Richard D. Smith

Chemist, Battelle Fellow

Biological Sciences

Biography

Dr. Smith's research interests span the 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. This has included creating and applying new ultra-sensitive technologies to quantitatively probe the entire arrays of proteins (i.e. 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, (the array of biomolecule measurements that include the proteome, metabolome, lipidome, and glycome, to augment biological research. To enable much more effective pan-omics applications, he has recently lead 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 more than 1100 peer-reviewed journal articles and is the recipient of 70 patents and 12 R&D 100 Awards.

Research Interest

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, metabolomics, and other pan-omics measurements to augment systems biology research

Education

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

2019 Marcel Golay Award
American Society for Mass Spectrometry Distinguished Contribution in Mass Spectrometry Award (2013)
2018 Federal Laboratory Consortium Award for Excellence in Technology Transfer for: Structures for Lossless Ion Manipulations (SLIM)
R&D Magazine 2010 Scientist of the Year
Twelve R&D 100 Awards:
- Structures for Lossless Ion Manipulations (SLIM) (2017)
- Subambient Pressure Ionization with Nanoelectrospray (SPIN) Source (2015)
- 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 (1989)
AWU-DOE Distinguished Lecturer
Battelle Inventor of the Year (2000)
Pacific Northwest National Laboratory Mentor of the Year
ACS Award for Analytical Chemistry (2003)
ICI List of most cited chemists
Serves on six scientific journal advisory boards

Publications

2021

Harrilal C.P., V.D. Gandhi, G. Nagy, X. Chen, M.G. Buchanan, R. Wojcik, and C.R. Conant, et al. 2021. "Measurement and Theory of Gas-Phase Ion Mobility Shifts Resulting from Isotopomer Mass Distribution Changes." Analytical Chemistry. PNNL-SA-161633. doi:10.1021/acs.analchem.1c01736
Bilbao Pena A., B.C. Gibbons, S.M. Stow, J.E. Kyle, K.J. Bloodsworth, S.H. Payne, and R.D. Smith, et al. 2021. "A Preprocessing Tool for Enhanced Ion Mobility–Mass Spectrometry-Based Omics Workflows." Journal of Proteome Research. PNNL-SA-161913. doi:10.1021/acs.jproteome.1c00425
Sims A.C., H.D. Mitchell, L. Gralinski, J.E. Kyle, K.E. Burnum-Johnson, M. Lam, and L.M. Fulcher, et al. 2021. "Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 12, no. 4:e01572-21. PNNL-SA-162254. doi:10.1128/mBio.01572-21
Martin K.D., T. Zhang, T. Lin, A.N. Habowski, R. Zhao, C. Tsai, and W.B. Chrisler, et al. 2021. "Facile one-pot nanoproteomics for label-free proteome profiling of 50-1000 mammalian cells." Journal of Proteome Research 20, no. 9:4452-4461. PNNL-SA-160823. doi:10.1021/acs.jproteome.1c00403
Jarsberg L.G., K. Kedia, T.G. Wendler, A.T. Wright, P.D. Piehowski, M.A. Gritsenko, and T. Shi, et al. 2021. "Nutritional markers and proteome in patients undergoing treatment for pulmonary tuberculosis differ by geographic region." PLOS ONE 16, no. 5:Article No. e0250586. PNNL-SA-156554. doi:10.1371/journal.pone.0250586
Hollerbach A.L., C.R. Conant, G. Nagy, M.E. Monroe, K. Gupta, M.T. Donor, and C.M. Giberson, et al. 2021. "Dynamic time-warping correction for shifts in ultrahigh resolving power ion mobility spectrometry and structures for lossless ion manipulations." Journal of the American Society for Mass Spectrometry 32, no. 4:996-1007. PNNL-SA-158160. doi:10.1021/jasms.1c00005
Lee J., A. Bilbao Pena, C.R. Conant, K.J. Bloodsworth, D.J. Orton, I.K. Webb, and A. Li, et al. 2021. "AutoCCS: Automated collision cross section calculation software for ion mobility spectrometry-mass spectrometry." Bioinformatics. PNNL-SA-155898. doi:10.1093/bioinformatics/btab429
Wang L., A. Karpova, M.A. Gritsenko, J.E. Kyle, S. Cao, Y. Li, and D. Rykunov, et al. 2021. "Proteogenomic and Metabolomic Characterization of Human Glioblastoma." Cancer Cell 39, no. 4:509-528.e20. PNNL-SA-151124. doi:10.1016/j.ccell.2021.01.006
Khadempour L., J.E. Kyle, B.M. Webb-Robertson, C.D. Nicora, F.B. Smith, R.D. Smith, and M.S. Lipton, et al. 2021. "From plants to ants: Fungal modification of leaf lipids for nutrition and communication in the leaf-cutter ant fungal garden ecosystem." mSystems 6, no. 2:e01307-20. PNNL-SA-147384. doi:10.1128/mSystems.01307-20
Tsai C., P. Zhang, D. Scholten, K.D. Martin, Y. Wang, R. Zhao, and W.B. Chrisler, et al. 2021. "Surfactant-assisted one-pot sample preparation for label-free single-cell proteomics." Communications Biology 4, no. 1:265. PNNL-SA-150656. doi:10.1038/s42003-021-01797-9
Conant C.R., I.K. Attah, V. Garimella, G. Nagy, A. Bilbao Pena, R.D. Smith, and Y.M. Ibrahim. 2021. "Evaluation of Waveform Profiles for Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations." Journal of the American Society for Mass Spectrometry 32, no. 1:225–236. PNNL-SA-154551. doi:10.1021/jasms.0c00282
Hollerbach A.L., C.M. Giberson, J. Lee, A.P. Huntley, R.D. Smith, and Y.M. Ibrahim. 2021. "Improving Signal to Noise Ratios in Ion Mobility Spectrometry and Structures for Lossless Ion Manipulations (SLIM) using a High Dynamic Range Analog-to-Digital Converter." Journal of the American Society for Mass Spectrometry. PNNL-SA-163799.

2020

Martin K.D., T. Zhang, P. Zhang, W.B. Chrisler, T.L. Fillmore, F. Liu, and T. Liu, et al. 2020. "Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells." Journal of Visualized Experiments (JoVE). PNNL-SA-153959. doi:10.3791/61797
Li A., C.R. Conant, X. Zheng, K.J. Bloodsworth, D.J. Orton, V. Garimella, and I.K. Attah, et al. 2020. "Assessing Collision Cross Section Calibration Strategies for Traveling Wave-based Ion Mobility Separations in Structures for Lossless Ion Manipulations." Analytical Chemistry 92, no. 22:14976-14982. PNNL-SA-154112. doi:10.1021/acs.analchem.0c02829
Zhang Y., Z. Ouyang, W. Qian, R.D. Smith, W. Wong, and R.W. Davis. 2020. "Meta-analysis of peptides to detect protein significance." Statistics and It's Interface 13, no. 4:465-474. PNNL-SA-152554. doi:10.4310/sii.2020.v13.n4.a4
Orwoll E.S., J. Wiedrick, C. Nielson, J.M. Jacobs, E.S. Baker, P.D. Piehowski, and V.A. Petyuk, et al. 2020. "Proteomic assessment of serum biomarkers of longevity in older men." Aging Cell 19, no. 11:Article No. e13253. PNNL-SA-155940. doi:10.1111/acel.13253
Petralia F., N. Tignor, B. Reva, M. Koptyra, S. Chowdhury, D. Rykunov, and A. Krek, et al. 2020. "Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer." Cell 183, no. 7:1962-1985. PNNL-SA-155153. doi:10.1016/j.cell.2020.10.044
Li A., G. Nagy, C.R. Conant, R.V. Norheim, J. Lee, C.M. Giberson, and A.L. Hollerbach, et al. 2020. "Ion Mobility Spectrometry with High Ion Utilization Efficiency Using Traveling Wave-Based Structures for Lossless Ion Manipulations." Analytical Chemistry 92, no. 22:14930-14938. PNNL-SA-166146. doi:10.1021/acs.analchem.0c02100
Hollerbach A.L., A. Prabhakaran Nair Syamala Amma, A. Li, G. Nagy, C.P. Harrilal, C.R. Conant, and R.V. Norheim, et al. 2020. "Ultra-High-Resolution Ion Mobility Separations Over Extended Path Lengths and Mobility Ranges Achieved using a Multilevel Structures for Lossless Ion Manipulations Module." Analytical Chemistry 92, no. 11:7972 - 7979. PNNL-SA-152421. doi:10.1021/acs.analchem.0c01397
Eguchi A., R. Yan, S. Pan, R. Wu, J. Kim, Y. Chen, and C.K. Ansong, et al. 2020. "Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1ß and IL-17 upregulation in alcoholic hepatitis mice." Journal of Molecular Medicine 98, no. 7:1021-1034. PNNL-SA-155939. doi:10.1007/s00109-020-01926-7
Xiang P., Y. Zhu, Y. Yang, Z. Zhao, S.M. Williams, R.J. Moore, and R.T. Kelly, et al. 2020. "Picoflow Liquid Chromatography-Mass Spectrometry for Ultrasensitive Bottom-up Proteomics using 2-µm i.d. Open Tubular Columns." Analytical Chemistry 92, no. 7:4711-4715. PNNL-SA-150120. doi:10.1021/acs.analchem.9b05639
Gao Y., Y. Wang, Y. Chen, H. Wang, D. Young, T. Shi, and Y. Song, et al. 2020. "Proteomic Tissue-based Classifier for Early Prediction of Prostate Cancer Progression." Cancers 12, no. 5:1268. PNNL-SA-149705. doi:10.3390/cancers12051268
Tsai C., R. Zhao, S.M. Williams, R.J. Moore, K.D. Schultz, W.B. Chrisler, and L. Pasa Tolic, et al. 2020. "An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics." Molecular and Cellular Proteomics 19, no. 5:828-838. PNNL-SA-149183. doi:10.1074/mcp.RA119.001857
Kagan J., R.L. Moritz, R. Mazurchuk, J. Lee, P. Kharchenko, O. Rozenblatt-Rosen, and E. Ruppin, et al. 2020. "National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions." Journal of Proteome Research 19, no. 5:1900–1912. PNNL-SA-152101. doi:10.1021/acs.jproteome.0c00021
McDermott J.E., O.A. Arshad, V.A. Petyuk, Y. Fu, M.A. Gritsenko, T.R. Clauss, and R.J. Moore, et al. 2020. "Proteogenomic characterization of ovarian HGSC implicates mitotic kinases, replication stress in observed chromosomal instability." Cell Reports Medicine 1, no. 1:Article No. 100004. PNNL-SA-145681. doi:10.1016/j.xcrm.2020.100004
Nagy G., I.K. Attah, C.R. Conant, W. Liu, V. Garimella, H.P. Gunawardena, and J.B. Shaw, et al. 2020. "Rapid and Simultaneous Characterization of Drug Conjugation in Heavy and Light Chains of a Monoclonal Antibody Revealed by High-Resolution Ion Mobility Separations in SLIM." Analytical Chemistry 92, no. 7:5004-5012. PNNL-SA-149352. doi:10.1021/acs.analchem.9b05209
Dou Y., E. Kawaler, D.C. Zhou, M.A. Gritsenko, C. Huang, L. Blumenberg, and A. Karpova, et al. 2020. "Proteogenomic Characterization of Endometrial Carcinoma." Cell 180, no. 4:729-748.e26. PNNL-SA-147326. doi:10.1016/j.cell.2020.01.026
Williams S.M., A.V. Liyu, C. Tsai, R.J. Moore, D.J. Orton, W.B. Chrisler, and M.J. Gaffrey, et al. 2020. "Automated coupling of nanodroplet sample preparation with liquid chromatography-mass spectrometry for high-throughput single-cell proteomics." Analytical Chemistry 92, no. 15:10588–10596. PNNL-SA-152553. doi:10.1021/acs.analchem.0c01551

2019

Stevens S., T. Liu, F.R. Bahjat, V.A. Petyuk, A.A. Schepmoes, R.L. Sontag, and M.A. Gritsenko, et al. 2019. "Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia that Is Associated with Neuroprotection." Translational Stroke Research 10, no. 4:440-448. PNWD-SA-10567. doi:10.1007/s12975-018-0670-7
Zhang Y., Y. Zhong, A.L. Connor, D.P. Miller, R. Cao, J. Shen, and B. Song, et al. 2019. "Folding and Assembly of Short a, ß, y-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures." Journal of the American Chemical Society 141, no. 36:14239-14248. PNNL-SA-140660. doi:10.1021/jacs.9b06094
Dou M., C.D. Chouinard, Y. Zhu, G. Nagy, A.V. Liyu, Y.M. Ibrahim, and R.D. Smith, et al. 2019. "Nanowell-mediated multidimensional separations combining nanoLC with SLIM IM-MS for rapid, high-peak-capacity proteomic analyses." Analytical and Bioanalytical Chemistry 411, no. 21:5363–5372. PNNL-SA-146403. doi:10.1007/s00216-018-1452-5
Stevens S.L., T. Liu, F.R. Bahjat, V.A. Petyuk, A.A. Schepmoes, R.L. Sontag, and M.A. Gritsenko, et al. 2019. "Preconditioning in the Rhesus Macaque Induces a Proteomic Signature Following Cerebral Ischemia That Is Associated With Neuroprotection." Translational Stroke Research 10, no. 4:440-448. PNNL-SA-153569. doi:10.1007/s12975-018-0670-7
Tsai C., J.S. Smith, K. Krajewski, R. Zhao, A.M. Moghieb, C.D. Nicora, and X. Xiong, et al. 2019. "Tandem Mass Tag Labeling Facilitates Reversed-Phase Liquid Chromatography-Mass Spectrometry Analysis of Hydrophilic Phosphopeptides." Analytical Chemistry 91, no. 18:11606-11613. PNNL-SA-142808. doi:10.1021/acs.analchem.9b01814
Attah I.K., V. Garimella, I.K. Webb, G. Nagy, R.V. Norheim, C.E. Schimelfenig, and Y.M. Ibrahim, et al. 2019. "Dual Polarity Ion Confinement and Mobility Separations." Journal of the American Society for Mass Spectrometry 30, no. 6:967-976. PNNL-SA-146246. doi:10.1007/s13361-019-02138-1
Zheng X., F.B. Smith, N.A. Aly, J. Cai, R.D. Smith, A.D. Patterson, and E.S. Baker. 2019. "Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry." Analytical and Bioanalytical Chemistry 411, no. 19:4673-4682. PNNL-SA-147447. doi:10.1007/s00216-019-01869-0
Wojcik R., G. Nagy, I.K. Attah, I.K. Webb, V. Garimella, K.K. Weitz, and A.L. Hollerbach, et al. 2019. "SLIM Ultrahigh Resolution Ion Mobility Spectrometry Separations of Isotopologues and Isotopomers Reveal Mobility Shifts due to Mass Distribution Changes." Analytical Chemistry 91, no. 18:11952-11962. PNNL-SA-147394. doi:10.1021/acs.analchem.9b02808
Zhang P., M.J. Gaffrey, Y. Zhu, W.B. Chrisler, T.L. Fillmore, L. Yi, and C.D. Nicora, et al. 2019. "Carrier-assisted single-tube processing approach for targeted proteomics analysis of low numbers of mammalian cells." Analytical Chemistry 91, no. 2:1441-1451. PNNL-SA-138130. doi:10.1021/acs.analchem.8b04258
Vasaikar S., C. Huang, X. Wang, V.A. Petyuk, S. Savage, B. Wen, and Y. Dou, et al. 2019. "Proteogenomic analysis of human colon cancer reveals new therapeutic opportunities." Cell 177, no. 4:1035-1049. PNNL-SA-137631. doi:10.1016/j.cell.2019.03.030
Kyle J.E., K.E. Burnum-Johnson, J.P. Wendler, A.J. Eisfeld, P.J. Halfmann, T. Watanabe, and F. Sahr, et al. 2019. "Plasma lipidome reveals critical illness and recovery from human Ebola virus disease." Proceedings of the National Academy of Sciences of the United States of America 116, no. 9:3919-3928. PNNL-SA-136689. doi:10.1073/pnas.1815356116
Dou M., G. Clair, C. Tsai, K. Xu, W.B. Chrisler, R.L. Sontag, and R. Zhao, et al. 2019. "High-Throughput Single Cell Proteomics Enabled by Multiplex Isobaric Labelling in a Nanodroplet Sample Preparation Platform." Analytical Chemistry 91, no. 20:13119-13127. PNNL-SA-146297. doi:10.1021/acs.analchem.9b03349
Dou M., C. Tsai, P.D. Piehowski, Y. Wang, T.L. Fillmore, R. Zhao, and R.J. Moore, et al. 2019. "Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples." Analytical Chemistry 91, no. 15:9707-9715. PNNL-SA-141437. doi:10.1021/acs.analchem.9b01248
Dickinson M., L.N. Anderson, B.M. Webb-Robertson, J.R. Hansen, R.D. Smith, A.T. Wright, and K. Hybiske. 2019. "Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites." PLoS Pathogens 15, no. 4:Article Number e1007698. PNNL-SA-132851. doi:10.1371/journal.ppat.1007698
Dirice E., S. Kahraman, D.F. De Jesus, A. El Ouaamari, G. Basile, R. Baker, and B. Yigit, et al. 2019. "Increased ß-cell proliferation before immune cell invasion prevents progression of type 1 diabetes." Nature Metabolism 1, no. 5:509–518. PNNL-SA-141695. doi:10.1038/s42255-019-0061-8
Yi L., C. Tsai, E. Dirice, A.C. Swensen, J. Chen, T. Shi, and M.A. Gritsenko, et al. 2019. "Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells." Analytical Chemistry 91, no. 9:5794-5801. PNNL-SA-140381. doi:10.1021/acs.analchem.9b00024
Nagarajan A., M. Zhou, A.Y. Nguyen, M.L. Liberton, K. Kedia, T. Shi, and P.D. Piehowski, et al. 2019. "Proteomic insights into phycobilisome degradation, a selective and tightly controlled process in the fast growing cyanobacterium Synechococcus elongatus UTEX 2973." Biomolecules 9, no. 8:Article Number 374. PNNL-SA-146394. doi:10.3390/biom9080374
Zhang Y., Y. Zhong, A.L. Connor, D.P. Miller, R. Cao, J. Shen, and B. Song, et al. 2019. "Folding and Assembly of Short a, ß, y-Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures." Journal of the American Chemical Society 141, no. 36:14239-14248. PNNL-SA-146170. doi:10.1021/jacs.9b06094
Garimella V., G. Nagy, Y.M. Ibrahim, and R.D. Smith. 2019. "Opening new paths for biological applications of ion mobility - Mass spectrometry using structures for lossless ion manipulations." Trends in Analytical Chemistry. TrAC 116. PNNL-SA-140349. doi:10.1016/j.trac.2019.04.021
Burnum-Johnson K.E., X. Zheng, J.N. Dodds, J. Ash, D. Fourches, C.D. Nicora, and J.P. Wendler, et al. 2019. "Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples." Trends in Analytical Chemistry. TrAC 116. PNNL-SA-140985. doi:10.1016/j.trac.2019.04.022
Attah I.K., G. Nagy, V. Garimella, R.V. Norheim, G.A. Anderson, Y.M. Ibrahim, and R.D. Smith. 2019. "Traveling-wave-based electrodynamic switch for concurrent dual-polarity ion manipulations in Structures for Lossless Ion Manipulations." Analytical Chemistry 91, no. 22:14712-14718. PNNL-SA-147653. doi:10.1021/acs.analchem.9b03987
Attah I.K., V. Garimella, I.K. Webb, G. Nagy, R.V. Norheim, C.E. Schimelfenig, and Y.M. Ibrahim, et al. 2019. "Dual Polarity Ion Confinement and Mobility Separations." Journal of the American Society for Mass Spectrometry 30, no. 6:967–976. PNNL-SA-132014. doi:10.1007/s13361-019-02138-1
Moghieb A.M., L. Tesfay, S. Nie, M.A. Gritsenko, T.L. Fillmore, J.M. Jacobs, and R.D. Smith, et al. 2019. "A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification." Scientific Reports 9, no. 1:Article No. 7264. PNNL-SA-138022. doi:10.1038/s41598-019-43756-9
Nagy G., K. Kedia, I.K. Attah, V. Garimella, Y.M. Ibrahim, V.A. Petyuk, and R.D. Smith. 2019. "Separation of ß-Amyloid Tryptic Peptide Species with Isomerized and Racemized L-Aspartic Residues with Ion Mobility in Structures for Lossless Ion Manipulations." Analytical Chemistry 91, no. 7:4374–4380. PNNL-SA-138885. doi:10.1021/acs.analchem.8b04696
Wakasaki R., K. Matsushita, K. Golgotiu, S. Anderson, M.B. Eiwaz, D.J. Orton, and S. Han, et al. 2019. "Glomerular filtrate proteins in acute cardiorenal syndrome." JCI Insight 4, no. 4:Article No. e122130. PNNL-SA-129539. doi:10.1172/jci.insight.122130
Nagy G., D. Velickovic, R.K. Chu, A.A. Carrell, D.J. Weston, Y.M. Ibrahim, and C.R. Anderton, et al. 2019. "Towards Resolving the Spatial Metabolome with Unambiguous Molecular Annotations in Complex Biological Systems by Coupling Mass Spectrometry Imaging with Structures for Lossless Ion Manipulations." Chemical Communications 55, no. 3:306-309. PNNL-SA-138045. doi:10.1039/C8CC07482H

