular & Cellular Proteomics. MCP 11(9):605-618.  doi:10.1074/mcp.M111.016121
  • Burnum KE, Y Hirota, ES Baker, M Yoshie, YM Ibrahim, ME Monroe, GA Anderson, RD Smith, T Daikoku, and SK Dey. 2012. "Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua." Endocrinology 153(9):4568-4579.  doi:10.1210/en.2012-1335
  • Cao L, DA Bryant, AA Schepmoes, K Vogl, RD Smith, MS Lipton, and SJ Callister. 2012. "Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically." Photosynthesis Research 110(3):153-168.  doi:10.1007/s11120-011-9711-8
  • Chauvigne-Hines LM, LN Anderson, HM Weaver, JN Brown, PK Koech, CD Nicora, BA Hofstad, RD Smith, MJ Wilkins, SJ Callister, and AT Wright. 2012. "Suite of Activity-Based Probes for Cellulose-Degrading Enzymes." Journal of the American Chemical Society 134(50):20521-20532.  doi:10.1021/ja309790w
  • Chauvin T, F Xie, T Liu, CD Nicora, F Yang, DG Camp, II, RD Smith, and KP Roberts. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction 87(6):Article No. 141.  doi:10.1095/biolreprod.112.104208
  • Diamond DL, A Krasnoselski, KE Burnum, ME Monroe, BJM Webb-Robertson, JE McDermott, MM Yeh, JF Golib-Dzib, N Susnow, S Strom , S Proll, S Belisle, DE Purdy, A Rasmussen, KA Walters, JM Jacobs, MA Gritsenko, DG Camp, II, R Bhattacharya, JD Perkins, RL Carithers, IW Liou, AM Larson, A Benecke, KM Waters, RD Smith, and MG Katze. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 56(1):28-38.  doi:10.1002/hep.25649
  • Karpievitch Y, AR Dabney, and RD Smith. 2012. "Normalization and missing value imputation for label-free LC-MS analysis." BMC Bioinformatics 13(Suppl 16):Article No. S5.  doi:10.1186/1471-2105-13-S16-S5
  • Lee JH, SW Hyung, DG Mun, HJ Jung, H Kim, H Lee, SJ Kim, KS Park, RJ Moore, RD Smith, and SW Lee. 2012. "Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses." Journal of Proteome Research 11(8):4373-4381.  doi:10.1021/pr3004166
  • Lerman JA, DR Hyduke, H Latif, VA Portnoy, NE Lewis, JD Orth, AC Rutledge, RD Smith, JN Adkins, K Zengler, and BO Palsson. 2012. "In silico method for modelling metabolism and gene product expression at genome scale." Nature Communications 3:Article No. 929.  doi:10.1038/ncomms1928
  • Liu T, M Hossain, AA Schepmoes, TL Fillmore, LJ Sokoll, SR Kronewitter, G Izmirlian, T Shi, W Qian, R Leach, IM Thompson, DW Chan, RD Smith, J Kagan, S Srinivastava, KD Rodland, and DG Camp, II. 2012. "Analysis of Serum Total and Free PSA Using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests." Journal of Proteomics 75(15):4747-4757.  doi:10.1016/j.jprot.2012.01.035
  • Liu X, Y Sirotkin, Y Shen, GA Anderson, YHS Tsai, YS Ting, DR Goodlett, RD Smith, V Bafna, and PA Pevzner. 2012. "Protein Identification Using Top-Down." Molecular & Cellular Proteomics. MCP 11(6):M111.008524.  doi:10.1074/mcp.M111.008524
  • Malouli D, ES Nakayasu, K Viswanathan, DG Camp, II, WL Chang, PA Barry, RD Smith, and K Fruh. 2012. "Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1." Journal of Virology 86(17):8959-8973.  doi:10.1128/JVI.01132-12
  • Maxwell E, Y Tan, Y Tan, H Hu, G Benson, K Aizikov, S Conley, GO Staples, GW Slysz, RD Smith, and J Zaia. 2012. "GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data ." PLoS One 7(9):e45474.  doi:10.1371/journal.pone.0045474
  • Merkley ED, BJ Anderson, JH Park, SM Belchik, L Shi, ME Monroe, RD Smith, and MS Lipton. 2012. "Detection and Identification of Heme c-Modified Peptides by Histidine Affinity Chromatography, High-Performance Liquid Chromatography-Mass Spectrometry, and Database Searching." Journal of Proteome Research 11(12):6147-6158.  doi:10.1021/pr3007914
  • Payne SH, S Bonissone, S Wu, RN Brown, D Ivankov, D Frishman, L Pasa-Tolic, RD Smith, and PA Pevzner. 2012. "Unexpected Diversity of Signal Peptides in Prokaryotes." mBio 3(6):Article No. e00339-12.  doi:10.1128/mBio.00339-12
  • Rutledge AC, G Fontes, MA Gritsenko, AD Norbeck, DJ Anderson, KM Waters, JN Adkins, RD Smith, V Poitout, and TO Metz. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Proteome Research 11(7):3520-32.  doi:10.1021/pr3002996
  • Rutledge AC, MB Jones, S Chauhan, SO Purvine, J Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, S Peterson, VL Motin, and JN Adkins. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7(3):Article No. E33903.  doi:10.1371/journal.pone.0033903
  • Sadler NC, TE Angel, MP Lewis, LM Pederson, LM Chauvigne-Hines, SD Wiedner, EM Zink, RD Smith, and AT Wright. 2012. "Activity-Based Protein Profiling Reveals Mitochondrial Oxidative Enzyme Impairment and Restoration in Diet-Induced Obese Mice." PLoS One 7(10):Article No. e47996.  doi:10.1371/journal.pone.0047996
  • Shi T, D Su, T Liu, K Tang, DG Camp, II, W Qian, and RD Smith. 2012. "Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics." Proteomics 12(8):1074-1092.  doi:10.1002/pmic.201100436
  • Shi T, J Zhou, MA Gritsenko, M Hossain, DG Camp, II, RD Smith, and W Qian. 2012. "IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery." Methods 56(2):246-253.  doi:10.1016/j.ymeth.2011.09.001
  • Shi T, TL Fillmore, X Sun, R Zhao, AA Schepmoes, M Hossain, F Xie, S Wu, JS Kim, NJ Jones, RJ Moore, L Pasa-Tolic, J Kagan, KD Rodland, T Liu, K Tang, DG Camp, II, RD Smith, and W Qian. 2012. "Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum." Proceedings of the National Academy of Sciences of the United States of America 109(38):15395-15400.  doi:10.1073/pnas.1204366109
  • Tolmachev AV, EW Robinson, RD Smith, FE Leach, III, JH Futrell, and L Pasa-Tolic. 2012. "A Conceptual Approach for FT-ICR cell Harmonization Utilizing External Shim Electrodes ." International Journal of Mass Spectrometry 325-327:45-50.  doi:10.1016/j.ijms.2012.06.027
  • Tolmachev AV, EW Robinson, S Wu, RD Smith, JH Futrell, and L Pasa-Tolic. 2012. "Angular Averaged Profiling of the Radial Electric Field in Compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 23(7):1169-1172.  doi:10.1007/s13361-012-0395-x
  • Varnum SM, BJM Webb-Robertson, JG Pounds, RJ Moore, RD Smith, C Frevert, SJ Skerret, and DS Wunschel. 2012. "Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp novicida." Journal of Proteome Research 11(7):3690-3703. 
  • Wang C, CS Lee, RD Smith, and K Tang. 2012. "Ultrasensitive Sample Quantitation via Selected Reaction Monitoring Using CITP/CZE-ESI-Triple Quadrupole MS." Analytical Chemistry 84(23):10395-10403.  doi:10.1021/ac302616m
  • Wang L, UK Aryal, Z Dai, AC Mason, ME Monroe, Z Tian, J Zhou, D Su, KK Weitz, T Liu, DG Camp, II, RD Smith, SE Baker, and W Qian. 2012. "Mapping N-linked Glycosylation Sites in the Secretome and Whole Cells of Aspergillus niger Using Hydrazide Chemistry and Mass Spectrometry." Journal of Proteome Research 11(1):143-56.  doi:10.1021/pr200916k
  • Wang X, GA Anderson, RD Smith, and AR Dabney. 2012. "A Hybrid Approach to Protein Differential Expression in Mass Spectrometry-Based Proteomics." Bioinformatics 28(12):1586-1591.  doi:10.1093/bioinformatics/bts193
  • Waters KM, T Liu, RD Quesenberry, AR Willse, S Bandyopadhyay, LE Kathmann, TJ Weber, RD Smith, HS Wiley, and BD Thrall. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data ." PLoS One 7(3):Article No. e34515.  doi:10.1371/journal.pone.0034515
  • Wiedner SD, KE Burnum, LM Pederson, LN Anderson, S Fortuin, LM Chauvigne-Hines, AK Shukla, C Ansong, EA Panisko, RD Smith, and AT Wright. 2012. "Multiplexed Activity-Based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes Upon Exposure to Human Serum." Journal of Biological Chemistry 287(40):33447-33459.  doi:10.1074/jbc.M112.394106
  • Xie F, RD Smith, and Y Shen. 2012. "Advanced proteomic liquid chromatography." Journal of Chromatography A 1261:78-90.  doi:10.1016/j.chroma.2012.06.098
  • Yang F, Y Shen, DG Camp, II, and RD Smith. 2012. "High pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis." Expert Review of Proteomics 9(2):129-134.  doi:10.1586/EPR.12.15
  • Yang F, KM Waters, BJM Webb-Robertson, MB Sowa, CH Freiin von Neubeck, JT Aldrich, LM Markillie, RM Wirgau, MA Gristenko, R Zhao, DG Camp, II, RD Smith, and DL Stenoien. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21(5):352-357.  doi:10.1111/j.1600-0625.2012.01470.x
  • Zhou J, GP Dann, T Shi, L Wang, X Gao, D Su, CD Nicora, AK Shukla, RJ Moore, T Liu, DG Camp, II, RD Smith, and W Qian. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84(6):2862-2867.  doi:10.1021/ac203394r

2011

  • Ansong C, N Tolic, SO Purvine, S Porwollik, MB Jones, H Yoon, SH Payne, JL Martin, MC Burnet, ME Monroe, P Venepally, RD Smith, S Peterson, F Heffron, M Mcclelland, and JN Adkins. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12:Art. No. 433.  doi:10.1186/1471-2164-12-433
  • Belov ME, S Prasad, DC Prior, WF Danielson, III, KK Weitz, YM Ibrahim, and RD Smith. 2011. "Pulsed Multiple Reaction Monitoring Approach to Enhancing Sensitivity of a Tandem Quadrupole Mass Spectrometer." Analytical Chemistry 83(6):2162-2171.  doi:10.1021/ac103006b
  • Kim YM, TO Metz, Z Hu, SD Wiedner, JS Kim, RD Smith, WF Morgan, and Q Zhang. 2011. "Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics ." Rapid Communications in Mass Spectrometry 25:2561-2564.  doi:10.1002/rcm.5134
  • Shen Y, N Tolic, F Xie, R Zhao, SO Purvine, AA Schepmoes, RJ Moore, GA Anderson, and RD Smith. 2011. "Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods." Journal of Proteome Research 10(9):3929-3943.  doi:10.1021/pr200052c
  • Shen Y, N Tolic, SO Purvine, and RD Smith. 2011. "Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information." Journal of Proteome Research doi:10.1021/pr200597j
  • Shukla AK, R Zhang, DJ Orton, R Zhao, TRW Clauss, RJ Moore, and RD Smith. 2011. "Formation of iron complexs from trifluoroacetic acid based liquid chromatography mobile phases as interference ions in liquid chromatography/electrospray ionization mass spectrometric analysis." Rapid Communications in Mass Spectrometry 25(10):1452-1456.  doi:10.1002/rcm.5017
  • Shvartsburg AA, AJ Creese, RD Smith, and HJ Cooper. 2011. "Separation of a Set of Peptide Sequence Isomers Using Differential Ion Mobility Spectrometry ." Analytical Chemistry 83(18):6918-6923.  doi:10.1021/ac201640d
  • Shvartsburg AA, and RD Smith. 2011. "Accelerated High-Resolution Differential Ion Mobility Separations Using Hydrogen." Analytical Chemistry 83(23):9159-9166.  doi:10.1021/ac202386w
  • Shvartsburg AA, and RD Smith. 2011. "Ultrahigh-Resolution Differential Ion Mobility Spectrometry Using Extended Separation Times." Analytical Chemistry 83(1):23-29.  doi:10.1021/ac102689p
  • Shvartsburg AA, D Singer, RD Smith, and R Hoffmann. 2011. "Ion Mobility Separation of Isomeric Phosphopeptides from a Protein with Variant Modification of Adjacent Residues." Analytical Chemistry 83(13):5078-5085.  doi:10.1021/ac200985s
  • Sun X, RT Kelly, K Tang, and RD Smith. 2011. "Membrane-Based Emitter for Coupling Microfluidics with Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry." Analytical Chemistry 83(4):5797-5803.  doi:10.1021/ac200960h