2018

Bilbao Pena A., B.C. Gibbons, G.W. Slysz, K.L. Crowell, M.E. Monroe, Y.M. Ibrahim, and R.D. Smith, et al. 2018. "An Algorithm to Correct Saturated Mass Spectrometry Ion Abundances for Enhanced Quantitation and Mass Accuracy in Omic Studies." International Journal of Mass Spectrometry 427. PNNL-SA-126312. doi:10.1016/j.ijms.2017.11.003
Garabedian A., P. Benigni, C. Ramirez, E.M. Baker, T. Liu, R.D. Smith, and F. Fernandez-Lima. 2018. "Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS." Journal of the American Society for Mass Spectrometry 29, no. 5:817-826. PNNL-SA-129610. doi:10.1007/s13361-017-1787-8
Kyle J.E., N.A. Aly, X. Zheng, K.E. Burnum-Johnson, R.D. Smith, and E.M. Baker. 2018. "Evaluating lipid mediator structural complexity using ion mobility spectrometry combined with mass spectrometry." Bioanalysis 10, no. 5:279-289. PNNL-SA-130733. doi:10.4155/bio-2017-0245
Menachery V.D., A. Schafer, K.E. Burnum-Johnson, H.D. Mitchell, A.J. Eisfeld-Fenney, K.B. Walters, and C.D. Nicora, et al. 2018. "MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape." Proceedings of the National Academy of Sciences of the United States of America 115, no. 5:E1012-E1021. PNNL-SA-126254. doi:10.1073/pnas.1706928115
Nicora C.D., K.E. Burnum-Johnson, E.S. Nakayasu, C.P. Casey, R.A. White, T. Roy Chowdhury, and J.E. Kyle, et al. 2018. "The MPLEx Protocol for Multi-Omic Analyses of Soil Samples." Journal of Visualized Experiments e57343, no. 135. PNNL-SA-129344. doi:10.3791/57343
Ortega C., A. Frando, B.M. Webb-Robertson, L.N. Anderson, N. Fleck, E.L. Flannery, and M. Fishbaugher, et al. 2018. "A global survey of ATPase activity in Plasmodium falciparum asexual blood stages and gametocytes." Molecular and Cellular Proteomics 17, no. 1:111-120. PNNL-SA-121236. doi:10.1074/mcp.RA117.000088
Orton D.J., M.M. Tfaily, R.J. Moore, B.L. Lamarche, X. Zheng, T.L. Fillmore, and R.K. Chu, et al. 2018. "A Customizable Flow Injection System for Automated, High Throughput and Time Sensitive Ion Mobility Spectrometry and Mass Spectrometry Measurements." Analytical Chemistry 90, no. 1:737-744. PNNL-SA-128111. doi:10.1021/acs.analchem.7b02986
Poad B.L., X. Zheng, T.A. Mitchell, R.D. Smith, E.M. Baker, and S.J. Blanksby. 2018. "Online ozonolysis combined with ion mobility-mass spectrometry provides a new platform for lipid isomer analyses." Analytical Chemistry 90, no. 2:1292-1300. PNNL-SA-129778. doi:10.1021/acs.analchem.7b04091
Prabhakaran Nair Syamala Amma A., A.M. Hamid, V. Garimella, B.R. Valenzuela, R.G. Ewing, Y.M. Ibrahim, and R.D. Smith. 2018. "A Hybrid Constant and Oscillatory Field Ion Mobility Analyzer in Structures for Lossless Ion Manipulations." Journal of the American Society for Mass Spectrometry 29, no. 2:342-351. PNNL-SA-126448. doi:10.1007/s13361-017-1841-6
Yi L., T. Shi, M.A. Gritsenko, C. Chan, T.L. Fillmore, B.M. Hess, and A.C. Swensen, et al. 2018. "Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway." Analytical Chemistry 90, no. 8:5256-5263. PNNL-SA-131519. doi:10.1021/acs.analchem.8b00071
Zheng X., R.D. Smith, and E.M. Baker. 2018. "Recent Advances in Lipid Separations and Structural Elucidation Using Mass Spectrometry Combined with Ion Mobility Spectrometry, Ion-Molecule Reactions and Fragmentation Approaches." Current Opinion in Chemical Biology 42. PNNL-SA-131398. doi:10.1016/j.cbpa.2017.11.009
Zhu Y., R. Zhao, P.D. Piehowski, R.J. Moore, S. Lim, V.J. Orphan, and L. Pasa Tolic, et al. 2018. "Subnanogram proteomics: impact of LC column selection, MS instrumentation and data analysis strategy on proteome coverage for trace samples." International Journal of Mass Spectrometry 427. PNNL-SA-125645. doi:10.1016/j.ijms.2017.08.016

2017

Baker E.M., R. Wojcik, I.K. Webb, V. Garimella, S.A. Prost, Y.M. Ibrahim, and R.D. Smith. 2017. "Lipid and Glycolipid Isomer Analyses Using Ultra-high Resolution Ion Mobility Spectrometry Separations." International Journal of Molecular Sciences 18, no. 1:183. PNNL-SA-122274. doi:10.3390/ijms18010183
Burnum-Johnson K.E., J.E. Kyle, A.J. Eisfeld, C.P. Casey, K.G. Stratton, J.F. Gonzalez, and F. Habyarimana, et al. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142, no. 3:442-448. PNNL-SA-116063. doi:10.1039/c6an02486f
Deng L., I.K. Webb, V. Garimella, A.M. Hamid, X. Zheng, R.V. Norheim, and S.A. Prost, et al. 2017. "Serpentine Ultralong Path with Extended Routing (SUPER) High Resolution Traveling Wave Ion Mobility-MS using Structures for Lossless Ion Manipulations." Analytical Chemistry89, no. 8:4628-4634. PNNL-SA-123438. doi:10.1021/acs.analchem.7b00185
Deng L., V. Garimella, A.M. Hamid, I.K. Webb, I.K. Attah, R.V. Norheim, and S.A. Prost, et al. 2017. "Compression Ratio Ion Mobility Programming (CRIMP) Accumulation and Compression of Billions of Ions for Ion Mobility-Mass Spectrometry Using Traveling Waves in Structures for Lossless Ion Manipulations (SLIM)." Analytical Chemistry 89, no. 12:6432-6439. PNNL-SA-123357. doi:10.1021/acs.analchem.7b00189
Dhondt I., V.A. Petyuk, S. Bauer, H.M. Brewer, R.D. Smith, G.G. Depuydt, and B.P. Braeckman. 2017. "Changes of Protein Turnover in Aging Caenorhabditis elegans." Molecular & Cellular Proteomics. MCP 16, no. 9:1621-1633. PNNL-SA-129634. doi:10.1074/mcp.RA117.000049
Eisfeld A.J., P. Halfmann, J.P. Wendler, J.E. Kyle, K.E. Burnum-Johnson, Z. Peralta, and T. Maemura, et al. 2017. "Multi-platform 'Omics Analysis of Human Ebola Virus Disease Pathogenesis." Cell Host & Microbe 22, no. 6:817-829. PNNL-SA-120881. doi:10.1016/j.chom.2017.10.011
Gao H., A. Makarov, and R.D. Smith. 2017. "2016 ASMS Workshop Review: Next Generation LC/MS: Critical Insights and Future Perspectives." Journal of the American Society for Mass Spectrometry 28, no. 7:1248-1249. PNNL-SA-125969. doi:10.1007/s13361-017-1664-5
Garimella V., I.K. Webb, A. Prabhakaran Nair Syamala Amma, I.K. Attah, Y.M. Ibrahim, and R.D. Smith. 2017. "Design of a TW-SLIM Module for Dual Polarity Confinement, Transport, and Reactions." Journal of the American Society for Mass Spectrometry 28, no. 7:1442-1449. PNNL-SA-123670. doi:10.1007/s13361-017-1680-5
Hasan Madar I., S. Ko, H. Kim, D. Mun, S. Kim, R.D. Smith, and S. Lee. 2017. "Multiplexed Post-Experimental Monoisotopic Mass Refinement (mPE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation." Analytical Chemistry 89, no. 2:1244-1253. PNNL-SA-129635. doi:10.1021/acs.analchem.6b03874
Ibrahim Y.M., A.M. Hamid, J.T. Cox, V. Garimella, and R.D. Smith. 2017. "Ion Elevators and Escalators in Multi-level Structures for Lossless Ion Manipulations." Analytical Chemistry 89, no. 3:1972-1977. PNNL-SA-122334. doi:10.1021/acs.analchem.6b04500
Ibrahim Y.M., A.M. Hamid, L. Deng, V. Garimella, I.K. Webb, E.M. Baker, and R.D. Smith. 2017. "New Frontiers for Mass Spectrometry based upon Structures for Lossless Ion Manipulations." Analyst 142, no. 7:1010-1021. PNNL-SA-123137. doi:10.1039/C7AN00031F
Kerkhoven E.J., Y. Kim, S. Wei, C.D. Nicora, T.L. Fillmore, S.O. Purvine, and B.M. Webb-Robertson, et al. 2017. "Leucine biosynthesis is involved in regulating high lipid accumulation in Yarrowia lipolytica." mBio 8, no. 3:Article No. e00857-17. PNNL-SA-122829. doi:10.1128/mBio.00857-17
Kyle J.E., C.P. Casey, K.G. Stratton, E.M. Zink, Y. Kim, X. Zheng, and M.E. Monroe, et al. 2017. "Comparing Identified and Statistically Significant Lipids and Metabolites in 15-Year Old Serum and Dried Blood Spot Samples for Longitudinal Studies." Rapid Communications in Mass Spectrometry 31, no. 5:447-456. PNNL-SA-121197. doi:10.1002/rcm.7808
Kyle J.E., K.L. Crowell, C.P. Casey, G.M. Fujimoto, S. Kim, S.E. Dautel, and R.D. Smith, et al. 2017. "LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data." Bioinformatics 33, no. 11:1744-1746. PNNL-SA-118436. doi:10.1093/bioinformatics/btx046
Liberton M.L., W.B. Chrisler, C.D. Nicora, R.J. Moore, R.D. Smith, D.W. Koppenaal, and H.B. Pakrasi, et al. 2017. "Phycobilisome Truncation Causes Widespread Proteome Changes in Synechocystis sp. PCC 6803." PLoS One 12, no. 3:e0173251. PNNL-SA-112677. doi:10.1371/journal.pone.0173251
Lobanov A.V., S.M. Heaphy, A.A. Turanov, M.V. Gerashchenko, S. Pucciarelli, R.R. Devaraj, and F. Xie, et al. 2017. "Position-dependent termination and widespread obligatory frameshifting in Euplotes translation." Nature Structural & Molecular Biology 24, no. 1:61-68. PNNL-SA-123907. doi:10.1038/nsmb.3330
Ma J., C.P. Casey, X. Zheng, Y.M. Ibrahim, C.S. Wilkins, R.S. Renslow, and D.G. Thomas, et al. 2017. "PIXiE: An Algorithm for Automated Ion Mobility Arrival Time Extraction and Collision Cross Section Calculation using Global Data Association." Bioinformatics 33, no. 17:2715-2722. PNNL-SA-122828. doi:10.1093/bioinformatics/btx305
Metz T.O., E.M. Baker, E.L. Schymanski, R.S. Renslow, D.G. Thomas, T.J. Causon, and I.K. Webb, et al. 2017. "Integrating Ion Mobility Spectrometry into Mass Spectrometry-based Exposome Measurements: What Can It Add and How Far Can It Go?." Bioanalysis 9, no. 1:81-98. PNNL-SA-121158. doi:10.4155/bio-2016-0244
Nie S., T. Shi, T.L. Fillmore, A.A. Schepmoes, H.M. Brewer, Y. Gao, and E. Song, et al. 2017. "Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues." Analytical Chemistry 89, no. 17:9139-9146. PNNL-SA-126297. doi:10.1021/acs.analchem.7b01878
Nielson C., J. Wiedrick, J. Shen, J.M. Jacobs, E.M. Baker, A. Baraff, and P.D. Piehowski, et al. 2017. "Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics." Journal of Bone and Mineral Research 32, no. 7:1559-1567. PNNL-SA-111322. doi:10.1002/jbmr.3125
Park J., P.D. Piehowski, C.S. Wilkins, M. Zhou, J.A. Mendoza, G.M. Fujimoto, and B.C. Gibbons, et al. 2017. "Informed-Proteomics: Open Source Software Package for Top-down Proteomics." Nature Methods 14, no. 9:909-914. PNNL-SA-120171. doi:10.1038/nmeth.4388
Shen Y., N. Tolic, P.D. Piehowski, A.K. Shukla, S. Kim, R. Zhao, and Y. Qu, et al. 2017. "High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics." Journal of Chromatography A 1498. PNNL-SA-104738. doi:10.1016/j.chroma.2017.01.008
Shi T., S. Quek, Y. Gao, C.D. Nicora, S. Nie, T.L. Fillmore, and T. Liu, et al. 2017. "Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins." Oncotarget 8, no. 60:101887-101898. PNNL-SA-128413. doi:10.18632/oncotarget.21710
Smith R.D. 2017. "Having it all, and with any mass spectrometer." LCGC North America 35, no. 8:514-515. PNNL-SA-127178.
Song E., Y. Gao, C. Wu, T. Shi, S. Nie, T.L. Fillmore, and A.A. Schepmoes, et al. 2017. "Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer." Scientific Data. PNNL-SA-122408. doi:10.1038/sdata.2017.91
Stow S., T.J. Causon, X. Zheng, R.T. Kurulugama Lekamlage, T. Mairinger, J.C. May, and E.E. Rennie, et al. 2017. "An Interlaboratory Evaluation of Drift Tube Ion Mobility-Mass Spectrometry Collision Cross Section Measurements." Analytical Chemistry 89, no. 17:9048-9055. PNNL-SA-129678. doi:10.1021/acs.analchem.7b01729
Wang J., Z. Ma, S.A. Carr, P. Mertins, H. Zhang, Z. Zhang, and D.W. Chan, et al. 2017. "Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction." Molecular & Cellular Proteomics. MCP 16, no. 1:121-134. PNNL-SA-124098. doi:10.1074/mcp.M116.060301
Wang S., F. Yang, V.A. Petyuk, A.K. Shukla, M.E. Monroe, M.A. Gritsenko, and K.D. Rodland, et al. 2017. "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease." The Journal of Pathology 243, no. 1:78-88. PNNL-SA-119241. doi:10.1002/path.4929
Yi L., P.D. Piehowski, T. Shi, R.D. Smith, and W. Qian. 2017. "Advances in Microscale Separations towards Nanoproteomics Applications." Journal of Chromatography A. 1523. PNNL-SA-125498. doi:10.1016/j.chroma.2017.07.055
Zheng X., L. Deng, E.M. Baker, Y.M. Ibrahim, V.A. Petyuk, and R.D. Smith. 2017. "Distinguishing D- and L-Aspartic and Isoaspartic Acids in Amyloid ß Peptides with Ultrahigh Resolution Ion Mobility Spectrometry." Chemical Communications 53, no. 56:7913-7916. PNNL-SA-124064. doi:10.1039/C7CC03321D
Zheng X., R. Wojcik, X. Zhang, Y.M. Ibrahim, K.E. Burnum-Johnson, D.J. Orton, and M.E. Monroe, et al. 2017. "Coupling Front-end Separations, Ion Mobility Spectrometry, and Mass Spectrometry for Enhanced Multidimensional Biological and Environmental Analyses." Annual Review of Analytical Chemistry 10. PNNL-SA-121198. doi:10.1146/annurev-anchem-061516-045212
Zheng X., R.S. Renslow, M.M. Makola, I.K. Webb, L. Deng, D.G. Thomas, and N. Govind, et al. 2017. "Structural Elucidation of cis/trans Dicaffeoylquinic Acid Photoisomerization Using Ion Mobility Spectrometry-Mass Spectrometry." The Journal of Physical Chemistry Letters 8, no. 7:1381-1388. PNNL-SA-123119. doi:10.1021/acs.jpclett.6b03015
Zheng X., X. Zhang, N. Schocker, R.S. Renslow, D.J. Orton, J. Khamsi, and R.A. Ashmus, et al. 2017. "Enhancing Glycan Isomer Separations with Metal Ions and Positive and Negative Polarity Ion Mobility Spectrometry-Mass Spectrometry Analyses." Analytical and Bioanalytical Chemistry 409. PNNL-SA-118977. doi:10.1007/s00216-016-9866-4
Zhou J., L. Chen, B. Zhang, Y. Tian, T. Liu, S.N. Thomas, and L. Chen, et al. 2017. "Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues." Journal of Proteome Research 16, no. 12:4523-4530. PNNL-SA-105677. doi:10.1021/acs.jproteome.7b00362

2016

Ahmad R., C.D. Nicora, A.K. Shukla, R.D. Smith, W. Qian, and A.Y. Liu. 2016. "An efficient method for native protein purification in the selected range from prostate cancer tissue digests." Chinese Clinical Oncology 5, no. 6:78. PNNL-SA-123158. doi:10.21037/cco.2016.12.03
Burnum-Johnson K.E., S. Nie, C.P. Casey, M.E. Monroe, D.J. Orton, Y.M. Ibrahim, and M.A. Gritsenko, et al. 2016. "Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Molecular and Cellular Proteomics 15, no. 12:3694-3705. PNNL-SA-118308. doi:10.1074/mcp.M116.061143
Chan C., M.A. Gritsenko, R.D. Smith, and W. Qian. 2016. "The Current State-of-the-Art of Quantitative Phosphoproteomics and Its Applications to Diabetes Research." Expert Review of Proteomics 13, no. 4:421-433. PNNL-SA-115406. doi:10.1586/14789450.2016.1164604
Chen T., Y.M. Ibrahim, I.K. Webb, V. Garimella, X. Zhang, A.M. Hamid, and L. Deng, et al. 2016. "Mobility-Selected Ion Trapping and Enrichment Using Structures for Lossless Ion Manipulations." Analytical Chemistry 88, no. 3:1728-1733. PNNL-SA-113681. doi:10.1021/acs.analchem.5b03910
Clair G., P.D. Piehowski, T. Nicola, J. Kitzmiller, E.L. Huang, E.M. Zink, and R.L. Sontag, et al. 2016. "Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples." Scientific Reports 6. PNNL-SA-119185. doi:10.1038/srep39223
Deng L., Y.M. Ibrahim, A.M. Hamid, V. Garimella, I.K. Webb, X. Zheng, and S.A. Prost, et al. 2016. "Ultra-High Resolution Ion Mobility Separations Utilizing Traveling Waves in a 13-m Serpentine Path Length Structures for Lossless Ion Manipulations Module." Analytical Chemistry 88, no. 18:8957-8964. PNNL-SA-118270. doi:10.1021/acs.analchem.6b01915
Deng L., Y.M. Ibrahim, E.S. Baker, N.A. Aly, A.M. Hamid, X. Zhang, and X. Zheng, et al. 2016. "Ion Mobility Separations of Isomers based upon Long Path Length Structures for Lossless Ion Manipulations Combined with Mass Spectrometry." ChemistrySelect 1, no. 10:2396-2399. PNNL-SA-116187. doi:10.1002/slct.201600460
Deng L., Y.M. Ibrahim, V. Garimella, I.K. Webb, A.M. Hamid, R.V. Norheim, and S.A. Prost, et al. 2016. "Greatly Increasing Trapped Ion Populations for Mobility Separations Using Traveling Waves in Structures for Lossless Ion Manipulations." Analytical Chemistry 88, no. 20:10143-10150. PNNL-SA-119618. doi:10.1021/acs.analchem.6b02678
Dhondt I., V.A. Petyuk, H. Cai, L. Vandemeulebroucke, A. Vierstraete, R.D. Smith, and G.G. Depuydt, et al. 2016. "FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans." Cell Reports 16, no. 11:3028-3040. PNNL-SA-121059. doi:10.1016/j.celrep.2016.07.088
Garimella V., A.M. Hamid, L. Deng, Y.M. Ibrahim, I.K. Webb, E.M. Baker, and S.A. Prost, et al. 2016. "Squeezing of Ion Populations and Peaks in Traveling Wave Ion Mobility Separations and Structures for Lossless Ion Manipulations using Compression Ratio Ion Mobility Programming." Analytical Chemistry 88, no. 23:11877-11885. PNNL-SA-121131. doi:10.1021/acs.analchem.6b03660
Garimella V., Y.M. Ibrahim, K. Tang, I.K. Webb, E.M. Baker, A.V. Tolmachev, and T. Chen, et al. 2016. "Spatial Ion Peak Compression and its Utility in Ion Mobility Spectrometry." Journal of the American Society for Mass Spectrometry 27, no. 6:1128-1135. PNNL-SA-114168. doi:10.1007/s13361-016-1371-7
Gritsenko M.A., Z. Xu, T. Liu, and R.D. Smith. 2016. "Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS." In Quantitative Proteomics by Mass Spectrometry, 2nd edition. Series: Methods in Molecular Biology, edited by S Sechi. 237-247. New York, New York:Springer. PNNL-SA-107351.
Hamid A.M., V. Garimella, Y.M. Ibrahim, L. Deng, X. Zheng, I.K. Webb, and G.A. Anderson, et al. 2016. "Achieving high resolution ion mobility separations using traveling waves in compact multi-turn Structures for Lossless Ion Manipulations modules." Analytical Chemistry 88, no. 18:8949-8956. PNNL-SA-118269. doi:10.1021/acs.analchem.6b01914
Hasin-Brumshtein Y., A.H. Khan, F. Hormozdiari, C. Pan, B. Parks, V.A. Petyuk, and P.D. Piehowski, et al. 2016. "Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes." eLife 2016, no. 5:e15614. PNNL-SA-120999. doi:10.7554/eLife.15614
Hoofnagle A.N., J.R. Whiteaker, S.A. Carr, E. Kuhn, T. Liu, S.A. Massoni, and S.N. Thomas, et al. 2016. "Recommendations for the generation, quantification, storage and handling of peptides used for mass spectrometry-based assays." Clinical Chemistry 62, no. 1:48-69. PNNL-SA-113208. doi:10.1373/clinchem.2015.250563
Huang E.L., P.D. Piehowski, D.J. Orton, R.J. Moore, W. Qian, C.P. Casey, and X. Sun, et al. 2016. "SNaPP: Simplified Nano-Proteomics Platform for reproducible global proteomic analysis of nanogram protein quantities." Endocrinology 157, no. 3:1307-14. PNNL-SA-111854. doi:10.1210/en.2015-1821
Ibrahim Y.M., V. Garimella, S.A. Prost, R. Wojcik, R.V. Norheim, E.M. Baker, and I. Rusyn, et al. 2016. "Development of an Ion Mobility Spectrometry-Orbitrap Mass Spectrometer Platform." Analytical Chemistry 88, no. 24:12152-12160. PNNL-SA-123568. doi:10.1021/acs.analchem.6b03027
Khadempour L., K.E. Burnum-Johnson, E.S. Baker, C.D. Nicora, B.M. Webb-Robertson, R.A. White, and M.E. Monroe, et al. 2016. "The fungal cultivar of leaf-cutter ants produces specific enzymes in response to different plant substrates." Molecular Ecology 25, no. 22:5795-5805. PNNL-SA-113016. doi:10.1111/mec.13872
Kyle J.E., X. Zhang, K.K. Weitz, M.E. Monroe, Y.M. Ibrahim, R.J. Moore, and J. Cha, et al. 2016. "Uncovering Biologically Significant Lipid Isomers with Liquid Chromatography, Ion Mobility Spectrometry and Mass Spectrometry." Analyst 141, no. 5:1649-1659. PNNL-SA-111991. doi:10.1039/C5AN02062J
Liberton M.L., R. Saha, J.M. Jacobs, A.Y. Nguyen, M.A. Gritsenko, R.D. Smith, and D.W. Koppenaal, et al. 2016. "Global Proteomic Analysis Reveals an Exclusive Role of Thylakoid Membranes in Bioenergetics of a Model Cyanobacterium." Molecular and Cellular Proteomics15, no. 6:2021-2032. PNNL-SA-121062. doi:10.1074/mcp.M115.057240
Liberton M.L., R. Saha, J.M. Jacobs, A.Y. Nguyen, M.A. Gritsenko, R.D. Smith, and D.W. Koppenaal, et al. 2016. "Proteomics analysis of isolated plasma membrane and thylakoid membrane from Synechocystis sp. PCC 6803." Molecular and Cellular Proteomics 15, no. 6:2021-2032. PNNL-SA-112674. doi:10.1074/mcp.M115.057240
Liu R., S. Cheng, E.S. Baker, R.D. Smith, X. Zeng, and B. Gong. 2016. "Surprising Impact of Remote Groups on the Folding-Unfolding and Dimer-Chain Equilibria of Bifunctionl H-Bonding Unimers." Chemical Communications 52, no. 19:3773-3776. PNNL-SA-115916. doi:10.1039/C6CC00224B
Nakayasu E.S., C.D. Nicora, A.C. Sims, K.E. Burnum-Johnson, Y. Kim, J.E. Kyle, and M.M. Matzke, et al. 2016. "MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses." mSystems 1, no. 3:e00043-16. PNNL-SA-114737. doi:10.1128/mSystems.00043-16
Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Free 25-Hydroxyvitamin D: Impact of Vitamin D Binding Protein Assays on Racial-Genotypic Associations." Journal of Clinical Endocrinology and Metabolism 101, no. 5:2226-2234. PNNL-SA-120076. doi:10.1210/jc.2016-1104
Nielson C., K. Jones, R.F. Chun, J.M. Jacobs, Y. Wang, M. Hewison, and J.S. Adams, et al. 2016. "Role of Assay Type in Determining Free 25-Hydroxyvitamin D Levels in Diverse Populations." The New England Journal of Medicine 374, no. 17:1695-1696. PNNL-SA-108708. doi:10.1056/NEJMc1513502
Ortega C., L.N. Anderson, A. Frando, N.C. Sadler, R.W. Brown, R.D. Smith, and A.T. Wright, et al. 2016. "Systematic Survey of Serine Hydrolase Activity in Mycobacterium tuberculosis Defines Changes Associated with Persistence." Cell Chemical Biology 23, no. 2:290-298. PNNL-SA-112430. doi:10.1016/j.chembiol.2016.01.003
Otwell A.E., S.J. Callister, E.M. Zink, R.D. Smith, and R.E. Richardson. 2016. "Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-positive Sulfate- and Metal-reducing Bacterium." Frontiers in Microbiology 7. PNNL-SA-115268. doi:10.3389/fmicb.2016.00191
Quaamari A., E. Dirice, N. Gedeon, J. Hu, J. Zhou, J. Shirakawa, and L. Hou, et al. 2016. "SerpinB1 Promotes Pancreatic ß Cell Proliferation." Cell Metabolism 23, no. 1:194-205. PNNL-SA-114412. doi:10.1016/j.cmet.2015.12.001
Ruggles K., Z. Tang, Z. Tang, X. Wang, H. Grover, M. Askenazi, and J. Teubl, et al. 2016. "An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer." Molecular and Cellular Proteomics 15, no. 3:1060-1071. PNNL-SA-105676. doi:10.1074/mcp.M115.056226
Sadler N.C., H.C. Bernstein, M.R. Melnicki, M.A. Charania, E.A. Hill, L.N. Anderson, and M.E. Monroe, et al. 2016. "Dinitrogenase Driven Photobiological Hydrogen Production Combats Oxidative Stress in Cyanothece sp. ATCC 51142." Applied Environmental Microbiology 82, no. 24:7227-7235. PNNL-SA-113160. doi:10.1128/AEM.02098-16
Shi T., E. Song, S. Nie, K.D. Rodland, T. Liu, W. Qian, and R.D. Smith. 2016. "Advances in targeted proteomics and applications to biomedical research." Proteomics 16, no. 15-16:2160-2182. PNNL-SA-120776. doi:10.1002/pmic.201500449
Shi T., M. Niepel, J.E. McDermott, Y. Gao, C.D. Nicora, W.B. Chrisler, and L.M. Markillie, et al. 2016. "Conservation of Protein Abundance Patterns Reveals the Regulatory Architecture of the of the EGFR-MAPK Pathway." Science Signaling 9, no. 436:rs6. PNNL-SA-115056. doi:10.1126/scisignal.aaf0891
Sigdel T.K., Y. Gao, J. He, A. Wang, C.D. Nicora, T.L. Fillmore, and T. Shi, et al. 2016. "Mining the Human Urine Proteome for Monitoring Renal Transplant Injury." Kidney International 89, no. 6:1244-1252. PNNL-SA-115293. doi:10.1016/j.kint.2015.12.049
Smith D., C.D. Nicora, P. Carini, M.S. Lipton, A.D. Norbeck, R.D. Smith, and S.J. Giovannoni. 2016. "Proteome Remodeling in Response to Sulfur Limitation in “Candidatus Pelagibacter ubique”." mSystems 1, no. 4:e00068-16. PNNL-SA-113512. doi:10.1128/mSystems.00068-16
Sun J., J.D. Todd, J. Thrash, Y. Qian, M.C. Qian, B. Temperton, and J. Guo, et al. 2016. "The abundant marine bacterium Pelagibacter simultaneously catabolizes dimethylsulfoniopropionate to the gases dimethyl sulfide and methanethiol." Nature Microbiology 1, no. 8:Article No. 16065. PNNL-SA-108154. doi:10.1038/nmicrobiol.2016.65
Tabb D.L., X. Wang, S.A. Carr, K. Clauser, P. Mertins, M.C. Chambers, and J.D. Holman, et al. 2016. "Reproducibility of differential proteomic technologies in CPTAC fractionated xenografts." Journal of Proteome Research 15, no. 3:691-706. PNNL-SA-113210. doi:10.1021/acs.jproteome.5b00859
Tisoncik-Go J., D.J. Gasper, J.E. Kyle, A.J. Eisfeld, C. Selinger, M. Hatta, and J. Morrison, et al. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19, no. 2:254-66. PNWD-SA-10483. doi:10.1016/j.chom.2016.01.002
van Baren M.J., C. Bachy, E. Reistetter, S.O. Purvine, J. Grimwood, S. Sudek, and H. Yu, et al. 2016. "Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants." BMC Genomics 17. PNNL-SA-114561. doi:10.1186/s12864-016-2585-6
Waltman P., J. Guo, E. Reistetter, S.O. Purvine, C. Ansong, M.J. van Baren, and C. Wong, et al. 2016. "Identifying Aspects of the Post-transcriptional Program Governing the Proteome of the Green Algal Micromonas pusilla." PLoS One 11, no. 7:Article No. e0155839. PNNL-SA-115265. doi:10.1371/journal.pone.0155839
Wang H., T. Shi, W. Qian, T. Liu, J. Kagan, S. Srivastava, and R.D. Smith, et al. 2016. "The Clinical Impact of Recent Advances in LC-MS for Cancer Biomarker Discovery and Verification." Expert Review of Proteomics 13, no. 1:99-114. PNNL-SA-113659. doi:10.1586/14789450.2016.1122529
Webb I.K., V. Garimella, R.V. Norheim, E.S. Baker, Y.M. Ibrahim, and R.D. Smith. 2016. "A Structures for Lossless Ion Manipulations (SLIM) Module for Collision Induced Dissociation." Journal of the American Society for Mass Spectrometry 27, no. 7:1285-1288. PNNL-SA-115654. doi:10.1007/s13361-016-1397-x
Whiteaker J.R., G. Halusa, A.N. Hoofnagle, V. Sharma, B. MacLean, P. Yan, and J. Wrobel, et al. 2016. "Using the CPTAC Assay Portal to identify and implement highly characterized targeted proteomics assays." In Quantitative Proteomics by Mass Spectrometry, 2nd edition. Series: Methods in Molecular Biology, edited by S Sechi. 223-263. New York, New York:Springer. PNNL-SA-110086. doi:10.1007/978-1-4939-3524-6_13
Wu C., J. Duan, T. Liu, R.D. Smith, and W. Qian. 2016. "Contributions of Immunoaffinity Chromatography to Deep Proteome Profiling of Human Biofluids." Journal of Chromatography B 1021. PNNL-SA-112289. doi:10.1016/j.jchromb.2016.01.015
Zhang H., T. Liu, Z. Zhang, S.H. Payne, B. Zhang, J.E. McDermott, and J. Zhou, et al. 2016. "Integrated proteogenomic characterization of human high grade serous ovarian cancer." Cell166, no. 3:755-765. PNNL-SA-107151. doi:10.1016/j.cell.2016.05.069
Zhang X., M.V. Romm, X. Zheng, E.M. Zink, Y. Kim, K.E. Burnum-Johnson, and D.J. Orton, et al. 2016. "SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in bio?uids." Clinical Mass Spectrometry 2. PNNL-SA-117436. doi:10.1016/j.clinms.2016.11.002