  • Aryal UK, J Stockel, RK Krovvidi, MA Gritsenko, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, HB Pakrasi, and JM Jacobs. 2011. "Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles." BMC Systems Biology 5:Article No. 194.  doi:10.1186/1752-0509-5-194
  • Burnum KE, SJ Callister, CD Nicora, SO Purvine, P Hugenholtz, F Warnecke, RH Scheffrahn, RD Smith, and MS Lipton. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5(1):161-164.  doi:10.1038/ismej.2010.97
  • Dresang LR, JR Teuton, H Feng, JM Jacobs, DG Camp, II, SO Purvine, MA Gritsenko, Z Li, RD Smith, B Sugden, PS Moore, and Y Chang. 2011. "Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes." BMC Genomics 12:Article No. 625.  doi:10.1186/1471-2164-12-625
  • Du X, SM Chowdhury, NP Manes, S Wu, MU Mayer, JN Adkins, GA Anderson, and RD Smith. 2011. "Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry." Journal of Proteome Research 10(3):923-931.  doi:10.1021/pr100848a
  • Frank AM, ME Monroe, AR Shah, JJ Carver, N Bandeira, RJ Moore, GA Anderson, RD Smith, and PA Pevzner. 2011. "Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra." Nature Methods 8(7):587-591.  doi:10.1038/nmeth.1609
  • Ghazalpour A, B Bennett, VA Petyuk, L Orazco, R Hagopian, I Mungrue, CR Farber, J Sinsheimer, HM Kang, N Furlotte, C Park, PZ Wen, HM Brewer, KK Weitz, DG Camp, II, C Pan, R Yordanova, I Neuhaus, C Tilford, N Siemers, P Gargalovic, E Eskin, T Kirchgessner, DJ Smith, RD Smith, and AJ Lusis. 2011. "Comparative Analysis of Proteome and Transcriptome Variation in Mouse." PLoS Genetics 7(6):Article No. e1001393.  doi:10.1371/journal.pgen.1001393
  • Gonzales RM, Q Zhang, RC Zangar, RD Smith, and TO Metz. 2011. "Development of a Fibrinogen-Specific Sandwich Enzyme-Linked Immunosorbent Assay Microarray Assay for Distinguishing Between Blood Plasma and Serum Samples." Analytical Biochemistry 414(1):99-102.  doi:10.1016/j.ab.2011.02.039
  • Heffron F, G Niemann, H Yoon, AS Kidwai, RN Brown, JE McDermott, RD Smith, and JN Adkins. 2011. "Salmonella-secreted Virulence Factors." Chapter 10 in Salmonella: From Genome to Function, ed. S Porwollik, pp. 187-223.  Caister Academic Press, Norfolk, United Kingdom. 
  • Hossain M, DT Kaleta, EW Robinson, T Liu, R Zhao, JS Page, RT Kelly, RJ Moore, K Tang, DG Camp, II, W Qian, and RD Smith. 2011. "Enhanced Sensitivity for Selected Reaction Monitoring-Mass Spectrometry-based Targeted Proteomics using a Dual-Stage Electrodynamic Ion Funnel Interface ." Molecular & Cellular Proteomics. MCP 10(2):, doi:10.1074/mcp.M000062-MCP201
  • Huang X, AV Tolmachev, Y Shen, M Liu, L Huang, Z Zhang, GA Anderson, RD Smith, WC Chan, S Hinrichs, K Fu, and SJ Ding. 2011. "UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling." Journal of Proteome Research 10(3):1228-1237.  doi:10.1021/pr1010058
  • Ibrahim YM, AA Shvartsburg, RD Smith, and ME Belov. 2011. "Ultrasensitive Identification of Localization Variants of Modified Peptides Using Ion Mobility Spectrometry ." Analytical Chemistry 83(14):5617 - 5623.  doi:10.1021/ac200719n
  • Johnson PV, R Hodyss, K Tang, W Brinckerhoff, and RD Smith. 2011. "The Laser Ablation Ion Funnel: Sampling for In Situ Mass Spectrometry on Mars." Planetary and Space Science 59(5-6):387-393.  doi:10.1016/j.pss.2011.01.004
  • Kim JS, TL Fillmore, T Liu, EW Robinson, M Hossain, BL Champion, RJ Moore, DG Camp, II, RD Smith, and W Qian. 2011. "18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry." Molecular & Cellular Proteomics. MCP 10(12):Article No. M110.007302.  doi:10.1074/mcp.M110.007302
  • Kingsinger CR, J Apffel, MS Baker, X Bian, CH Borchers, RA Bradshaw, MY Brusniak, DW Chan, EW Deutsch, B Domon, J Gorman, R Grimm, WS Hancock, H Hermjakob, D Horn, C Hunter, P Kolar, HJ Kraus, H Langen, R Linding, RL Moritz, GS Omenn, R Orlando, A Pandey, P Ping, A Rahbar, R Rivers, SL Seymour, RJ Simpson, D Slotta, RD Smith, SE Stein, DL Tabb, D Tagle, JR Yates, and H Rodriguez. 2011. "Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles)." Proteomics - Clinical Applications 5(11-12):580-589.  doi:10.1002/prca.201100097
  • Lee B, D Lopez-Ferrer, BC Kim, HB Na, YI Park, KK Weitz, MG Warner, T Hyeon, SW Lee, RD Smith, and J Kim. 2011. "Rapid and Efficient Protein Digestion using Trypsin Coated Magnetic Nanoparticles under Pressure Cycles." Proteomics 11(2):309-318.  doi:10.1002/pmic.201000378
  • Lopez-Ferrer D, K Petritis, EW Robinson, KK Hixson, Z Tian, JH Lee, SW Lee, N Tolic, KK Weitz, ME Belov, RD Smith, and L Pasa-Tolic. 2011. "Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics." Molecular & Cellular Proteomics. MCP 10(2):, doi:10.1074/mcp.M110.001479
  • Lopez-Ferrer D, KK Hixson, ME Belov, and RD Smith. 2011. "Ultra-Fast Sample Preparation for High-Throughput Proteomics." Chapter 8 in Sample Preparation in Biological Mass Spectrometry, ed. AR Ivanov and AV Lazarev, pp. 125-139.  Springer, Dordrecht, Germany. 