2015

Aylward F.O., L. Khadempour, D. Tremmel, B.R. McDonald, C.D. Nicora, S. Wu, and R.J. Moore, et al. 2015. "Enrichment and Broad Representation of Plant Biomass-Degrading Enzymes in the Specialized Hyphal Swellings of Leucoagaricus gongylophorus, the Fungal Symbiont of Leaf-Cutter Ants." PLoS One 10, no. 8:e0134752. PNNL-SA-108498. doi:10.1371/journal.pone.0134752
Baker E.S., K.E. Burnum-Johnson, Y.M. Ibrahim, D.J. Orton, M.E. Monroe, R.T. Kelly, and R.J. Moore, et al. 2015. "Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations." Proteomics 15, no. 16:2766-2776. PNNL-SA-107785. doi:10.1002/pmic.201500048
Bhatt S., M. Gupta, M. Khamaisi, R. Martinez, M.A. Gritsenko, B. Wagner, and P. Guye, et al. 2015. "Preserved DNA Damage Checkpoint Pathway Protects against Complications in Long-Standing Type 1 Diabetes." Cell Metabolism 22, no. 2:239-252. PNNL-SA-113658. doi:10.1016/j.cmet.2015.07.015
Burnet M.C., A. Dohnalkova, A.P. Neumann, M.S. Lipton, R.D. Smith, G. Suen, and S.J. Callister. 2015. "Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85." PLoS One 10, no. 12:e0143809. PNNL-SA-111279. doi:10.1371/journal.pone.0143809
Chen T., I.K. Webb, S.A. Prost, M.B. Harrer, R.V. Norheim, K. Tang, and Y.M. Ibrahim, et al. 2015. "Rectangular Ion Funnel: A New Ion Funnel Interface for Structures for Lossless Ion Manipulations." Analytical Chemistry 87, no. 1:716-722. PNNL-SA-105304. doi:10.1021/ac503564c
Chen T., T.L. Fillmore, S.A. Prost, R.J. Moore, Y.M. Ibrahim, and R.D. Smith. 2015. "Orthogonal Injection Ion Funnel Interface Providing Enhanced Performance for Selected Reaction Monitoring-Triple Quadruple Mass Spectrometry." Analytical Chemistry 87, no. 14:7326-7331. PNNL-SA-109430. doi:10.1021/acs.analchem.5b01482
Chen Y., F.E. Leach, N.K. Kaiser, X. Dang, Y.M. Ibrahim, R.V. Norheim, and G.A. Anderson, et al. 2015. "Improved ion optics for introduction of ions into a 9.4-T Fourier transform ion cyclotron resonance mass spectrometer." Journal of Mass Spectrometry 50, no. 1:280-284. PNNL-SA-104452. doi:10.1002/jms.3523
Cox J.T., I. Marginean, R.D. Smith, and K. Tang. 2015. "On the Ionization and Ion Transmission Efficiencies of Different ESI-MS Interfaces." Journal of the American Society for Mass Spectrometry 26, no. 1:55-62. PNNL-SA-103142. doi:10.1007/s13361-014-0998-5
Duan J., V.K. Kodali, M.J. Gaffrey, J. Guo, R.K. Chu, D.G. Camp, and R.D. Smith, et al. 2015. "Quantitative Profiling of Protein S-Glutathionylation Reveals Redox-Dependent Regulation of Macrophage Function During Nanoparticle-Induced Oxidative Stress." ACS Nano 10, no. 1:524-538. PNNL-SA-112721. doi:10.1021/acsnano.5b05524
EL Ouaaman A., J. Zhou, C. Liew, J. Shirakawa, E. Dirice, N. Gedeon, and S. Kahraman, et al. 2015. "Compensatory Islet Response to Insulin Resistance Revealed by Quantitative Proteomics." Journal of Proteome Research 14, no. 8:3111-3122. PNNL-SA-100672. doi:10.1021/acs.jproteome.5b00587
Garimella V., Y.M. Ibrahim, I.K. Webb, A.B. Ipsen, T. Chen, A.V. Tolmachev, and E.S. Baker, et al. 2015. "ION MANIPULATIONS IN STRUCTURES FOR LOSSLESS ION MANIPULATIONS (SLIM): COMPUTATIONAL EVALUATION OF A 90o TURN AND A SWITCH." Analyst 140, no. 20:6845-6852. PNNL-SA-107773. doi:10.1039/c5an00844a
Hamid A.M., Y.M. Ibrahim, V. Garimella, I.K. Webb, L. Deng, T. Chen, and G.A. Anderson, et al. 2015. "Characterization of Traveling Wave Ion Mobility Separations in Structures for Lossless Ion Manipulations." Analytical Chemistry 87, no. 22:11301-11308. PNNL-SA-111147. doi:10.1021/acs.analchem.5b02481
He J., A.A. Schepmoes, T. Shi, C. Wu, T.L. Fillmore, Y. Gao, and R.D. Smith, et al. 2015. "Analytical platform evaluation for quantification of ERG in prostate cancer using protein and mRNA detection methods." Journal of Translational Medicine 13. PNNL-SA-107827. doi:10.1186/s12967-015-0418-z
Ibrahim Y.M., E.M. Baker, W.F. Danielson, R.V. Norheim, D.C. Prior, G.A. Anderson, and M.E. Belov, et al. 2015. "Development of a New Ion Mobility Time-of-Flight Mass Spectrometer." International Journal of Mass Spectrometry 377. PNNL-SA-119651. doi:10.1016/j.ijms.2014.07.034
Ibrahim Y.M., E.S. Baker, W.F. Danielson, R.V. Norheim, D.C. Prior, G.A. Anderson, and M.E. Belov, et al. 2015. "Development of a New Ion Mobility (Quadrupole) Time-of-Flight Mass Spectrometer." International Journal of Mass Spectrometry 377. PNNL-SA-102133. doi:10.1016/j.ijms.2014.07.034
Kebaabetswe L.P., A.K. Haick, M.A. Gritsenko, T.L. Fillmore, R.K. Chu, S.O. Purvine, and B.M. Webb-Robertson, et al. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438. PNWD-SA-10439. doi:10.1016/j.virol.2015.03.045
Lin T., G.A. Anderson, R.V. Norheim, S.A. Prost, B.L. Lamarche, F.E. Leach, and K.J. Auberry, et al. 2015. "An Adaptable Multiple Power Source for Mass Spectrometry and other Scientific Instruments." Review of Scientific Instruments 86, no. 9:Article No. 094102. PNNL-SA-110063. doi:10.1063/1.4930967
Liu Y., J.K. Fredrickson, N.C. Sadler, P. Nandhikonda, R.D. Smith, and A.T. Wright. 2015. "Advancing Understanding of Microbial Bioenergy Conversion Processes by Activity-Based Protein Profiling." Biotechnology for Biofuels 8. PNNL-SA-107650. doi:10.1186/s13068-015-0343-7
Merkley E.D., K.C. Wrighton, C. Castelle, B.J. Anderson, M.J. Wilkins, V. Shah, and T. Arbour, et al. 2015. "Changes in protein expression across laboratory and field experiments in Geobacter bemidjiensis." Journal of Proteome Research 14, no. 3:1361-1375. PNNL-SA-104781. doi:10.1021/pr500983v
Nakayasu E.S., M.A. Sydor, R.N. Brown, R.L. Sontag, T. Sobreira, G.W. Slysz, and D.R. Humphrys, et al. 2015. "Identification of Salmonella Typhimurium deubiquitinase SseL substrates by immunoaffinity enrichment and quantitative proteomic analysis." Journal of Proteome Research 14, no. 9:4029-4038. PNNL-SA-101042. doi:10.1021/acs.jproteome.5b00574
Payne S.H., M.E. Monroe, C.C. Overall, G.R. Kiebel, M.G. Degan, B.C. Gibbons, and G.M. Fujimoto, et al. 2015. "The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity." Scientific Data 2. PNNL-SA-108944. doi:10.1038/sdata.2015.41
Sigdel T.K., Y. NG, S. Lee, C.D. Nicora, W. Qian, R.D. Smith, and D.G. Camp, et al. 2015. "Perturbations in the Urinary Exosome in Transplant Rejection." Frontiers of Medicine 1. PNNL-SA-106428. doi:10.3389/fmed.2014.00057
Ting Y.S., J.D. Egertson, S.H. Payne, S. Kim, B. MacLean, L. Kall, and R. Aebersold, et al. 2015. "Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data." Molecular and Cellular Proteomics 14. PNNL-SA-107046. doi:10.1074/mcp.O114.047035
Vrablik T.L., V.A. Petyuk, E.M. Larson, R.D. Smith, and J. Watts. 2015. "Lipidomic and proteomic analysis of Caenorhabditis elegans lipid droplets and identi?cation of ACS-4 as a lipid droplet-associated protein." Biochimica and Biophysica Acta. Molecular and Cell Biology of Lipids. 1851, no. 10:1337-1345. PNNL-SA-108157. doi:10.1016/j.bbalip.2015.06.004
Webb-Robertson B.M., H.K. Wiberg, M.M. Matzke, J.N. Brown, J. Wang, J.E. McDermott, and R.D. Smith, et al. 2015. "Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics." Journal of Proteome Research 14, no. 5:1993-2001. PNWD-SA-10158. doi:10.1021/pr501138h
Wu C., M.E. Monroe, Z. Xu, G.W. Slysz, S.H. Payne, K.D. Rodland, and T. Liu, et al. 2015. "An Optimized Informatics Pipeline for Mass Spectrometry-Based Peptidomics." Journal of the American Society for Mass Spectrometry 26, no. 12:2002-2008. PNNL-SA-108032. doi:10.1007/s13361-015-1169-z
Wu C., T. Liu, E.S. Baker, K.D. Rodland, and R.D. Smith. 2015. "Mass spectrometry for biomarker development." In General Methods in Biomarker Research and their Applications. Biomarkers in Disease: Methods, Discoveries and Applications, edited by V Preedy and V Patel. 17-48. Heidelberg:Springer. PNNL-SA-97608.
Xu Z., C. Wu, F. Xie, G.W. Slysz, N. Tolic, M.E. Monroe, and V.A. Petyuk, et al. 2015. "Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes." Journal of Proteome Research 14, no. 1:422-433. PNNL-SA-103951. doi:10.1021/pr500840w
Yu J., M.L. Liberton, P. Cliften, R. Head, J.M. Jacobs, R.D. Smith, and D.W. Koppenaal, et al. 2015. "Synechococcus elongatus UTEX 2973, a fast growing cyanobacterial chassis for biosynthesis using light and CO2." Scientific Reports 5. PNNL-SA-105375. doi:10.1038/srep08132
Zhang X., V. Garimella, S.A. Prost, I.K. Webb, T. Chen, K. Tang, and A.V. Tolmachev, et al. 2015. "Ion Trapping, Storage, and Ejection in Structures for Lossless Ion Manipulations." Analytical Chemistry 87, no. 12:6010-6016. PNNL-SA-107651. doi:10.1021/acs.analchem.5b00214
Zhang X., Y.M. Ibrahim, T. Chen, J.E. Kyle, R.V. Norheim, M.E. Monroe, and R.D. Smith, et al. 2015. "Enhancing Biological Analyses with Three Dimensional Field Asymmetric Ion Mobility, Low Field Drift Time Ion Mobility and Mass Spectrometry (µFAIMS/IMS-MS) Separations." Analyst 140. PNNL-SA-110080. doi:10.1039/c5an00897b

2014

Aevermann B., B.E. Pickett, S. Kumar, E.B. Klem, S. Agnihothram, P.S. Askovich, and A. Bankhead, et al. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1. PNNL-SA-101269. doi:10.1038/sdata.2014.33
Amidan B.G., D.J. Orton, B.L. Lamarche, M.E. Monroe, R.J. Moore, A.M. Venzin, and R.D. Smith, et al. 2014. "Signatures for Mass Spectrometry Data Quality." Journal of Proteome Research 13, no. 4:2215-2222. PNNL-SA-97216. doi:10.1021/pr401143e
Ansong C., N.C. Sadler, E.A. Hill, M.P. Lewis, E.M. Zink, R.D. Smith, and A.S. Beliaev, et al. 2014. "Characterization of protein redox dynamics induced during light-to-dark transitions and nutrient limitation in cyanobacteria." Frontiers in Microbiology 5. PNNL-SA-101966. doi:10.3389/fmicb.2014.00325
Aryal U.K., S.J. Callister, B.H. McMahon, L.A. McCue, J.N. Brown, J. Stockel, and M.L. Liberton, et al. 2014. "Proteomic profiles of five strains of oxygenic photosynthetic cyanobacteria of the genus Cyanothece." Journal of Proteome Research 13, no. 7:3262-3276. PNNL-SA-102687. doi:10.1021/pr5000889
Baker E.S., K.E. Burnum-Johnson, J.M. Jacobs, D.L. Diamond, R.N. Brown, Y.M. Ibrahim, and D.J. Orton, et al. 2014. "Advancing the High Throughput Identification of Liver Fibrosis Protein Signatures Using Multiplexed Ion Mobility Spectrometry." Molecular and Cellular Proteomics13, no. 4:1119-1127. PNNL-SA-90826. doi:10.1074/mcp.M113.034595
Brown J.N., H.M. Brewer, C.D. Nicora, K.K. Weitz, M.J. Morris, A.J. Skabelund, and J.N. Adkins, et al. 2014. "Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea." BMC Medical Genomics 7. PNWD-SA-10347. doi:10.1186/1755-8794-7-58
Cox J.T., I. Marginean, R.T. Kelly, R.D. Smith, and K. Tang. 2014. "Improving the Sensitivity of Mass Spectrometry by Using a New Sheath Flow Electrospray Emitter Array at Subambient Pressures." Journal of the American Society for Mass Spectrometry 25, no. 12:2028-37. PNNL-SA-96045. doi:10.1007/s13361-014-0856-5
Cox J.T., S.R. Kronewitter, A.K. Shukla, R.J. Moore, R.D. Smith, and K. Tang. 2014. "High Sensitivity Combined with Extended Structural Coverage of Labile Compounds via Nanoelectrospray Ionization at Subambient Pressures." Analytical Chemistry 86, no. 19:9504-9511. PNNL-SA-102134. doi:10.1021/ac502767y
Depuydt G.G., F. Xie, V.A. Petyuk, A. Smolders, H.M. Brewer, D.G. Camp, and R.D. Smith, et al. 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, no. 4:1938-1956. PNNL-SA-86677. doi:10.1021/pr401081b
Dominy S., J.N. Brown, M.I. Ryder, M.A. Gritsenko, J.M. Jacobs, and R.D. Smith. 2014. "Proteomic Analysis of Saliva in HIV-positive Heroin Addicts Reveals Proteins Correlated with Cognition." PLoS One 9, no. 4:e89366. PNNL-SA-95909. doi:10.1371/journal.pone.0089366
Fujimoto G.M., M.E. Monroe, L.M. Rodriguez, C. Wu, B. MacLean, R.D. Smith, and M. MacCoss, et al. 2014. "Accounting for population variation in targeted proteomics." Journal of Proteome Research 13, no. 1:321-323. PNNL-SA-99100. doi:10.1021/pr4011052
Garimella V., Y.M. Ibrahim, I.K. Webb, A.V. Tolmachev, X. Zhang, S.A. Prost, and G.A. Anderson, et al. 2014. "Simulation of Electric Potentials and Ion Motion in Planar Electrode Structures for Lossless Ion Manipulations (SLIM)." Journal of the American Society for Mass Spectrometry 25, no. 11:1890-1896. PNNL-SA-103104. doi:10.1007/s13361-014-0976-y
Granholm V., S. Kim, J.C. Navarro, E. Sjolund, R.D. Smith, and L. Kall. 2014. "Fast and accurate database searches with MS-GF+Percolator." Journal of Proteome Research 13, no. 2:890-897. PNNL-SA-96119. doi:10.1021/pr400937n
Guo J., M.J. Gaffrey, D. Su, T. Liu, D.G. Camp, R.D. Smith, and W. Qian. 2014. "Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications." Nature Protocols 9, no. 1:64-75. PNNL-SA-96060. doi:10.1038/nprot.2013.161
He J., X. Sun, T. Shi, A.A. Schepmoes, T.L. Fillmore, V.A. Petyuk, and F. Xie, et al. 2014. "Antibody-independent Targeted Quantification of TMPRSS2-ERG Fusion Protein Products in Prostate Cancer." Molecular Oncology 8, no. 7:1169-1180. PNNL-SA-97917. doi:10.1016/j.molonc.2014.02.004
Huang E.L., F.O. Aylward, Y. Kim, B.M. Webb-Robertson, C.D. Nicora, Z. Hu, and T.O. Metz, et al. 2014. "The fungus gardens of leaf-cutter ants undergo a distinct physiological transition during biomass degradation." Environmental Microbiology Reports 6, no. 4:389-95. PNNL-SA-96938. doi:10.1111/1758-2229.12163
Hyung S., P.D. Piehowski, R.J. Moore, D.J. Orton, A.A. Schepmoes, T.R. Clauss, and R.K. Chu, et al. 2014. "Microscale Depletion of High Abundance Proteins in Human Biofluids using IgY14 Immunoaffinity Resin: Analysis of Human Plasma and Cerebrospinal Fluid." Analytical and Bioanalytical Chemistry 406, no. 28:7117-7125. PNNL-SA-92758. doi:10.1007/s00216-014-8058-3
Ibrahim Y.M., V. Garimella, A.V. Tolmachev, E.S. Baker, and R.D. Smith. 2014. "Improving Ion Mobility Measurement Sensitivity by Utilizing Helium in an Ion Funnel-Trap." Analytical Chemistry 86, no. 11:5295-5299. PNNL-SA-100190. doi:10.1021/ac404250z
Jonkers W., A.C. Leeder, C. Ansong, Y. Wang, F. Yang, T.L. Starr, and D.G. Camp, et al. 2014. "HAM-5 functions as a MAP kinase scaffold during cell fusion in Neurospora crassa." PLoS Genetics 10, no. 11:Article No. e1004783. PNNL-SA-103955. doi:10.1371/journal.pgen.1004783
Kronewitter S.R., G.W. Slysz, I. Marginean, C.D. Hagler, B.L. Lamarche, R. Zhao, and M.Y. Harris, et al. 2014. "GlyQ-IQ: Glycomics Quintavariate-Informed Quantification with High-Performance Computing and GlycoGrid 4D Visualization." Analytical Chemistry 86, no. 13:6268-6276. PNNL-SA-100272. doi:10.1021/ac501492f
Kronewitter S.R., I. Marginean, J.T. Cox, R. Zhao, C.D. Hagler, A.K. Shukla, and T.S. Carlson, et al. 2014. "Polysialylated N-Glycans Identified in Human Serum Through Combined Developments in Sample Preparation, Separations and Electrospray ionization-mass spectrometry." Analytical Chemistry 86, no. 17:8700-10. PNNL-SA-102819. doi:10.1021/ac501839b
Malouli D., S.G. Hansen, E.S. Nakayasu, E.E. Marshall, C.M. Hughes, A.B. Ventura, and R.M. Gilbride, et al. 2014. "Cytomegalovirus pp65 limits dissemination but is dispensable for persistence." Journal of Clinical Investigation 124, no. 5:1928-1944. PNNL-SA-91084. doi:10.1172/JCI67420
Marginean I., K. Tang, R.D. Smith, and R.T. Kelly. 2014. "Picoelectrospray Ionization Mass Spectrometry Using Narrow-bore Chemically Etched Emitters." Journal of the American Society for Mass Spectrometry 25, no. 1:30-36. PNNL-SA-97221. doi:10.1007/s13361-013-0749-z
Martin J.L., P.A. Yates, R. Soysa, J.F. Alfaro, F. Yang, K.E. Burnum-Johnson, and V.A. Petyuk, et al. 2014. "Metabolic Reprogramming During Purine Stress in the Protozoan Pathogen Leishmania donovani." PLoS Pathogens 10, no. 2:e1003938. PNNL-SA-96975. doi:10.1371/journal.ppat.1003938
Menachery V., A.J. Eisfeld, A. Schafer, L. Josset, A.C. Sims, S. Proll, and S. Fan, et al. 2014. "Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-Stimulated Gene Responses." mBio 5, no. 3:Article No. e01174-14. PNWD-SA-9990. doi:10.1128/mBio.01174-14
Merkley E.D., T.O. Metz, R.D. Smith, J. Baynes, and N. Frizell. 2014. "The Succinated Proteome." Mass Spectrometry Reviews 33, no. 22:98-109. PNNL-SA-92730. doi:10.1002/mas.21382
Mertins P., F. Yang, T. Liu, D. Mani, V.A. Petyuk, M. Gillette, and K. Clauser, et al. 2014. "Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels." Molecular & Cellular Proteomics. MCP 13, no. 7:1690-1704. PNNL-SA-98702. doi:10.1074/mcp.M113.036392
Nakayasu E.S., S. Wu, M.A. Sydor, A.K. Shukla, K.K. Weitz, R.J. Moore, and K.K. Hixson, et al. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014. PNNL-SA-96571. doi:10.1155/2014/730725
Prost S.A., K.L. Crowell, E.S. Baker, Y.M. Ibrahim, B.H. Clowers, M.E. Monroe, and G.A. Anderson, et al. 2014. "Detecting and Removing Data Artifacts in Hadamard Transform Ion Mobility-Mass Spectrometry Measurements." Journal of the American Society for Mass Spectrometry 25, no. 12:2020-2027. PNNL-SA-100086. doi:10.1007/s13361-014-0895-y
Ryu S., W. Qian, D.G. Camp, R.D. Smith, R.G. Tompkins, R.W. Davis, and W. Xiao. 2014. "Detecting differential protein expression in large-scale population proteomics." Bioinformatics30, no. 19:2741-2746. PNNL-SA-100193. doi:10.1093/bioinformatics/btu341
Sadler N.C., M.R. Melnicki, M.H. Serres, E.D. Merkley, W.B. Chrisler, E.A. Hill, and M.F. Romine, et al. 2014. "Live Cell Chemical Profiling of Temporal Redox Dynamics in a Photoautotrophic Cyanobacterium." ACS Chemical Biology 9, no. 1:291-300. PNNL-SA-93812. doi:10.1021/cb400769v
Shen Y., L. Pasa-Tolic, E.W. Robinson, J.N. Adkins, and R.D. Smith. 2014. "New challenges for proteomics technologies: a mini perspective review." Austin Journal of Proteomics, Bioinformatics & Genomics 1, no. 1:Article No. 3. PNNL-SA-106057.
Shi T., Y. Gao, M.J. Gaffrey, C.D. Nicora, T.L. Fillmore, W.B. Chrisler, and M.A. Gritsenko, et al. 2014. "Sensitive Targeted Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells without Affinity Enrichment." Analytical Chemistry 87, no. 2:1103-1110. PNNL-SA-103421. doi:10.1021/ac503797x
Shi T., Y. Gao, S. Quek, T.L. Fillmore, C.D. Nicora, D. Su, and R. Zhao, et al. 2014. "A highly sensitive targeted mass spectrometric assay for quantification of low-abundance AGR2 in human urine and serum." Journal of Proteome Research 13, no. 2:875-882. PNWD-SA-10119. doi:10.1021/pr400912c
Shin A.C., M. Fasshauer, N. Filatova, L.A. Grundell, E. Zielinski, J. Zhou, and T. Scherer, et al. 2014. "Brain insulin lowers circulating BCAA levels by inducing hepatic BCAA catabolism." Cell Metabolism 20, no. 5:898-909. PNNL-SA-103823. doi:10.1016/j.cmet.2014.09.003
Shvartsburg A.A., Y.M. Ibrahim, and R.D. Smith. 2014. "Differential Ion Mobility Separations in up to 100% Helium Using Microchips." Journal of the American Society for Mass Spectrometry25, no. 3:480-489. PNNL-SA-97871. doi:10.1007/s13361-013-0797-4
Sigdel T.K., N. Salomonis, C.D. Nicora, S. Ryu, J. He, V. Dinh, and D.J. Orton, et al. 2014. "The Identification of Novel Potential Injury Mechanisms and Candidate Biomarkers in Renal Allograft Rejection by Quantitative Proteomics." Molecular & Cellular Proteomics. MCP 13, no. 2:621-631. PNWD-SA-10124. doi:10.1074/mcp.M113.030577
Slysz G.W., L.A. Steinke, D.M. Ward, C.G. Klatt, T.R. Clauss, S.O. Purvine, and S.H. Payne, et al. 2014. "Automated data extraction from in situ protein stable isotope probing studies." Journal of Proteome Research 13, no. 3:1200-1210. PNNL-SA-96672. doi:10.1021/pr400633j
Smith J.S., T.E. Angel, C. Chavkin, D.J. Orton, R.J. Moore, and R.D. Smith. 2014. "Characterization of individual mouse cerebrospinal fluid proteomes." Proteomics 14, no. 9:1102-1106. PNNL-SA-93378. doi:10.1002/pmic.201300241
Su D., M.J. Gaffrey, J. Guo, K.E. Hatchell, R.K. Chu, T.R. Clauss, and J.T. Aldrich, et al. 2014. "Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling." Free Radical Biology & Medicine 67. PNNL-SA-96702. doi:10.1016/j.freeradbiomed.2013.12.004
Tolmachev A.V., I.K. Webb, Y.M. Ibrahim, V. Garimella, X. Zhang, G.A. Anderson, and R.D. Smith. 2014. "Characterization of Ion Dynamics in Structures for Lossless Ion Manipulations." Analytical Chemistry 86, no. 18:9162-9168. PNNL-SA-103154. doi:10.1021/ac502054p
Wang S., F. Yang, D.G. Camp, K.D. Rodland, W. Qian, T. Liu, and R.D. Smith. 2014. "Proteomic Approaches for Site-specific O-GlcNAcylation Analysis." Bioanalysis 6, no. 19:2571-2580. PNNL-SA-102529. doi:10.4155/bio.14.239
Webb I.K., T. Chen, W.F. Danielson, Y.M. Ibrahim, K. Tang, G.A. Anderson, and R.D. 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, no. 4:563-571. PNNL-SA-98909. doi:10.1007/s13361-013-0815-6
Webb I.K., V. Garimella, A.V. Tolmachev, T. Chen, X. Zhang, J.T. Cox, and R.V. Norheim, et al. 2014. "Mobility-Resolved Ion Selection in Uniform Drift Field Ion Mobility Spectrometry/Mass Spectrometry; Dynamic Switching in Structures for Lossless Ion Manipulations." Analytical Chemistry 86, no. 19:9632-9637. PNNL-SA-103347. doi:10.1021/ac502139e
Webb I.K., V. Garimella, A.V. Tolmachev, T. Chen, X. Zhang, R.V. Norheim, and S.A. Prost, et al. 2014. "Experimental Evaluation and Optimization of Structures for Lossless Ion Manipulations for Ion Mobility Spectrometry with Time-of-Flight Mass Spectrometry." Analytical Chemistry 86, no. 18:9169-9176. PNNL-SA-103224. doi:10.1021/ac502055e
Webb-Robertson B.M., M.M. Matzke, S. Datta, S.H. Payne, J. Kang, L.M. Bramer, and C.D. Nicora, et al. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13, no. 12:3639-3646. PNNL-SA-95335. doi:10.1074/mcp.M113.030932
Welkie D.G., X. Zhang, L.M. Markillie, R.C. Taylor, G. Orr, J.M. Jacobs, and K. Bhide, et al. 2014. "Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle." BMC Genomics15. PNNL-SA-104956.
Whiteaker J.R., G. Halusa, A.N. Hoofnagle, V. Sharma, B. MacLean, P. Yan, and J. Wrobel, et al. 2014. "CPTAC Assay Portal: a repository of targeted proteomic assays." Nature Methods11, no. 7:703-704. PNNL-SA-103950. doi:10.1038/nmeth.3002
Wiedner S.D., L.N. Anderson, N.C. Sadler, W.B. Chrisler, V.K. Kodali, R.D. Smith, and A.T. Wright. 2014. "Organelle-Specific Activity-Based Protein Profiling in Living Cells." Angewandte Chemie International Edition 53, no. 11:2919-2922. PNNL-SA-98713. doi:10.1002/anie.201309135
Woo S., S. Cha, S. Na, C. Guest, T. Liu, R.D. Smith, and K.D. Rodland, et al. 2014. "Proteogenomic strategies for identification of aberrant cancer peptides using large-scale Next Generation Sequencing data." Proteomics 14, no. 23-24:2719-2730. PNNL-SA-105664. doi:10.1002/pmic.201400206
Wu C., T. Shi, J.N. Brown, J. He, Y. Gao, T.L. Fillmore, and A.K. Shukla, et al. 2014. "Expediting SRM assay development for large-scale targeted proteomics experiments." Journal of Proteome Research 13, no. 10:4479-87. PNNL-SA-102906. doi:10.1021/pr500500d
Wu S., J.N. Brown, N. Tolic, D. Meng, X. Liu, H. Zhang, and R. Zhao, et al. 2014. "Quantitative Analysis of Human Salivary Gland-Derived Intact Proteome Using Top-Down Mass Spectrometry." Proteomics 14, no. 10:1211-1222. PNNL-SA-83095. doi:10.1002/pmic.201300378
Xiong Y., S.T. Coradetti, X. Li, M.A. Gritsenko, T.R. Clauss, V.A. Petyuk, and D.G. Camp, et al. 2014. "The proteome and phosphoproteome of Neurospora crassa in response to cellulose, sucrose and carbon starvation." Fungal Genetics and Biology : FG & B 72. PNNL-SA-103196. doi:10.1016/j.fgb.2014.05.005
Zaborin A., J. Defazio, M. Kade, B. Kaiser, N. Belogortseva, D.G. Camp, and R.D. Smith, et al. 2014. "Phosphate-Containing Polyethylene Glycol Polymers Prevent Lethal Sepsis by Multidrug-Resistant Pathogens." Antimicrobial Agents and Chemotherapy 58, no. 2:966. PNNL-SA-95501. doi:10.1128/AAC.02183-13
Zhang Q., M.M. Matzke, A.A. Schepmoes, R.J. Moore, B.M. Webb-Robertson, Z. Hu, and M.E. Monroe, et al. 2014. "High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model." PLoS One 9, no. 3:Article No. e92332. PNNL-SA-98075. doi:10.1371/journal.pone.0092332