  • Niemann G, RN Brown, JK Gustin, A Stufkens, AS Shaikh-Kidwai, J Li, JE McDermott, HM Brewer, AA Schepmoes, RD Smith, JN Adkins, and F Heffron. 2011. "Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants." Infection and Immunity 79(1):33-43.  doi:10.1128/IAI.00771-10
  • Qian W, BO Petritis, CD Nicora, and RD Smith. 2011. "Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics." Chapter 3 in Gel-Free Proteomics, Methods and Protocols: Methods in Molecular Biology, vol. 753, ed. K Gevaert and J Vandekerckhove, pp. 43-54.  Humana Press Inc., Totowa, NJ. 
  • Rasmussen A, DL Diamond, JE McDermott, X Gao, TO Metz, MM Matzke, V Carter, S Belisle, MJ Korth, KM Waters, RD Smith, and MG Katze. 2011. "Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enyzme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis." Journal of Virology 85(22):11646-11654.  doi:10.1128/JVI.05605-11
  • Schoenherr RM, KS Kelly-Spratt, CW Lin, JR Whiteaker, T Liu, T Holzman, I Coleman, LC Feng, TD Lorentzen, AL Krasnoselsky, P Wang, Y Liu, KE Gurley, LM Amon, AA Schepmoes, RJ Moore, DG Camp, II, LA Chodosh, RD Smith, PS Nelson, M McIntosh, C Kemp, and AG Paulovich. 2011. "Proteome and Transcriptome Profiles of a Her2/Neu-driven Mouse Model of Breast Cancer." Proteomics - Clinical Applications 5(3-4):179-188.  doi:10.1002/prca.201000037
  • Schutzer SE, TE Angel, T Liu, AA Schepmoes, TRW Clauss, JN Adkins, DG Camp, II, BK Holland, J Bergquist, PK Coyle, RD Smith, BA Fallon, and B Natelson. 2011. "Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome." PLoS One 6(2):Article No. e17287.  doi:10.1371/journal.pone.0017287
  • Shvartsburg AA, G Isaac, N Leveque, RD Smith, and TO Metz. 2011. "Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry." Journal of the American Society for Mass Spectrometry 22(7):1146-1155.  doi:10.1007/s13361-011-0114-z
  • Stanley JR, JN Adkins, GW Slysz, ME Monroe, SO Purvine, YV Karpievitch, GA Anderson, RD Smith, and AR Dabney. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83(16):6135-6140.  doi:10.1021/ac2009806
  • Stockel J, JM Jacobs, TR Elvitigala, ML Liberton, EA Welsh, AD Polpitiya, MA Gritsenko, CD Nicora, DW Koppenaal, RD Smith, and HB Pakrasi. 2011. "Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142." PLoS One 6(2):Article No.: e16680.  doi:10.1371/journal.pone.0016680
  • Sun X, RT Kelly, WF Danielson, III, N Agrawal, K Tang, and RD Smith. 2011. "Hydrodynamic injection with pneumatic valving for microchip electrophoresis with total analyte utilization." Electrophoresis 32(13):1610-1618.  doi:10.1002/elps.201000522
  • Tang K, JS Page, I Marginean, RT Kelly, and RD Smith. 2011. "Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface." Journal of the American Society for Mass Spectrometry 22(8):1318-1325.  doi:10.1007/s13361-011-0135-7
  • Tolmachev AV, EW Robinson, S Wu, RD Smith, and L Pasa-Tolic. 2011. "Trapping radial electric field optimization in compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 22(8):1334-1342.  doi:10.1007/s13361-011-0167-z
  • Varnum SM, BJM Webb-Robertson, N Hessol, RD Smith, and RC Zangar. 2011. "Plasma Biomarkers for Detecting Hodgkin's Lymphoma in HIV Patients." PLoS One 6(12):Article No. e29263.  doi:10.1371/journal.pone.0029263
  • Venter E, RD Smith, and SH Payne. 2011. "Proteogenomic analysis of bacteria and archaea: A 46 organism case study." PLoS One 6(11):Article No. e27587.  doi:10.1371/journal.pone.0027587
  • Wang Y, F Yang, MA Gritsenko, Y Wang, TRW Clauss, T Liu, Y Shen, ME Monroe, D Lopez-Ferrer, T Reno, RJ Moore, RL Klemke, DG Camp, II, and RD Smith. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11(10):2019-2026.  doi:10.1002/pmic.201000722
  • Wang Y, F Yang, Y Fu, X Huang, W Wang, X Jiang, MA Gritsenko, R Zhao, ME Monroe, OC Pertz, SO Purvine, DJ Orton, JM Jacobs, DG Camp, II, RD Smith, and RL Klemke. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286(20):18190-18201. 
  • Xie F, T Liu, W Qian, VA Petyuk, and RD Smith. 2011. "Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics." Journal of Biological Chemistry 286(29):25443-25449. 
  • Yoon H, C Ansong, JE McDermott, MA Gritsenko, RD Smith, F Heffron, and JN Adkins. 2011. "Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella ." BMC Systems Biology 5:Article No. 100.  doi:10.1186/1752-0509-5-100
  • Zhang H, F Yang, W Qian, RN Brown, Y Wang, ED Merkley, JH Park, ME Monroe, SO Purvine, RJ Moore, L Shi, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2011. "Identification of c-Type Heme-Containing Peptides Using Non-Activated Immobilized Metal Affinity Cchromatography Resin Enrichment and Higher-Energy Collisional Dissociation." Analytical Chemistry 83(19):7260-7268.  doi:10.1021/ac2000829
  • Zhang H, KE Burnum, ML Luna, BO Petritis, JS Kim, W Qian, RJ Moore, A Heredia-Langner, BJM Webb-Robertson, BD Thrall, DG Camp, II, RD Smith, JG Pounds, and T Liu. 2011. "Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size." Proteomics 11(23):4569-4577.  doi:10.1002/pmic.201100037
  • Zhang Q, ME Monroe, AA Schepmoes, TRW Clauss, MA Gritsenko, D Meng, VA Petyuk, RD Smith, and TO Metz. 2011. "Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects." Journal of Proteome Research 10(7):3076-3088. 
  • Zhou J, GP Dann, CW Liew, RD Smith, RN Kulkarni, and W Qian. 2011. "Unraveling pancreatic islet biology by quantitative proteomics." Expert Review of Proteomics 8(4):495-504.  doi:10.1586/epr.11.39

2010

  • Belov ME, YM Ibrahim, and RD Smith. 2010. "Ion Accumulation Approaches for Increasing Sensitivity and Dynamic Range in the Analysis of Complex Samples." Chapter 7 in Practical Aspects of Trapped Ion Mass Spectrometry: Theory and Instrumentation , vol. IV, ed. RE March and JFJ Todd, pp. 401-432.  CRC Press, Boca Raton, FL. 
  • Brown RN, MF Romine, AA Schepmoes, RD Smith, and MS Lipton. 2010. "Mapping the Subcellular Proteome of Shewanella oneidensis MR-1 using Sarkosyl-based fractionation and LC-MS/MS protein identification." Journal of Proteome Research 9(9):4454-4463.  doi:10.1021/pr100215h
  • Lourette NM, HS Smallwood, S Wu, EW Robinson, TC Squier, RD Smith, and L Pasa-Tolic. 2010. "A Top-Down LC-FTICR MS-Based Strategy for Characterizing Oxidized Calmodulin in Activated Macrophages ." Journal of the American Society for Mass Spectrometry 21(6):930-939. 
  • Marginean I, JS Page, AV Tolmachev, K Tang, and RD Smith. 2010. "Achieving 50% ionization efficiency in sub-ambient pressure ionization with nanoelectrospray." Analytical Chemistry 82(22):9344-9349. 
  • Shen Y, N Tolic, SO Purvine, and RD Smith. 2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de Novo-Protein Unique Sequence Tags Approach." Journal of Proteome Research 9(8):4053-4060. 
  • Shvartsburg AA, A Creese, RD Smith, and HJ Cooper. 2010. "Separation of Peptide Isomers with Variant Modified Sites by High-Resolution Differential Ion Mobility Spectrometry." Analytical Chemistry 82(19):8327-8334.  doi:10.1021/ac101878a
  • Shvartsburg AA, DC Prior, K Tang, and RD Smith. 2010. "High-Resolution Differential Ion Mobility Separations Using Planar Analyzers at Elevated Dispersion Fields." Analytical Chemistry 82(18):7649-7655.  doi:10.1021/ac101413k
  • Shvartsburg AA, DE Clemmer, and RD Smith. 2010. "Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry ." Analytical Chemistry 82(19):8047-8051.  doi:10.1021/ac101992d
  • Shvartsburg AA, K Tang, and RD Smith. 2010. "Differential Ion Mobility Separations of Peptides with Resolving Power Exceeding 50." Analytical Chemistry 82(1):32-35.  doi:10.1021/ac902133n
  • Sorensen CM, J Ding, Q Zhang, T Alquier, R Zhao, PW Mueller, RD Smith, and TO Metz. 2010. "Perturbations in the Lipid Profile of Individuals with Newly Diagnosed Type 1 Diabetes Mellitus: Lipidomics Analysis of a Diabetes Antibody Standardization Program Sample Subset." Clinical Biochemistry 43(12):948-956. 
  • Sun X, RT Kelly, K Tang, and RD Smith. 2010. "Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry using Poly(dimethylsiloxane) Microchips with Monolithically Integrated Emitters." Analyst 135(9):2296-2302. 
  • Tian Z, R Zhao, N Tolic, RJ Moore, DL Stenoien, EW Robinson, RD Smith, and L Pasa-Tolic. 2010. "Two-dimensional liquid chromatography system for online top-down mass spectrometry." Proteomics 10(20):3610-3620.  doi:10.1002/pmic.201000367
  • Adkins JN, H Mottaz, TO Metz, CK Ansong, NP Manes, RD Smith, and F Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." Chapter 2 in Peptidomics: Methods and Protocols, Methods in Molecular Biology, vol. 615, ed. Mikhail Soloviev, pp. 13-27.  Humana Press, Inc., New York, NY. 
  • Ahn HK, BC Kim, SH Jun, MS Chang, D Lopez-Ferrer, RD Smith, MB Gu, SW Lee, BS Kim, and J Kim. 2010. "Robust Trypsin Coating on Electrospun Polymer Nanofibers in Rigorous Conditions and Its Uses for Protein Digestion." Biotechnology and Bioengineering 107(6):917-923. 
  • Alpert AJ, K Petritis, LJ Kangas, RD Smith, K Mechtler, G Mitulovic, S Mohammed, and AJ Heck. 2010. "Peptide Orientation Affects Selectivity in Ion-Exchange Chromatography." Analytical Chemistry 82(12):5253-5259. 
  • Angel TE, BJ Luft, X Yang, CD Nicora, DG Camp, II, JM Jacobs, and RD Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5(11):Article No.: e13800.  doi:10.1371/journal.pone.0013800
  • Auberry KJ, GR Kiebel, ME Monroe, JN Adkins, GA Anderson, and RD Smith. 2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3(1):1-4. 
  • Baker ES, EA Livesay, DJ Orton, RJ Moore, WF Danielson, DC Prior, YM Ibrahim, BL Lamarche, AM Mayampurath, AA Schepmoes, DF Hopkins, K Tang, RD Smith, and ME Belov. 2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." Journal of Proteome Research 9(2):997-1006.  doi:10.1021/pr900888b
  • Brown JN, R Estep, D Lopez-Ferrer, HM Brewer, TRW Clauss, NP Manes, M O'Connor, H Li, JN Adkins, S Wong, and RD Smith. 2010. "CHARACTERIZATION OF MACAQUE PULMONARY FLUID PROTEOME DURING MONKEYPOX INFECTION: DYNAMICS OF HOST RESPONSE." Molecular & Cellular Proteomics. MCP 9(12):2760-2771.  doi:10.1074/mcp.M110.001875
  • Brown JN, R Palermo, CR Baskin, MA Gritsenko, PJ Sabourin, JP Long, CL Sabourin, H Bielefeldt-Ohmann, A Garcia-Sastre, R Albrecht, TM Tumpey, JM Jacobs, RD Smith, and MG Katze. 2010. "Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections." Journal of Virology 84(22):12058-12068. 