2013

Anderson L.N., D.E. Culley, B.A. Hofstad, L.M. Chauvigne-Hines, E.M. Zink, S.O. Purvine, and R.D. Smith, et al. 2013. "Activity-based protein profiling of secreted cellulolytic enzyme activity dynamics in Trichoderma reesei QM6a, NG14, and RUT-C30." Molecular Biosystems 9, no. 12:2992-3000. PNNL-SA-97265. doi:10.1039/c3mb70333a
Ansong C., A.C. Rutledge, H.D. Mitchell, S. Chauhan, M.B. Jones, Y. Kim, and K. Mcateer, et al. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9, no. 1:44-54. PNNL-SA-89164. doi:10.1039/C2MB25287B
Ansong C., C. Ortega, S.H. Payne, D.H. Haft, L.M. Chauvigne-Hines, M.P. Lewis, and A.R. Ollodart, et al. 2013. "Identification of widespread adenosine nucleotide binding in Mycobacterium tuberculosis." Chemistry & Biology 20, no. 1:123-133. PNNL-SA-88963. doi:10.1016/j.chembiol.2012.11.008
Ansong C., S. Wu, D. Meng, X. Liu, H.M. Brewer, B. Kaiser, and E.S. Nakayasu, et al. 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, no. 25:10153-10158. PNNL-SA-92306. doi:10.1073/pnas.1221210110
Aryal U.K., S.J. Callister, S. Mishra, X. Zhang, J.I. Shutthanandan, T.E. Angel, and A.K. Shukla, et al. 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, no. 4:1070-1077. PNNL-SA-90813. doi:10.1128/AEM.02864-12
Aylward F.O., K.E. Burnum-Johnson, S.G. Tringe, C. Teiling, D. Tremmel, J. Moeller, and J.J. Scott, et al. 2013. "Leucoagaricus gongylophorus Produces Diverse Enzymes for the Degradation of Recalcitrant Plant Polymers in Leaf-Cutter Ant Fungus Gardens." Applied and Environmental Microbiology 79, no. 12:3770-3778. PNNL-SA-92750. doi:10.1128/AEM.03833-12
Conlon B.P., E.S. Nakayasu, L.E. Fleck, M.D. LaFleur, V.M. Isabella, K. Coleman, and S.N. Leonard, et al. 2013. "Activated ClpP kills persisters and eradicates a chronic biofilm infection." Nature 503, no. 7476:365-370. PNNL-SA-98792. doi:10.1038/nature12790
Crowell K.L., E.S. Baker, S.H. Payne, Y.M. Ibrahim, M.E. Monroe, G.W. Slysz, and B.L. Lamarche, et al. 2013. "Increasing Confidence of LC-MS Identifications by Utilizing Ion Mobility Spectrometry." International Journal of Mass Spectrometry 354-355. PNNL-SA-95461. doi:10.1016/j.ijms.2013.06.028
Crowell K.L., G.W. Slysz, E.S. Baker, B.L. Lamarche, M.E. Monroe, Y.M. Ibrahim, and S.H. Payne, et al. 2013. "LC-IMS-MS Feature Finder: Detecting Multidimensional Liquid Chromatography, Ion Mobility, and Mass Spectrometry Features in Complex Datasets." Bioinformatics 29, no. 21:2804-2805. PNNL-SA-95214. doi:10.1093/bioinformatics/btt465
Dai Z., U.K. Aryal, A.K. Shukla, W. Qian, R.D. Smith, J.K. Magnuson, and W.S. Adney, et al. 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. PNNL-SA-93855. doi:10.1016/j.fgb.2013.09.004
Depuydt G.G., F. Xie, V.A. Petyuk, N. Shanmugam, A. Smolders, I. Dhondt, and H.M. Brewer, et al. 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, no. 12:3624-3639. PNNL-SA-98548. doi:10.1074/mcp.M113.027383
Ellis M., M. Gillette, S.A. Carr, A.G. Paulovich, R.D. Smith, K.D. Rodland, and R. Townsend, et al. 2013. "Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium." Cancer Discovery 3, no. 10:1108-1112. PNNL-SA-98856. doi:10.1158/2159-8290.CD-13-0219
Finnerty C.C., M.G. Jeschke, W. Qian, A. Kaushal, W. Xiao, T. Liu, and M.A. Gritsenko, et al. 2013. "DETERMINATION OF BURN PATIENT OUTCOME BY LARGE-SCALE QUANTITATIVE DISCOVERY PROTEOMICS." Critical Care Medicine 41, no. 6:1421-1434. PNWD-SA-9845. doi:10.1097/CCM.0b013e31827c072e
Gibbs D.L., A. Baratt, R. Baric, Y. Kawaoka, R.D. Smith, E.S. Orwoll, and M.G. Katze, et al. 2013. "Protein Co-Expression Network Analysis (ProCoNA)." Journal of Clinical Bioinformatics3. PNNL-SA-92592. doi:10.1186/2043-9113-3-11
Gralinski L., A. Bankhead, S. Jeng, V. Menachery, S. Proll, S. Belisle, and M.M. Matzke, et al. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 4, no. 4:Article No. e00271-13. PNWD-SA-9804. doi:10.1128/mBio.00271-13
Kaiser B., J. Li, J.A. Sanford, Y. Kim, S.R. Kronewitter, M.B. Jones, and C. Peterson, et al. 2013. "A Multi-Omic View of Host-Pathogen-Commensal Interplay in Salmonella-Mediated Intestinal Infection." PLoS One 8, no. 6:Article No. e67155. PNNL-SA-85342. doi:10.1371/journal.pone.0067155
Kim J., M.E. Monroe, D.G. Camp, R.D. Smith, and W. Qian. 2013. "In-Source Fragmentation and the Sources of Partially Tryptic Peptides in Shotgun Proteomics." Journal of Proteome Research 12, no. 2:910-916. PNNL-SA-91081. doi:10.1021/pr300955f
Kim J., Z. Dai, U.K. Aryal, R.J. Moore, D.G. Camp, S.E. Baker, and R.D. Smith, et al. 2013. "Resin-assisted Enrichment of N-terminal Peptides for Characterizing Proteolytic Processing." Analytical Chemistry 85, no. 14:6826-6832. PNNL-SA-92785. doi:10.1021/ac401000q
Kim Y., B. Schmidt, A.S. Kidwai, M.B. Jones, B.L. Deatherage, H.M. Brewer, and H.D. Mitchell, et al. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9, no. 6:1522-1534. PNNL-SA-89810. doi:10.1039/C3MB25598K
Lamarche B.L., K.L. Crowell, N. Jaitly, V.A. Petyuk, A.R. Shah, A.D. Polpitiya, and J.D. Sandoval, et al. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14. PNNL-SA-89778. doi:10.1186/1471-2105-14-49
Latif H., J.A. Lerman, V.A. Portnoy, Y. Tarasova, H. Nagarajan, A.C. Rutledge, and R.D. Smith, et al. 2013. "The Genome Organization of Thermotoga maritima Reflects Its Lifestyle." PLoS Genetics 9, no. 4:Article No. e1003485. PNNL-SA-94268. doi:10.1371/journal.pgen.1003485
Matzke M.M., J.N. Brown, M.A. Gritsenko, T.O. Metz, J.G. Pounds, K.D. Rodland, and A.K. Shukla, et al. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13, no. 3-4:493-503. PNNL-SA-88866. doi:10.1002/pmic.201200269
Merkley E.D., E.S. Baker, K.L. Crowell, D.J. Orton, T. Taverner, C. Ansong, and Y.M. Ibrahim, et al. 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, no. 3:444-449. PNNL-SA-88464. doi:10.1007/s13361-012-0565-x
Mitchell H.D., A.J. Eisfeld, A. Sims, J.E. McDermott, M.M. Matzke, B.M. Webb-Robertson, and S.C. Tilton, et al. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8, no. 7:e69374. PNNL-SA-92748. doi:10.1371/journal.pone.0069374
Nakayasu E.S., C. Ansong, J.N. Brown, F. Yang, D. Lopez-Ferrer, W. Qian, and R.D. Smith, et al. 2013. "Evaluation of selected binding domains for the analysis of ubiquitinated proteomes." Journal of the American Society for Mass Spectrometry 24, no. 8:1214-1223. PNNL-SA-83169. doi:10.1007/s13361-013-0619-8
Nakayasu E.S., R. Tempel, X.A. Cambronne, V.A. Petyuk, M.B. Jones, M.A. Gritsenko, and M.E. Monroe, et al. 2013. "Comparative phosphoproteomics reveals components of host cell invasion and post-transcriptional regulation during Francisella infection." Molecular and Cellular Proteomics 12, no. 11:3297-3309. PNNL-SA-93942. doi:10.1074/mcp.M113.029850
Nakayasu E.S., R.N. Brown, C. Ansong, M.A. Sydor, S. Imtiaz, C. Mihai, and R.L. Sontag, et al. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12, no. 8:2136-2147. PNNL-SA-88392. doi:10.1074/mcp.M112.026138
Nicora C.D., B.J. Anderson, S.J. Callister, A.D. Norbeck, S.O. Purvine, J.K. Jansson, and O.U. Mason, et al. 2013. "Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies." Proteomics 13, no. 18-19:2776-2785. PNNL-SA-92783. doi:10.1002/pmic.201300003
Niemann G., R.N. Brown, I.T. Mushamiri, N.T. Nguyen, R. Taiwo, A. Stufkens, and R.D. Smith, et al. 2013. "RNA Type III Secretion Signals that require Hfq." Journal of Bacteriology 195, no. 10:2119-2125. PNNL-SA-90112. doi:10.1128/JB.00024-13
Piehowski P.D., V.A. Petyuk, D.J. Orton, F. Xie, R.J. Moore, M. Ramirez Restrepo, and A. Engel, et al. 2013. "Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis." Journal of Proteome Research 12, no. 5:2128-2137. PNNL-SA-92104. doi:10.1021/pr301146m
Piehowski P.D., V.A. Petyuk, J.D. Sandoval, K.E. Burnum, G.R. Kiebel, M.E. Monroe, and G.A. Anderson, et al. 2013. "STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results." Proteomics 13, no. 5:766-770. PNNL-SA-86051. doi:10.1002/pmic.201200096
Pincus D.E., C. Ryan, R.D. 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, no. 3:Article No. e56544. PNNL-SA-90320. doi:10.1371/journal.pone.0056544
Price R.W., J. Peterson, D. Fuchs, T.E. Angel, H. Zetterberg, L. Hagberg, and S.S. Spudich, et al. 2013. "Approach to Cerebrospinal Fluid (CSF) Biomarker Discovery and Evaluation in HIV Infection." Journal of Neuroimmune Pharmacology 8, no. 5:1147-1158. PNNL-SA-98546. doi:10.1007/s11481-013-9491-3
Schutzer S.E., T.E. Angel, T. Liu, A.A. Schepmoes, F. Xie, J.P. Bergquist, and L. Vecsei, et al. 2013. "Gray Matter Is Targeted in First-Attack Multiple Sclerosis." PLoS One 8, no. 9:E6617. PNNL-SA-98547. doi:10.1371/journal.pone.0066117
Seok J., H.S. Warren, A.G. Cuenca, M. Mindrinos, H.V. Baker, W. Xu, and D.R. Richards, et al. 2013. "Genomic responses in mouse models poorly mimic human inflammatory diseases." Proceedings of the National Academy of Sciences of the United States of America 110, no. 9:3507-3512. PNWD-SA-10475. doi:10.1073/pnas.1222878110
Shi T., T.L. Fillmore, Y. Gao, R. Zhao, J. He, A.A. Schepmoes, and C.D. Nicora, et al. 2013. "Long-Gradient Separations Coupled with Selected Reaction Monitoring for Highly Sensitive, Large Scale Targeted Protein Quantification in a Single Analysis." Analytical Chemistry 85, no. 19:9196-9203. PNNL-SA-96700. doi:10.1021/ac402105s
Shi T., X. Sun, Y. Gao, T.L. Fillmore, A.A. Schepmoes, R. Zhao, and J. He, et al. 2013. "Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion." Journal of Proteome Research 12, no. 7:3353-3361. PNNL-SA-92544. doi:10.1021/pr400178v
Shvartsburg A.A., and R.D. Smith. 2013. "High-Resolution Differential Ion Mobility Spectrometry of a Protein." Analytical Chemistry 85, no. 1:10-13. PNNL-SA-91957. doi:10.1021/ac3029129
Shvartsburg A.A., and R.D. Smith. 2013. "Separation of Protein Conformers by Differential Ion Mobility in Hydrogen-Rich Gases." Analytical Chemistry 85, no. 14:6967-6973. PNNL-SA-95662. doi:10.1021/ac4015963
Shvartsburg A.A., G.A. Anderson, and R.D. Smith. 2013. "Pushing the Frontier of High-Definition Ion Mobility Spectrometry Using FAIMS." Mass Spectrometry Society of Japan. Journal 2. PNNL-SA-95627. doi:10.5702/massspectrometry.S0011
Shvartsburg A.A., T.A. Seim, W.F. Danielson, R.V. Norheim, R.J. Moore, G.A. Anderson, and R.D. Smith. 2013. "High-Definition Differential Ion Mobility Spectrometry with Resolving Power up to 500." Journal of the American Society for Mass Spectrometry 24, no. 1:109-114. PNNL-SA-88665. doi:10.1007/s13361-012-0517-5
Sims A.C., S.C. Tilton, V. Menachery, L. Gralinski, A. Schafer, M.M. Matzke, and B.M. Webb-Robertson, et al. 2013. "Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells." Journal of Virology 87, no. 7:3885-902. PNWD-SA-9741. doi:10.1128/JVI.02520-12
Su D., A.K. Shukla, B. Chen, J. Kim, E.S. Nakayasu, Y. Qu, and U.K. Aryal, et al. 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. PNNL-SA-89035. doi:10.1016/j.freeradbiomed.2012.12.010
Sun X., K. Tang, R.D. Smith, and R.T. Kelly. 2013. "Controlled Dispensing and Mixing of Pico- to Nanoliter Volumes Using On-Demand Droplet-Based Microfluidics." Microfluidics and Nanofluidics 15, no. 1:117-126. PNNL-SA-90505. doi:10.1007/s10404-012-1133-1
Tchitchek N., A.J. Eisfeld, J. Tisoncik-Go, L. Josset, L. Gralinski, C. Becavin, and S.C. Tilton, et al. 2013. "Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice." BMC Systems Biology 7. PNNL-SA-94011. doi:10.1186/1752-0509-7-69
Wang C., C.S. Lee, R.D. 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, no. 15:7308-7315. PNNL-SA-95213. doi:10.1021/ac401202c
Wiedner S.D., C. Ansong, B.M. Webb-Robertson, L.M. Pederson, S. Fortuin, B.A. Hofstad, and A.K. Shukla, et al. 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, no. 7:1791-1805. PNNL-SA-91969. doi:10.1074/mcp.M112.026534
Zhang Q., T.L. Fillmore, A.A. Schepmoes, T.R. Clauss, M.A. Gritsenko, P.W. Mueller, and M. Rewers, et al. 2013. "Serum proteomics reveals systemic dysregulation of innate immunity in type 1 diabetes." The Journal of Experimental Medicine 210, no. 1:191-203. PNNL-SA-89853. doi:10.1084/jem.20111843
Zhou J., R.K. Krovvidi, Y. Gao, H. Gao, B.O. Petritis, A. De, and C. Miller-Graziano, et al. 2013. "Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling." Proteomics - Clinical Applications 7, no. 7-8:571-583. PNWD-SA-9434. doi:10.1002/prca.201200109

2012

Alfaro J.F., C. Gong, M.E. Monroe, J.T. Aldrich, T.R. Clauss, S.O. Purvine, and Z. Wang, et al. 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, no. 19:7280-7285. PNNL-SA-84997. doi:10.1073/pnas.1200425109
Andreev V.P., V.A. Petyuk, H.M. Brewer, Y. Karpievitch, F. Xie, J. Clarke, and D.G. Camp, et al. 2012. "Label-Free Quantitative LC-MS Proteomics of Alzheimer’s Disease and Normally Aged Human Brains." Journal of Proteome Research 11, no. 6:3053-3067. PNNL-SA-90452. doi:10.1021/pr3001546
Angel T.E., J.M. Jacobs, R.P. Smith, M.S. Pasternack, S. Elias, M.A. Gritsenko, and A.K. Shukla, et al. 2012. "Cerebrospinal Fluid Proteome of Patients with Acute Lyme Disease." Journal of Proteome Research 11, no. 10:4814-4822. PNNL-SA-79143. doi:10.1021/pr300577p
Angel T.E., J.M. Jacobs, S.S. Spudich, M.A. Gritsenko, D. Fuchs, T. Liegler, and H. Zetterberg, et al. 2012. "The cerebrospinal fluid proteome in HIV infection: change associated with disease severity." Clinical Proteomics 9. PNNL-SA-81597. doi:10.1186/1559-0275-9-3
Angel T.E., U.K. Aryal, S.M. Hengel, E.S. Baker, R.T. Kelly, E.W. Robinson, and R.D. Smith. 2012. "Mass spectrometry-based proteomics: existing capabilities and future directions." Chemical Society Reviews 41, no. 10:3912-3928. PNNL-SA-84530. doi:10.1039/C2CS15331A
Aryal U.K., J. Stockel, E.A. Welsh, M.A. Gritsenko, C.D. Nicora, D.W. Koppenaal, and R.D. Smith, et al. 2012. "Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light." Journal of Proteome Research 11, no. 2:609-619. PNNL-SA-80375. doi:10.1021/pr200959x
Aylward F.O., K.E. Burnum, J.J. Scott, G. Suen, S.G. Tringe, S.M. Adams, and K.W. Barry, et al. 2012. "Metagenomic and metaproteomic insights into bacterial communities in leaf-cutter ant fungus gardens." The ISME Journal 6, no. 9:1688-1701. PNNL-SA-82393. doi:10.1038/ismej.2012.10
Baker E.S., T. Liu, V.A. Petyuk, K.E. Burnum-Johnson, Y.M. Ibrahim, G.A. Anderson, and R.D. Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4. PNNL-SA-86783. doi:10.1186/gm364
Bordbar A., M.L. Mo, E.S. Nakayasu, A.C. Rutledge, Y. Kim, T.O. Metz, and M.B. Jones, et al. 2012. "Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation." Molecular Systems Biology 8. PNNL-SA-87903. doi:10.1038/msb.2012.21
Brown J.N., G.M. Ortiz, T.E. Angel, J.M. Jacobs, M.A. Gritsenko, E.Y. Chan, and D.E. Purdy, et al. 2012. "Morphine Produces Immunosuppressive Effects in Non-human Primates at the Proteomic and Cellular Levels." Molecular & Cellular Proteomics. MCP 11, no. 9:605-618. PNNL-SA-83778. doi:10.1074/mcp.M111.016121
Brown R.N., J.A. Sanford, J.H. Park, B.L. Deatherage, B.L. Champion, R.D. Smith, and F. Heffron, et al. 2012. "A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions." International Journal of Proteomics 2012. PNNL-SA-86438. doi:10.1155/2012/123076
Burnum K.E., Y. Hirota, E.S. Baker, M. Yoshie, Y.M. Ibrahim, M.E. Monroe, and G.A. Anderson, et al. 2012. "Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua." Endocrinology 153, no. 9:4568-4579. PNNL-SA-87211. doi:10.1210/en.2012-1335
Cao L., D.A. Bryant, A.A. Schepmoes, K. Vogl, R.D. Smith, M.S. Lipton, and S.J. Callister. 2012. "Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically." Photosynthesis Research 110, no. 3:153-168. PNNL-SA-81058. doi:10.1007/s11120-011-9711-8
Chauvigne-Hines L.M., L.N. Anderson, H.M. Weaver, J.N. Brown, P.K. Koech, C.D. Nicora, and B.A. Hofstad, et al. 2012. "Suite of Activity-Based Probes for Cellulose-Degrading Enzymes." Journal of the American Chemical Society 134, no. 50:20521-20532. PNNL-SA-91066. doi:10.1021/ja309790w
Chauvin T., F. Xie, T. Liu, C.D. Nicora, F. Yang, D.G. Camp, and R.D. Smith, et al. 2012. "A Systematic Analysis of a Deep Mouse Epididymal Sperm Proteome." Biology of Reproduction87, no. 6:Article No. 141. PNNL-SA-90200. doi:10.1095/biolreprod.112.104208
Diamond D.L., A. Krasnoselski, K.E. Burnum, M.E. Monroe, B.M. Webb-Robertson, J.E. McDermott, and M.M. Yeh, et al. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 56, no. 1:28-38. PNWD-SA-9552. doi:10.1002/hep.25649
Gao X., Q. Zhang, D. Meng, G. Isaac, R. Zhao, T.L. Fillmore, and R.K. Chu, et al. 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, no. 9:2923-2933. PNWD-SA-9553.
Karpievitch Y., A.R. Dabney, and R.D. Smith. 2012. "Normalization and missing value imputation for label-free LC-MS analysis." BMC Bioinformatics 13, no. Suppl 16:Article No. S5. PNNL-SA-94014. doi:10.1186/1471-2105-13-S16-S5
Lee J., S. Hyung, D. Mun, H. Jung, H. Kim, H. Lee, and S. Kim, et al. 2012. "Fully automated multifunctional ultrahigh pressure liquid chromatography system for advanced proteome analyses." Journal of Proteome Research 11, no. 8:4373-4381. PNNL-SA-88005. doi:10.1021/pr3004166
Lerman J.A., D.R. Hyduke, H. Latif, V.A. Portnoy, N.E. Lewis, J.D. Orth, and A.C. Rutledge, et al. 2012. "In silico method for modelling metabolism and gene product expression at genome scale." Nature Communications 3. PNNL-SA-79962. doi:10.1038/ncomms1928
Liu T., M. Hossain, A.A. Schepmoes, T.L. Fillmore, L.J. Sokoll, S.R. Kronewitter, and G. Izmirlian, et al. 2012. "Analysis of Serum Total and Free PSA Using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests." Journal of Proteomics 75, no. 15:4747-4757. PNNL-SA-83777. doi:10.1016/j.jprot.2012.01.035
Liu X., Y. Sirotkin, Y. Shen, G.A. Anderson, Y.S. Tsai, Y.S. Ting, and D.R. Goodlett, et al. 2012. "Protein Identification Using Top-Down." Molecular & Cellular Proteomics. MCP 11, no. 6:M111.008524. PNNL-SA-77772. doi:10.1074/mcp.M111.008524
Malouli D., E.S. Nakayasu, K. Viswanathan, D.G. Camp, W.L. Chang, P.A. Barry, and R.D. Smith, et al. 2012. "Reevaluation of the Coding Potential and Proteomic Analysis of the BAC Derived Rhesus Cytomegalovirus Strain 68-1." Journal of Virology 86, no. 17:8959-8973. PNNL-SA-87442. doi:10.1128/JVI.01132-12
Marginean I., S.R. Kronewitter, R.J. Moore, G.W. Slysz, M.E. Monroe, G.A. Anderson, and K. Tang, et al. 2012. "Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure." Analytical Chemistry 84, no. 21:9208-9213. PNNL-SA-89077. doi:10.1021/ac301961u
Maxwell E., Y. Tan, Y. Tan, H. Hu, G. Benson, K. Aizikov, and S. Conley, et al. 2012. "GlycReSoft: A Software Package for Automated Recognition of Glycans from LC/MS Data." PLoS One 7, no. 9:e45474. PNNL-SA-92977. doi:10.1371/journal.pone.0045474
Merkley E.D., B.J. Anderson, J.H. Park, S.M. Belchik, L. Shi, M.E. Monroe, and R.D. Smith, et al. 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, no. 12:6147-6158. PNNL-SA-89362. doi:10.1021/pr3007914
Payne S.H., S. Bonissone, S. Wu, R.N. Brown, D. Ivankov, D. Frishman, and L. Pasa-Tolic, et al. 2012. "Unexpected Diversity of Signal Peptides in Prokaryotes." mBio 3, no. 6:Article No. e00339-12. PNWD-SA-9881. doi:10.1128/mBio.00339-12
Rutledge A.C., G. Fontes, M.A. Gritsenko, A.D. Norbeck, D.J. Anderson, K.M. Waters, and J.N. Adkins, et al. 2012. "Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics." Journal of Proteome Research 11, no. 7:3520-32. PNNL-SA-77193. doi:10.1021/pr3002996
Rutledge A.C., M.B. Jones, S. Chauhan, S.O. Purvine, J. Sanford, M.E. Monroe, and H.M. Brewer, et al. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7, no. 3:Article No. E33903. PNNL-SA-79961. doi:10.1371/journal.pone.0033903
Sadler N.C., T.E. Angel, M.P. Lewis, L.M. Pederson, L.M. Chauvigne-Hines, S.D. Wiedner, and E.M. Zink, et al. 2012. "Activity-Based Protein Profiling Reveals Mitochondrial Oxidative Enzyme Impairment and Restoration in Diet-Induced Obese Mice." PLoS One 7, no. 10:Article No. e47996. PNNL-SA-88011. doi:10.1371/journal.pone.0047996
Shen Y., N. Tolic, S.O. Purvine, and R.D. 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, no. 2:668-677. PNNL-SA-79420.
Shi T., D. Su, T. Liu, K. Tang, D.G. Camp, W. Qian, and R.D. Smith. 2012. "Advancing the sensitivity of selected reaction monitoring-based targeted quantitative proteomics." Proteomics12, no. 8:1074-1092. PNNL-SA-82133. doi:10.1002/pmic.201100436
Shi T., J. Zhou, M.A. Gritsenko, M. Hossain, D.G. Camp, R.D. Smith, and W. Qian. 2012. "IgY14 and SuperMix immunoaffinity separations coupled with liquid chromatography-mass spectrometry for human plasma proteomic biomarker discovery." Methods 56, no. 2:246-253. PNNL-SA-80317. doi:10.1016/j.ymeth.2011.09.001
Shi T., T.L. Fillmore, X. Sun, R. Zhao, A.A. Schepmoes, M. Hossain, and F. Xie, et al. 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, no. 38:15395-15400. PNNL-SA-83776. doi:10.1073/pnas.1204366109
Shvartsburg A.A., and R.D. Smith. 2012. "Protein Analyses Using Differential Ion Mobility Microchips with Mass Spectrometry." Analytical Chemistry 84, no. 17:7297-7300. PNWD-SA-9895. doi:10.1021/ac3018636
Shvartsburg A.A., Y. Zheng, R.D. Smith, and N. Kelleher. 2012. "Ion Mobility Separation of Variant Histone Tails Extending to the “Middle-down” Range." Analytical Chemistry 84, no. 10:4271-4276. PNNL-SA-86196. doi:10.1021/ac300612y
Shvartsburg A.A., Y. Zheng, R.D. Smith, and N. Kelleher. 2012. "Separation of Variant Methylated Histone Tails by Differential Ion Mobility." Analytical Chemistry 84, no. 15:6317-6320. PNNL-SA-88466. doi:10.1021/ac301541r
Smith R.D. 2012. "Mass spectrometry in biomarker applications: from untargeted discovery to targeted verification, and implications for platform convergence and clinical application." Clinical Chemistry 58, no. 3:528-530. PNNL-SA-84378. doi:10.1373/clinchem.2011.180596
Sun X., K. Tang, R.D. Smith, and R.T. Kelly. 2012. "Robust Extraction Interface for Coupling Droplet-Based and Continuous Flow Microfluidics." In Advances in Microfluidics, edited by R Kelly. 155-170. Rijeka:InTech. PNNL-SA-83129.
Taverner T., Y. Karpievitch, A.D. Polpitiya, J.N. Brown, A.R. Dabney, G.A. Anderson, and R.D. Smith. 2012. "DanteR: an extensible R-based tool for quantitative analysis of -omics data." Bioinformatics 28, no. 18:2404-2406. PNNL-SA-82126. doi:10.1093/bioinformatics/bts449
Tian Z., N. Tolic, R. Zhao, R.J. Moore, S.M. Hengel, E.W. Robinson, and D.L. Stenoien, et al. 2012. "Enhanced top-down characterization of histone post-translational modifications." Genome Biology 13, no. 10:R86. PNNL-SA-90867. doi:10.1186/gb-2012-13-10-r86
Tolmachev A.V., E.W. Robinson, R.D. Smith, F.E. Leach, J.H. 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. PNNL-SA-89137. doi:10.1016/j.ijms.2012.06.027
Tolmachev A.V., E.W. Robinson, S. Wu, R.D. Smith, J.H. 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, no. 7:1169-1172. PNNL-SA-86041. doi:10.1007/s13361-012-0395-x
Varnum S.M., B.M. Webb-Robertson, J.G. Pounds, R.J. Moore, R.D. Smith, C. Frevert, and S.J. Skerret, et al. 2012. "Proteomic analysis of bronchoalveolar lavage fluid proteins from mice infected with Francisella tularensis ssp novicida." Journal of Proteome Research 11, no. 7:3690-3703. PNNL-SA-86269.
Wang C., C.S. Lee, R.D. Smith, and K. Tang. 2012. "Ultrasensitive Sample Quantitation via Selected Reaction Monitoring Using CITP/CZE-ESI-Triple Quadrupole MS." Analytical Chemistry 84, no. 23:10395-10403. PNNL-SA-90482. doi:10.1021/ac302616m
Wang L., U.K. Aryal, Z. Dai, A.C. Mason, M.E. Monroe, Z. Tian, and J. Zhou, et al. 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, no. 1:143-56. PNNL-SA-82556. doi:10.1021/pr200916k
Wang X., G.A. Anderson, R.D. Smith, and A.R. Dabney. 2012. "A Hybrid Approach to Protein Differential Expression in Mass Spectrometry-Based Proteomics." Bioinformatics 28, no. 12:1586-1591. PNNL-SA-84117. doi:10.1093/bioinformatics/bts193
Waters K.M., T. Liu, R.D. Quesenberry, A.R. Willse, S. Bandyopadhyay, L.E. Kathmann, and T.J. Weber, et al. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data." PLoS One 7, no. 3:Article No. e34515. PNNL-SA-85737. doi:10.1371/journal.pone.0034515
Wiedner S.D., K.E. Burnum, L.M. Pederson, L.N. Anderson, S. Fortuin, L.M. Chauvigne-Hines, and A.K. Shukla, et al. 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, no. 40:33447-33459. PNNL-SA-87258. doi:10.1074/jbc.M112.394106
Xie F., R.D. Smith, and Y. Shen. 2012. "Advanced proteomic liquid chromatography." Journal of Chromatography A 1261. PNNL-SA-86948. doi:10.1016/j.chroma.2012.06.098
Yang F., K.M. Waters, B.M. Webb-Robertson, M.B. Sowa, C.H. Freiin von Neubeck, J.T. Aldrich, and L.M. Markillie, et al. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology21, no. 5:352-357. PNNL-SA-79030. doi:10.1111/j.1600-0625.2012.01470.x
Yang F., Y. Shen, D.G. Camp, and R.D. Smith. 2012. "High pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis." Expert Review of Proteomics 9, no. 2:129-134. PNNL-SA-83356. doi:10.1586/EPR.12.15
Zhou J., G.P. Dann, T. Shi, L. Wang, X. Gao, D. Su, and C.D. Nicora, et al. 2012. "Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications." Analytical Chemistry 84, no. 6:2862-2867. PNNL-SA-84751. doi:10.1021/ac203394r