  • Buchko GW, G Niemann, ES Baker, ME Belov, RD Smith, F Heffron, JN Adkins, and JE McDermott. 2010. "A multi-pronged search for a common structural motif in the secretion signal of Salmonella enterica serovar Typhimurium type III effector proteins." Molecular Biosystems 6(12):2448-2458.  doi:10.1039/c0mb00097c
  • Callister SJ, MJ Wilkins, CD Nicora, KH Williams, JF Banfield, N VerBerkmoes, RL Hettich, AL N'Guessan, P Mouser, H Elifantz, RD Smith, DR Lovley, MS Lipton, and PE Long. 2010. "Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles." Environmental Science & Technology 44(23):8897-8903.  doi:10.1021/es101029f
  • Diamond DL, AJ Syder, JM Jacobs, CM Sorensen, KA Walters, S Proll, JE McDermott, MA Gritsenko, Q Zhang, R Zhao, TO Metz, DG Camp, II, KM Waters, RD Smith, CM Rice, and MG Katze. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics ." PLoS Pathogens 6(1):Art. No. e1000719.  doi:10.1371/journal.ppat.1000719
  • Gupta N, KK Hixson, DE Culley, RD Smith, and PA Pevzner. 2010. "Analyzing Protease Specificity and Detecting in Vivo Proteolytic Events Using Tandem Mass Spectrometry." Proteomics 10(15):2833-2844. 
  • Ham BM, H Jayachandran, F Yang, N Jaitly, AD Polpitiya, ME Monroe, L Wang, R Zhao, SO Purvine, EA Livesay, DG Camp, II, SS Rossie, and RD Smith. 2010. "Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis." Journal of Proteome Research 9(2):945-953.  doi:10.1021/pr9008207
  • Ibrahim YM, DC Prior, ES Baker, RD Smith, and ME Belov. 2010. "Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation- Tandem Time-of-Flight Mass Spectrometry Approach." International Journal of Mass Spectrometry 293(1-3):34-44. 
  • Jun SH, MS Chang, BC Kim, HJ An, D Lopez-Ferrer, R Zhao, RD Smith, SW Lee, and J Kim. 2010. "Trypsin coatings on electrospun and alcohol-dispersed polymer nanofibers for trypsin digestion column." Analytical Chemistry 82(18):7828 - 7834.  doi:10.1021/ac101633e
  • Jung HJ, SO Purvine, H Kim, VA Petyuk, SW Hyung, ME Monroe, DG Mun, KC Kim, JM Park, SJ Kim, N Tolic, GW Slysz, RJ Moore, R Zhao, JN Adkins, GA Anderson, H Lee, DG Camp, II, MH Yu, RD Smith, and SW Lee. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82(20):8510-8518.  doi:10.1021/ac101388b
  • Karpievitch YV, AD Polpitiya, GA Anderson, RD Smith, and AR Dabney. 2010. "Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects." The Annals of Applied Statistics 4(4):1797-1823. 
  • Kelly RT, AV Tolmachev, JS Page, K Tang, and RD Smith. 2010. "The Ion Funnel: Theory, Implementations and Applications." Mass Spectrometry Reviews 29(2):294-312.  doi:10.1002/mas.20232
  • Kim J, BC Kim, D Lopez-Ferrer, K Petritis, and RD Smith. 2010. "Nanobiocatalysis for protein digestion in proteomic analysis ." Proteomics 10(4 SP ISS):687-699. 
  • Kotz KT, W Xiao, C Miller-Graziano, W Qian, A Russom, EA Warner, LL Moldawer, A De, PE Bankey, BO Petritis, DG Camp, II, AE Rosenbach, J Goverman, SP Fagan, BH Brownstein, D Irimia, W Xu, J Wilhelmy, M Mindrinos, RD Smith, RW Davis, RG Tompkins, and M Toner. 2010. "Clinical Microfluidics for Neutrophil Genomics and Proteomics." Nature Medicine 16(9):1042-1048.  doi:10.1038/nm.2205
  • Lewis NE, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, JN Adkins, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, R Eils, R Konig, RD Smith, and BO Palsson. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6:Article No. 390.  doi:10.1038/msb.2010.47
  • Liu M, J Hou, L Huang, X Huang, TH Heibeck, R Zhao, L Pasa-Tolic, RD Smith, Y Li, K Fu, Z Zhang, S Hinrichs, and SJ Ding. 2010. "Site-Specific Proteomics Approach for Study Protein S-Nitrosylation." Analytical Chemistry 82(17):7160-7168.  doi:10.1021/ac100569d
  • Petyuk VA, W Qian, RD Smith, and DJ Smith. 2010. "Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry." Methods 50(2):77-84. 
  • Qian W, BO Petritis, A Kaushal, CC Finnerty, MG Jescheke, ME Monroe, RJ Moore, AA Schepmoes, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DN Herndon, DG Camp, II, and RD Smith. 2010. "Plasma Proteome Response to Severe Burn Injury Revealed by 18O-Labeled "Universal" Reference-based Quantitative Proteomics." Journal of Proteome Research 9(9):4779-4789. 
  • Rana GSJB, TP York, JS Edmiston, BK Zedler, JG Pounds, JN Adkins, RD Smith, Z Liu, G Li, BT Webb, EL Murrelle, and JW Flora. 2010. "Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD) ." Analytical and Bioanalytical Chemistry 397:1809-1819.  doi:10.1007/s00216-010-3742-4
  • Schutzer SE, T Liu, B Natelson, TE Angel, AA Schepmoes, SO Purvine, KK Hixson, MS Lipton, DG Camp, II, PK Coyle, RD Smith, and J Bergquist. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid ." PLoS One 5(6):e10980-.  doi:10.1371/journal.pone.0010980
  • Shah AR, K Agarwal, ES Baker, M Singhal, AM Mayampurath, YM Ibrahim, LJ Kangas, ME Monroe, R Zhao, ME Belov, GA Anderson, and RD Smith. 2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry ." Bioinformatics 26(13):1601-1607.  doi:10.1093/bioinformatics/btq245
  • Shah AR, JL Davidson, ME Monroe, AM Mayampurath, WF Danielson, III, Y Shi, AC Robinson, BH Clowers, ME Belov, GA Anderson, and RD Smith. 2010. "An efficient data format for mass spectrometry based proteomics." Journal of the American Society for Mass Spectrometry 21(10):1784-1788.  doi:10.1016/j.jasms.2010.06.014
  • Shah AR, N Jaitly, N Zuljevic, ME Monroe, AV Liyu, AD Polpitiya, JN Adkins, ME Belov, GA Anderson, RD Smith, and I Gorton. 2010. "An architecture for real time data acquisition and online signal processing for high throughput tandem mass spectrometry." In 5th IEEE International Conference on e-Science, pp. 88 - 93.  IEEE, Piscataway, NJ.  doi:10.1109/e-Science.2009.21
  • Shen Y, N Tolic, T Liu, R Zhao, BO Petritis, MA Gritsenko, DG Camp, II, RJ Moore, SO Purvine, FJ Esteva, and RD Smith. 2010. " Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5(10):Article No.: e13133.  doi:10.1371/journal.pone.0013133
  • Shen Y, T Liu, N Tolic, BO Petritis, R Zhao, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma ." Journal of Proteome Research 9(5):2339-2346.  doi:10.1021/pr901083m
  • Shvartsburg AA, WF Danielson, III, and RD Smith. 2010. "High-Resolution Differential Ion Mobility Separations Using Helium-Rich Gases." Analytical Chemistry 82(6):2456-2462. 
  • Sigdel TK, A Kaushal, MA Gritsenko, AD Norbeck, W Qian, W Xiao, DG Camp, II, RD Smith, and MM Sarwal. 2010. "Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection." Proteomics - Clinical Applications 4(1):32-47.  doi:10.1002/prca.200900124
  • Smith DP, JB Kitner, AD Norbeck, TRW Clauss, MS Lipton, MS Schwalbach, L Steindler, CD Nicora, RD Smith, and SJ Giovannoni. 2010. "Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique." PLoS One 5(5):Article Number: e10487. 
  • Tang Z, H Wu, D Du, J Wang, H Wang, W Qian, DJ Bigelow, JG Pounds, RD Smith, and Y Lin. 2010. "Sensitive Immunoassays of Nitrated Fibrinogen in Human Biofluids." Talanta 81(4-5):1662-1669. 
  • True LD, H Zhang, M Ye, CY Huang, PS Nelson, PD Von Haller, LW Tjoelker, JS Kim, W Qian, RD Smith, WJ Ellis, ES Liebeskind, and AY Liu. 2010. "CD90/THY1 is over-expressed in prostate cancer-associated fibroblasts and could serve as a cancer biomarker." Modern Pathology 23(10):1346-1356. 
  • Wegener KM, AK Singh, JM Jacobs, TR Elvitigala, EA Welsh, NS Keren, MA Gritsenko, BK Ghosh, DG Camp, II, RD Smith, and HB Pakrasi. 2010. "Global Proteomics Reveal An Atypical Strategy for Carbon/Nitrogen Assimilation by a Cyanobacterium Under Diverse Environmental Perturbations." Molecular & Cellular Proteomics. MCP 9(12):2678-89.  doi:10.1074/mcp.M110.000109
  • Yang F, KM Waters, JH Miller, MA Gritsenko, R Zhao, X Du, EA Livesay, SO Purvine, ME Monroe, Y Wang, DG Camp, II, RD Smith, and DL Stenoien. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5(11):e14152.  doi:10.1371/journal.pone.0014152
  • Zhang H, RN Brown, W Qian, ME Monroe, SO Purvine, RJ Moore, MA Gritsenko, L Shi, MF Romine, JK Fredrickson, L Pasa-Tolic, RD Smith, and MS Lipton. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9(5):2160-2169. 
  • Zhang X, J Zhou, MH Chin, AA Schepmoes, VA Petyuk, KK Weitz, BO Petritis, ME Monroe, DG Camp, II, SA Wood, WP Melega, DJ Bigelow, DJ Smith, W Qian, and RD Smith. 2010. " Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson's Disease Mouse Model ." Journal of Proteome Research 9(3):1496-1509.  doi:10.1021/pr901024z
  • Zhang X, ME Monroe, B Chen, MH Chin, TH Heibeck, AA Schepmoes, F Yang, BO Petritis, DG Camp, II, JG Pounds, JM Jacobs, DJ Smith, DJ Bigelow, RD Smith, and W Qian. 2010. "Endogenous 3, 4- Dihydroxyphenylalanine and Dopaquinone Modifications on Protein Tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical." Molecular & Cellular Proteomics. MCP 9(6):1199-1208. 
  • Zhou J, AA Schepmoes, X Zhang, RJ Moore, ME Monroe, JH Lee, DG Camp, II, RD Smith, and W Qian. 2010. "Improved LC-MS/MS Spectral Counting Statistics by Recovering Low Scoring Spectra Matched to Confidently Identified Peptide Sequences." Journal of Proteome Research 9(11):5698-5704.  doi:10.1021/pr100508p

2009

  • Chowdhury SM, X Du, N Tolic, S Wu, RJ Moore, MU Mayer, RD Smith, and JN Adkins. 2009. "Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry." Analytical Chemistry 81(13):5524-5532.  doi:10.1021/ac900853k
  • Marginean I, JS Page, RT Kelly, K Tang, and RD Smith. 2009. "Effect of pressure on electrospray characteristics." Applied Physics Letters 95(18):Article Number: 184103 . 
  • 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. 
  • Petritis BO, W Qian, DG Camp, II, and RD Smith. 2009. "A Simple Procedure for Effective Quenching of Trypsin Activity and Prevention of 18O-Labeling Back-Exchange." Journal of Proteome Research 8(5):2157-2163.  doi:10.1021/pr800971w
  • Prasad S, K Tang, D Manura, D Papanastasiou, and RD Smith. 2009. "Simulation of Ion Motion in FAIMS through Combined Use of SIMION and Modified SDS." Analytical Chemistry 81(21):8749-8757.  doi:10.1021/ac900880v
  • Shen Y, JS Page, and RD Smith. 2009. "Advanced Capillary Liquid Chromatography-Mass Spectrometry for Proteomics ." Chapter 2 in Advances in Chromatography, vol. 47, ed. E Grushka and N Grinberg, pp. 31-58.  CRC Press, Boca Raton, FL. 