2011

Ansong C., N. Tolic, S.O. Purvine, S. Porwollik, M.B. Jones, H. Yoon, and S.H. Payne, et al. 2011. "Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium." BMC Genomics 12. PNNL-SA-77195. doi:10.1186/1471-2164-12-433
Aryal U.K., J. Stockel, R.K. Krovvidi, M.A. Gritsenko, M.E. Monroe, R.J. Moore, and D.W. Koppenaal, et al. 2011. "Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles." BMC Systems Biology 5. PNNL-SA-81418. doi:10.1186/1752-0509-5-194
Belov M.E., S. Prasad, D.C. Prior, W.F. Danielson, K.K. Weitz, Y.M. Ibrahim, and R.D. Smith. 2011. "Pulsed Multiple Reaction Monitoring Approach to Enhancing Sensitivity of a Tandem Quadrupole Mass Spectrometer." Analytical Chemistry 83, no. 6:2162-2171. PNNL-SA-74498. doi:10.1021/ac103006b
Burnum K.E., S.J. Callister, C.D. Nicora, S.O. Purvine, P. Hugenholtz, F. Warnecke, and R.H. Scheffrahn, et al. 2011. "Proteome Insights into the Symbiotic Relationship Between a Captive Colony of Nasutitermes corniger and its Hindgut Microbiome." The ISME Journal 5, no. 1:161-164. PNNL-SA-68831. doi:10.1038/ismej.2010.97
Dresang L.R., J.R. Teuton, H. Feng, J.M. Jacobs, D.G. Camp, S.O. Purvine, and M.A. Gritsenko, et al. 2011. "Coupled Transcriptome and Proteome Analysis of Human Lymphotropic Tumor Viruses: Insights on the Detection and Discovery of Viral Genes." BMC Genomics 12. PNNL-SA-84775. doi:10.1186/1471-2164-12-625
Du X., S.M. Chowdhury, N.P. Manes, S. Wu, M.U. Mayer, J.N. Adkins, and G.A. Anderson, et al. 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, no. 3:923-931. PNNL-SA-70094. doi:10.1021/pr100848a
Frank A.M., M.E. Monroe, A.R. Shah, J.J. Carver, N. Bandeira, R.J. Moore, and G.A. Anderson, et al. 2011. "Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra." Nature Methods 8, no. 7:587-591. PNNL-SA-79495. doi:10.1038/nmeth.1609
Ghazalpour A., B. Bennett, V.A. Petyuk, L. Orazco, R. Hagopian, I. Mungrue, and C.R. Farber, et al. 2011. "Comparative Analysis of Proteome and Transcriptome Variation in Mouse." PLoS Genetics 7, no. 6:Article No. e1001393. PNWD-SA-9360. doi:10.1371/journal.pgen.1001393
Gonzales R.M., Q. Zhang, R.C. Zangar, R.D. Smith, and T.O. 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, no. 1:99-102. PNNL-SA-75597. doi:10.1016/j.ab.2011.02.039
Heffron F., G. Niemann, H. Yoon, A.S. Kidwai, R.N. Brown, J.E. McDermott, and R.D. Smith, et al. 2011. "Salmonella-secreted Virulence Factors." In Salmonella: From Genome to Function, edited by S Porwollik. 187-223. Norfolk:Caister Academic Press. PNNL-SA-71401.
Hossain M., D.T. Kaleta, E.W. Robinson, T. Liu, R. Zhao, J.S. Page, and R.T. Kelly, et al. 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, no. 2. PNNL-SA-70166. doi:10.1074/mcp.M000062-MCP201
Huang X., A.V. Tolmachev, Y. Shen, M. Liu, L. Huang, Z. Zhang, and G.A. Anderson, et al. 2011. "UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling." Journal of Proteome Research 10, no. 3:1228-1237. PNNL-SA-74145. doi:10.1021/pr1010058
Ibrahim Y.M., A.A. Shvartsburg, R.D. Smith, and M.E. Belov. 2011. "Ultrasensitive Identification of Localization Variants of Modified Peptides Using Ion Mobility Spectrometry." Analytical Chemistry 83, no. 14:5617 - 5623. PNNL-SA-78723. doi:10.1021/ac200719n
Johnson P.V., R. Hodyss, K. Tang, W. Brinckerhoff, and R.D. Smith. 2011. "The Laser Ablation Ion Funnel: Sampling for In Situ Mass Spectrometry on Mars." Planetary and Space Science59, no. 5-6:387-393. PNWD-SA-9055. doi:10.1016/j.pss.2011.01.004
Kim J., T.L. Fillmore, T. Liu, E.W. Robinson, M. Hossain, B.L. Champion, and R.J. Moore, et al. 2011. "18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry." Molecular & Cellular Proteomics. MCP 10, no. 12:Article No. M110.007302. PNNL-SA-77028. doi:10.1074/mcp.M110.007302
Kim Y., T.O. Metz, Z. Hu, S.D. Wiedner, J. Kim, R.D. Smith, and W.F. Morgan, et al. 2011. "Formation of dehydroalanine from mimosine and cysteine: artifacts in gas chromatography/mass spectrometry based metabolomics." Rapid Communications in Mass Spectrometry 25. PNNL-SA-78517. doi:10.1002/rcm.5134
Kingsinger C.R., J. Apffel, M.S. Baker, X. Bian, C.H. Borchers, R.A. Bradshaw, and M. Brusniak, et al. 2011. "Recommendations for mass spectrometry data quality metrics for open access data(corollary to the Amsterdam principles)." Proteomics - Clinical Applications 5, no. 11-12:580-589. PNNL-SA-85425. doi:10.1002/prca.201100097
Lee B., D. Lopez-Ferrer, B. Kim, H. Na, Y.I. Park, K.K. Weitz, and M.G. Warner, et al. 2011. "Rapid and Efficient Protein Digestion using Trypsin Coated Magnetic Nanoparticles under Pressure Cycles." Proteomics 11, no. 2:309-318. PNNL-SA-72833. doi:10.1002/pmic.201000378
Lopez-Ferrer D., K. Petritis, E.W. Robinson, K.K. Hixson, Z. Tian, J. Lee, and S. Lee, et al. 2011. "Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics." Molecular & Cellular Proteomics. MCP 10, no. 2. PNNL-SA-71649. doi:10.1074/mcp.M110.001479
Lopez-Ferrer D., K.K. Hixson, M.E. Belov, and R.D. Smith. 2011. "Ultra-Fast Sample Preparation for High-Throughput Proteomics." In Sample Preparation in Biological Mass Spectrometry, edited by AR Ivanov and AV Lazarev. 125-139. Dordrecht:Springer. PNNL-SA-69697.
Niemann G., R.N. Brown, J.K. Gustin, A. Stufkens, A.S. Shaikh-Kidwai, J. Li, and J.E. McDermott, et al. 2011. "Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants." Infection and Immunity 79, no. 1:33-43. PNNL-SA-71385. doi:10.1128/IAI.00771-10
Qian W., B.O. Petritis, C.D. Nicora, and R.D. Smith. 2011. "Trypsin-catalyzed oxygen-18 labeling for quantitative proteomics." In Gel-Free Proteomics, Methods and Protocols: Methods in Molecular Biology, edited by K Gevaert and J Vandekerckhove. 43-54. Totowa, New Jersey:Humana Press Inc. PNNL-SA-78931.
Rasmussen A., D.L. Diamond, J.E. McDermott, X. Gao, T.O. Metz, M.M. Matzke, and V. Carter, et al. 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, no. 22:11646-11654. PNWD-SA-9324. doi:10.1128/JVI.05605-11
Schoenherr R.M., K.S. Kelly-Spratt, C. Lin, J.R. Whiteaker, T. Liu, T. Holzman, and I. Coleman, et al. 2011. "Proteome and Transcriptome Profiles of a Her2/Neu-driven Mouse Model of Breast Cancer." Proteomics - Clinical Applications 5, no. 3-4:179-188. PNNL-SA-72407. doi:10.1002/prca.201000037
Schutzer S.E., T.E. Angel, T. Liu, A.A. Schepmoes, T.R. Clauss, J.N. Adkins, and D.G. Camp, et al. 2011. "Distinct Cerebrospinal Fluid Proteomes Differentiate Post-Treatment Lyme Disease from Chronic Fatigue Syndrome." PLoS One 6, no. 2:Article No. e17287. PNWD-SA-9128. doi:10.1371/journal.pone.0017287
Shen Y., N. Tolic, F. Xie, R. Zhao, S.O. Purvine, A.A. Schepmoes, and R.J. Moore, et al. 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, no. 9:3929-3943. PNNL-SA-75441. doi:10.1021/pr200052c
Shen Y., N. Tolic, S.O. Purvine, and R.D. Smith. 2011. "Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information." Journal of Proteome Research. PNNL-SA-81060. doi:10.1021/pr200597j
Shukla A.K., R. Zhang, D.J. Orton, R. Zhao, T.R. Clauss, R.J. Moore, and R.D. 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, no. 10:1452-1456. PNNL-SA-68066. doi:10.1002/rcm.5017
Shvartsburg A.A., A.J. Creese, R.D. Smith, and H.J. Cooper. 2011. "Separation of a Set of Peptide Sequence Isomers Using Differential Ion Mobility Spectrometry." Analytical Chemistry83, no. 18:6918-6923. PNNL-SA-81065. doi:10.1021/ac201640d
Shvartsburg A.A., and R.D. Smith. 2011. "Accelerated High-Resolution Differential Ion Mobility Separations Using Hydrogen." Analytical Chemistry 83, no. 23:9159-9166. PNNL-SA-82720. doi:10.1021/ac202386w
Shvartsburg A.A., and R.D. Smith. 2011. "Ultrahigh-Resolution Differential Ion Mobility Spectrometry Using Extended Separation Times." Analytical Chemistry 83, no. 1:23-29. PNWD-SA-9232. doi:10.1021/ac102689p
Shvartsburg A.A., D. Singer, R.D. Smith, and R. Hoffmann. 2011. "Ion Mobility Separation of Isomeric Phosphopeptides from a Protein with Variant Modification of Adjacent Residues." Analytical Chemistry 83, no. 13:5078-5085. PNNL-SA-79163. doi:10.1021/ac200985s
Shvartsburg A.A., G. Isaac, N. Leveque, R.D. Smith, and T.O. Metz. 2011. "Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry." Journal of the American Society for Mass Spectrometry 22, no. 7:1146-1155. PNNL-SA-75443. doi:10.1007/s13361-011-0114-z
Stanley J.R., J.N. Adkins, G.W. Slysz, M.E. Monroe, S.O. Purvine, Y.V. Karpievitch, and G.A. Anderson, et al. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83, no. 16:6135-6140. PNNL-SA-72379. doi:10.1021/ac2009806
Stockel J., J.M. Jacobs, T.R. Elvitigala, M.L. Liberton, E.A. Welsh, A.D. Polpitiya, and M.A. Gritsenko, et al. 2011. "Diurnal Rhythms Result in Significant Changes in the Cellular Protein Complement in the Cyanobacterium Cyanothece 51142." PLoS One 6, no. 2:Article No.: e16680. PNNL-SA-78209. doi:10.1371/journal.pone.0016680
Sun X., R.T. Kelly, K. Tang, and R.D. Smith. 2011. "Membrane-Based Emitter for Coupling Microfluidics with Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry." Analytical Chemistry 83, no. 4:5797-5803. PNNL-SA-79137. doi:10.1021/ac200960h
Sun X., R.T. Kelly, W.F. Danielson, N. Agrawal, K. Tang, and R.D. Smith. 2011. "Hydrodynamic injection with pneumatic valving for microchip electrophoresis with total analyte utilization." Electrophoresis 32, no. 13:1610-1618. PNNL-SA-76945. doi:10.1002/elps.201000522
Tang K., J.S. Page, I. Marginean, R.T. Kelly, and R.D. Smith. 2011. "Improving liquid chromatography-mass spectrometry sensitivity using a subambient pressure ionization with nanoelectrospray (SPIN) interface." Journal of the American Society for Mass Spectrometry22, no. 8:1318-1325. PNNL-SA-77025. doi:10.1007/s13361-011-0135-7
Tolmachev A.V., E.W. Robinson, S. Wu, R.D. Smith, and L. Pasa-Tolic. 2011. "Trapping radial electric field optimization in compensated FTICR Cells." Journal of the American Society for Mass Spectrometry 22, no. 8:1334-1342. PNNL-SA-77848. doi:10.1007/s13361-011-0167-z
Varnum S.M., B.M. Webb-Robertson, N. Hessol, R.D. Smith, and R.C. Zangar. 2011. "Plasma Biomarkers for Detecting Hodgkin's Lymphoma in HIV Patients." PLoS One 6, no. 12:Article No. e29263. PNNL-SA-81553. doi:10.1371/journal.pone.0029263
Venter E., R.D. Smith, and S.H. Payne. 2011. "Proteogenomic analysis of bacteria and archaea: A 46 organism case study." PLoS One 6, no. 11:Article No. e27587. PNNL-SA-75723. doi:10.1371/journal.pone.0027587
Wang Y., F. Yang, M.A. Gritsenko, Y. Wang, T.R. Clauss, T. Liu, and Y. Shen, et al. 2011. "Reversed-Phase Chromatography with Multiple Fraction Concatenation Strategy for Proteome Profiling of Human MCF10A Cells." Proteomics 11, no. 10:2019-2026. PNNL-SA-75439. doi:10.1002/pmic.201000722
Wang Y., F. Yang, Y. Fu, X. Huang, W. Wang, X. Jiang, and M.A. Gritsenko, et al. 2011. "Spatial Phosphoprotein Profiling Reveals a Compartmentalized Extracellular Signal-regulated Kinase Switch Governing Neurite Growth and Retraction." Journal of Biological Chemistry 286, no. 20:18190-18201. PNNL-SA-79165.
Xie F., T. Liu, W. Qian, V.A. Petyuk, and R.D. Smith. 2011. "Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics." Journal of Biological Chemistry 286, no. 29:25443-25449. PNNL-SA-76123.
Yoon H., C. Ansong, J.E. McDermott, M.A. Gritsenko, R.D. Smith, F. Heffron, and J.N. Adkins. 2011. "Systems analysis of multiple regulator perturbations allows discovery of virulence factors in Salmonella." BMC Systems Biology 5. PNNL-SA-77197. doi:10.1186/1752-0509-5-100
Zhang H., F. Yang, W. Qian, R.N. Brown, Y. Wang, E.D. Merkley, and J.H. Park, et al. 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, no. 19:7260-7268. PNNL-SA-77198. doi:10.1021/ac2000829
Zhang H., K.E. Burnum, M.L. Luna, B.O. Petritis, J. Kim, W. Qian, and R.J. Moore, et al. 2011. "Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size." Proteomics 11, no. 23:4569-4577. PNNL-SA-74159. doi:10.1002/pmic.201100037
Zhang Q., M.E. Monroe, A.A. Schepmoes, T.R. Clauss, M.A. Gritsenko, D. Meng, and V.A. Petyuk, et al. 2011. "Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects." Journal of Proteome Research 10, no. 7:3076-3088. PNNL-SA-77801.
Zhou J., G.P. Dann, C.W. Liew, R.D. Smith, R.N. Kulkarni, and W. Qian. 2011. "Unraveling pancreatic islet biology by quantitative proteomics." Expert Review of Proteomics 8, no. 4:495-504. PNNL-SA-77799. doi:10.1586/epr.11.39