  • Shvartsburg AA, K Tang, RD Smith, M Holden, M Rush, A Thompson, and D Toutoungi. 2009. "Ultrafast Differential Ion Mobility Spectrometry at Extreme Electric Fields Coupled to Mass Spectrometry." Analytical Chemistry 81(19):8048-8053.  doi:10.1021/ac901479e
  • 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. 
  • 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
  • Chan EY, JN Sutton, JM Jacobs, A Bondarenko, RD Smith, and MG Katze. 2009. "Dynamic Host Energetics and Cytoskeletal Proteomes in HIV-1 -Infected Human Primary CD4 Cells: Analysis by Multiplexed Label-free Mass Spectrometry." Journal of Virology 83(18):9283-9295. 
  • 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 10:87.  doi:10.1186/1471-2105-10-87
  • 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. "A statistical framework for protein quantitation in bottom-up MS-based proteomics ." Bioinformatics 25(16):2028-2034.  doi:10.1093/bioinformatics/btp362
  • 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. "A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics." Bioinformatics 25(16):2028-2034. 
  • 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, S 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):1893-900. 
  • 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
  • Page JS, I Marginean, ES Baker, RT Kelly, K Tang, and RD Smith. 2009. "Biases in Ion Transmission Through an Electrospray Ionization-Mass Spectrometry Capillary Inlet." Journal of the American Society for Mass Spectrometry 20(12):2265-2272.  doi:10.1016/j.jasms.2009.08.018
  • Park CC, VA Petyuk, W Qian, RD Smith, and DJ Smith. 2009. "Dual spatial maps of transcript and protein abundance in the mouse brain." Expert Review of Proteomics 6(3):243-249. 
  • Petyuk VA, AM Mayampurath, ME Monroe, AD Polpitiya, SO Purvine, GA Anderson, DG Camp, II, and RD Smith. 2009. "DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets." Molecular & Cellular Proteomics. MCP 9.3:486-496.  doi:10.1074/mcp.M900217-MCP200
  • 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. 
  • Schepmoes AA, Q Zhang, BO Petritis, W Qian, and RD Smith. 2009. "N-Terminal Enrichment: Developing a Protocol to Detect Specific Proteolytic Fragments." Journal of Biomolecular Techniques:JBT 20(5):263-265. 
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • 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. 
  • Zhou J, BO Petritis, K Petritis, AD Norbeck, KK Weitz, RJ Moore, DG Camp, II, RN Kulkarni, RD Smith, and W Qian. 2009. "Mouse-Specific Tandem IgY7-SuperMix Immunoaffinity Separations for Improved LC-MS/MS Coverage of the Plasma Proteome ." Journal of Proteome Research 8(11):5387-5395. 

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, WF 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. 
  • 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
  • Page JS, K Tang, RT Kelly, and RD Smith. 2008. "A subambient pressure ionization with nanoelectrospray (SPIN) source and interface for improved sensitivity in mass spectrometry." Analytical Chemistry 80(5):1800-1805.  doi:10.1021/ac702354b
  • 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.  doi:10.1371/journal.pone.0001542
  • 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 SJ, Y Wang, JM Jacobs, W Qian, F Yang, AV Tolmachev, X Du, W Wang, RJ Moore, ME Monroe, SO Purvine, KM Waters, TH Heibeck, JN Adkins, DG Camp, II, RL Klemke, and RD Smith. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step 18O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7(10):4215-24.  doi:10.1021/pr7007785
  • 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, K Petritis, NM Lourette, BH Clowers, KK Hixson, TH Heibeck, DC Prior, L Pasa-Tolic, DG Camp, II, ME Belov, and RD Smith. 2008. "Fast On-Line Digestion System for Protein Characterization ." Analytical Chemistry 80(23):8930-8936.  doi:10.1021/ac800927v
  • 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
  • Pasa-Tolic L, JM Jacobs, W Qian, and RD Smith. 2008. "Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry." Chapter 7 in Clinical Proteomics: From Diagnosis to Therapy, ed. JE Van Eyk and MJ Dunn, pp. 89-100.  Wiley-VCH, Weinheim, Germany. 
  • 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
  • Prichard MN, E Sztul, SL Daily, AL Perry, SL Frederick, RB Gill, CB Hartline, DN Streblow, SM Varnum, RD Smith, and ER Kern. 2008. "Human Cytomegalovirus UL97 Kinase Activity Is Required for the Hyperphosphorylation of Retinoblastoma Protein and Inhibits the Formation of Nuclear Aggresomes." Journal of Virology 82(10):5054-5067. 
  • 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. 
  • 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.  doi:10.2217/17460913.3.6.625
  • 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
  • Smith RD. 2007. "Forward: Jean H. Futrell." International Journal of Mass Spectrometry 265(2-3):75-79.  doi:10.1016/j.ijms.2007.06.022
  • 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, W Qian, DG Camp, II, and RD Smith. 2007. "The Use of a Quantitative Cysteinyl-peptide Enrichment Technology for High-Throughput Quantitative Proteomics." In Quantitative Proteomics by Mass Spectrometry, Methods in Molecular Biology, vol. 359, pp. 107-24.  Humana Press, Totowa, NJ. 
  • 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. 
  • 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: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. 
  • 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 Separation Methods in Proteomics, ed. GB Smejkal and A Lazareu, pp. 363-385.  CRC Taylor & Francis, Boca Raton, FL. 
  • 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
  • Simpson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Mottaz, 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
  • 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, JH 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 H, P Loriaux, JK Eng, D Campbell, A Keller, P Moss, RA Bonneau, N Zhang, Y Zhou, B Wollscheid, K Cooke, EC Yi, H Lee, ER Peskind, J Zhang, RD Smith, and R Aebersold. 2006. "UniPep-A database for human N-linked glycosites: a resource for biomarker discovery." Genome Biology 7(8):Article No. R73.  doi:10.1186/gb-2006-7-8-r73
  • 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, 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. 
  • 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, EF 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, EF 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 DynamicsPNNL-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, 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.  doi:10.1110/ps.29401
  • 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. 

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