2010

Adkins J.N., H. Mottaz, T.O. Metz, C.K. Ansong, N.P. Manes, R.D. Smith, and F. Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." In Peptidomics: Methods and Protocols, Methods in Molecular Biology, edited by Mikhail Soloviev. 13-27. New York, New York:Humana Press, Inc. PNNL-SA-59136.
Ahn H., B. Kim, S. Jun, M. Chang, D. Lopez-Ferrer, R.D. Smith, and M. Gu, et al. 2010. "Robust Trypsin Coating on Electrospun Polymer Nanofibers in Rigorous Conditions and Its Uses for Protein Digestion." Biotechnology and Bioengineering 107, no. 6:917-923. PNNL-SA-72385.
Alpert A.J., K. Petritis, L.J. Kangas, R.D. Smith, K. Mechtler, G. Mitulovic, and S. Mohammed, et al. 2010. "Peptide Orientation Affects Selectivity in Ion-Exchange Chromatography." Analytical Chemistry 82, no. 12:5253-5259. PNNL-SA-73938.
Angel T.E., B.J. Luft, X. Yang, C.D. Nicora, D.G. Camp, J.M. Jacobs, and R.D. Smith. 2010. "Proteome Analysis of Borrelia burgdorferi Response to Environmental Change." PLoS One 5, no. 11:Article No.: e13800. PNNL-SA-74148. doi:10.1371/journal.pone.0013800
Auberry K.J., G.R. Kiebel, M.E. Monroe, J.N. Adkins, G.A. Anderson, and R.D. Smith. 2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3, no. 1:1-4. PNNL-SA-75729.
Baker E.S., E.A. Livesay, D.J. Orton, R.J. Moore, W.F. Danielson, D.C. Prior, and Y.M. Ibrahim, et al. 2010. "An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies." Journal of Proteome Research 9, no. 2:997-1006. PNNL-SA-67461. doi:10.1021/pr900888b
Belov M.E., Y.M. Ibrahim, and R.D. Smith. 2010. "Ion Accumulation Approaches for Increasing Sensitivity and Dynamic Range in the Analysis of Complex Samples." In Practical Aspects of Trapped Ion Mass Spectrometry: Theory and Instrumentation, edited by RE March and JFJ Todd. 401-432. Boca Raton, Florida:CRC Press. PNNL-SA-60908.
Brown J.N., R. Estep, D. Lopez-Ferrer, H.M. Brewer, T.R. Clauss, N.P. Manes, and M. O'Connor, et al. 2010. "CHARACTERIZATION OF MACAQUE PULMONARY FLUID PROTEOME DURING MONKEYPOX INFECTION: DYNAMICS OF HOST RESPONSE." Molecular & Cellular Proteomics. MCP 9, no. 12:2760-2771. PNWD-SA-8911. doi:10.1074/mcp.M110.001875
Brown J.N., R. Palermo, C.R. Baskin, M.A. Gritsenko, P.J. Sabourin, P.J. Sabourin, and J.P. Long, et al. 2010. "Macaque Proteome Response to Highly Pathogenic Avian Influenza and 1918 Reassortant Influenza Virus Infections." Journal of Virology 84, no. 22:12058-12068. PNWD-SA-9238.
Brown R.N., M.F. Romine, A.A. Schepmoes, R.D. Smith, and M.S. 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, no. 9:4454-4463. PNNL-SA-70091. doi:10.1021/pr100215h
Buchko G.W., G. Niemann, E.S. Baker, M.E. Belov, R.D. Smith, F. Heffron, and J.N. Adkins, et al. 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, no. 12:2448-2458. PNNL-SA-73691. doi:10.1039/c0mb00097c
Callister S.J., M.J. Wilkins, C.D. Nicora, K.H. Williams, J.F. Banfield, N. VerBerkmoes, and R.L. Hettich, et al. 2010. "Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles." Environmental Science & Technology 44, no. 23:8897-8903. PNNL-SA-71892. doi:10.1021/es101029f
Diamond D.L., A.J. Syder, J.M. Jacobs, C.M. Sorensen, K. Walters, S. Proll, and J.E. McDermott, et al. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics." PLoS Pathogens 6, no. 1:Art. No. e1000719. PNWD-SA-8678. doi:10.1371/journal.ppat.1000719
Gupta N., K.K. Hixson, D.E. Culley, R.D. Smith, and P.A. Pevzner. 2010. "Analyzing Protease Specificity and Detecting in Vivo Proteolytic Events Using Tandem Mass Spectrometry." Proteomics 10, no. 15:2833-2844. PNNL-SA-68815.
Ham B.M., H. Jayachandran, F. Yang, N. Jaitly, A.D. Polpitiya, M.E. Monroe, and L. Wang, et al. 2010. "Novel Ser/Thr Protein Phosphatase 5 (PP5) Regulated Targets during DNA Damage Identified by Proteomics Analysis." Journal of Proteome Research 9, no. 2:945-953. PNNL-SA-69020. doi:10.1021/pr9008207
Ibrahim Y.M., D.C. Prior, E.S. Baker, R.D. Smith, and M.E. Belov. 2010. "Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation- Tandem Time-of-Flight Mass Spectrometry Approach." International Journal of Mass Spectrometry 293, no. 1-3:34-44. PNNL-SA-68112.
Jun S., M. Chang, B. Kim, H. An, D. Lopez-Ferrer, R. Zhao, and R.D. Smith, et al. 2010. "Trypsin coatings on electrospun and alcohol-dispersed polymer nanofibers for trypsin digestion column." Analytical Chemistry 82, no. 18:7828 - 7834. PNNL-SA-72383. doi:10.1021/ac101633e
Jung H., S.O. Purvine, H. Kim, V.A. Petyuk, S. Hyung, M.E. Monroe, and D. Mun, et al. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82, no. 20:8510-8518. PNNL-SA-74157. doi:10.1021/ac101388b
Karpievitch Y.V., A.D. Polpitiya, G.A. Anderson, R.D. Smith, and A.R. Dabney. 2010. "Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects." The Annals of Applied Statistics 4, no. 4:1797-1823. PNNL-SA-75440.
Kelly R.T., A.V. Tolmachev, J.S. Page, K. Tang, and R.D. Smith. 2010. "The Ion Funnel: Theory, Implementations and Applications." Mass Spectrometry Reviews 29, no. 2:294-312. PNNL-SA-60508. doi:10.1002/mas.20232
Kim J., B.C. Kim, D. Lopez-Ferrer, K. Petritis, and R.D. Smith. 2010. "Nanobiocatalysis for protein digestion in proteomic analysis." Proteomics 10, no. 4 SP ISS:687-699. PNNL-SA-68067.
Kotz K.T., W. Xiao, C. Miller-Graziano, W. Qian, A. Russom, E.A. Warner, and L.L. Moldawer, et al. 2010. "Clinical Microfluidics for Neutrophil Genomics and Proteomics." Nature Medicine16, no. 9:1042-1048. PNWD-SA-8973. doi:10.1038/nm.2205
Lewis N.E., K.K. Hixson, T.M. Conrad, J.A. Lerman, P. Charusanti, P. Charusanti, and A.D. Polpitiya, et al. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6. PNNL-SA-68816. doi:10.1038/msb.2010.47
Liu M., J. Hou, L. Huang, X. Huang, T.H. Heibeck, R. Zhao, and L. Pasa-Tolic, et al. 2010. "Site-Specific Proteomics Approach for Study Protein S-Nitrosylation." Analytical Chemistry82, no. 17:7160-7168. PNNL-SA-75223. doi:10.1021/ac100569d
Lourette N.M., H.S. Smallwood, S. Wu, E.W. Robinson, T.C. Squier, R.D. 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, no. 6:930-939. PNNL-SA-69765.
Marginean I., J.S. Page, A.V. Tolmachev, K. Tang, and R.D. Smith. 2010. "Achieving 50% ionization efficiency in sub-ambient pressure ionization with nanoelectrospray." Analytical Chemistry 82, no. 22:9344-9349. PNNL-SA-74231.
Petyuk V.A., W. Qian, R.D. Smith, and D.J. Smith. 2010. "Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry." Methods 50, no. 2:77-84. PNNL-SA-68829.
Qian W., B.O. Petritis, A. Kaushal, C.C. Finnerty, M.G. Jescheke, M.E. Monroe, and R.J. Moore, et al. 2010. "Plasma Proteome Response to Severe Burn Injury Revealed by 18O-Labeled “Universal” Reference-based Quantitative Proteomics." Journal of Proteome Research 9, no. 9:4779-4789. PNWD-SA-9014.
Rana G., G. Rana, T.P. York, J.S. Edmiston, B.K. Zedler, J.G. Pounds, and J.N. Adkins, et al. 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. PNWD-SA-9006. doi:10.1007/s00216-010-3742-4
Schutzer S.E., T. Liu, B. Natelson, T.E. Angel, A.A. Schepmoes, S.O. Purvine, and K.K. Hixson, et al. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid." PLoS One 5, no. 6:e10980-. PNWD-SA-8931. doi:10.1371/journal.pone.0010980
Shah A.R., J.L. Davidson, M.E. Monroe, A.M. Mayampurath, W.F. Danielson, Y. Shi, and A.C. Robinson, et al. 2010. "An efficient data format for mass spectrometry based proteomics." Journal of the American Society for Mass Spectrometry 21, no. 10:1784-1788. PNNL-SA-69363. doi:10.1016/j.jasms.2010.06.014
Shah A.R., K. Agarwal, E.S. Baker, M. Singhal, A.M. Mayampurath, Y.M. Ibrahim, and L.J. Kangas, et al. 2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry." Bioinformatics 26, no. 13:1601-1607. PNWD-SA-8802. doi:10.1093/bioinformatics/btq245
Shah A.R., N. Jaitly, N. Zuljevic, M.E. Monroe, A.V. Liyu, A.D. Polpitiya, and J.N. Adkins, et al. 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, 88 - 93. Piscataway, New Jersey:IEEE. PNNL-SA-67849. doi:10.1109/e-Science.2009.21
Shen Y., N. Tolic, S.O. Purvine, and R.D. Smith. 2010. "Identification of Disulfide Bonds in Protein Proteolytic Degradation Products Using de Novo-Protein Unique Sequence Tags Approach." Journal of Proteome Research 9, no. 8:4053-4060. PNNL-SA-73098.
Shen Y., N. Tolic, T. Liu, R. Zhao, B.O. Petritis, M.A. Gritsenko, and D.G. Camp, et al. 2010. "Blood Peptidome-Degradome Profile of Breast Cancer." PLoS One 5, no. 10:Article No.: e13133. PNNL-SA-70095. doi:10.1371/journal.pone.0013133
Shen Y., T. Liu, N. Tolic, B.O. Petritis, R. Zhao, R.J. Moore, and S.O. Purvine, et al. 2010. "A strategy for degradomic-peptidomic analysis of the human blood plasma." Journal of Proteome Research 9, no. 5:2339-2346. PNNL-SA-71375. doi:10.1021/pr901083m
Shvartsburg A.A., A. Creese, R.D. Smith, and H.J. Cooper. 2010. "Separation of Peptide Isomers with Variant Modified Sites by High-Resolution Differential Ion Mobility Spectrometry." Analytical Chemistry 82, no. 19:8327-8334. PNNL-SA-74158. doi:10.1021/ac101878a
Shvartsburg A.A., D.C. Prior, K. Tang, and R.D. Smith. 2010. "High-Resolution Differential Ion Mobility Separations Using Planar Analyzers at Elevated Dispersion Fields." Analytical Chemistry 82, no. 18:7649-7655. PNNL-SA-72822. doi:10.1021/ac101413k
Shvartsburg A.A., D.E. Clemmer, and R.D. Smith. 2010. "Isotopic Effect on Ion Mobility and Separation of Isotopomers by High-Field Ion Mobility Spectrometry." Analytical Chemistry 82, no. 19:8047-8051. PNNL-SA-72381. doi:10.1021/ac101992d
Shvartsburg A.A., K. Tang, and R.D. Smith. 2010. "Differential Ion Mobility Separations of Peptides with Resolving Power Exceeding 50." Analytical Chemistry 82, no. 1:32-35. PNWD-SA-8758. doi:10.1021/ac902133n
Shvartsburg A.A., W.F. Danielson, and R.D. Smith. 2010. "High-Resolution Differential Ion Mobility Separations Using Helium-Rich Gases." Analytical Chemistry 82, no. 6:2456-2462. PNWD-SA-8910.
Sigdel T.K., A. Kaushal, M.A. Gritsenko, A.D. Norbeck, W. Qian, W. Xiao, and D.G. Camp, et al. 2010. "Shotgun Proteomics Identifies Proteins Specific for Acute Renal Transplant Rejection." Proteomics - Clinical Applications 4, no. 1:32-47. PNNL-SA-68069. doi:10.1002/prca.200900124
Smith D.P., J.B. Kitner, A.D. Norbeck, T.R. Clauss, M.S. Lipton, M.S. Schwalbach, and L. Steindler, et al. 2010. "Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus Pelagibacter ubique." PLoS One 5, no. 5:Article Number: e10487. PNNL-SA-72424.
Sorensen C.M., J. Ding, Q. Zhang, T. Alquier, R. Zhao, P.W. Mueller, and R.D. Smith, et al. 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, no. 12:948-956. PNNL-SA-70097.
Sun X., R.T. Kelly, K. Tang, and R.D. Smith. 2010. "Ultrasensitive Nanoelectrospray Ionization-Mass Spectrometry using Poly(dimethylsiloxane) Microchips with Monolithically Integrated Emitters." Analyst 135, no. 9:2296-2302. PNNL-SA-70123.
Tang Z., H. Wu, D. Du, J. Wang, H. Wang, W. Qian, and D.J. Bigelow, et al. 2010. "Sensitive Immunoassays of Nitrated Fibrinogen in Human Biofluids." Talanta 81, no. 4-5:1662-1669. PNNL-SA-71863.
Tian Z., R. Zhao, N. Tolic, R.J. Moore, D.L. Stenoien, E.W. Robinson, and R.D. Smith, et al. 2010. "Two-dimensional liquid chromatography system for online top-down mass spectrometry." Proteomics 10, no. 20:3610-3620. PNNL-SA-73468. doi:10.1002/pmic.201000367
True L.D., H. Zhang, M. Ye, C. Huang, P.S. Nelson, P.D. Von Haller, and L.W. Tjoelker, et al. 2010. "CD90/THY1 is over-expressed in prostate cancer-associated fibroblasts and could serve as a cancer biomarker." Modern Pathology 23, no. 10:1346-1356. PNNL-SA-74146.
Wegener K.M., A.K. Singh, J.M. Jacobs, T.R. Elvitigala, E.A. Welsh, N.S. Keren, and M.A. Gritsenko, et al. 2010. "Global Proteomics Reveal An Atypical Strategy for Carbon/Nitrogen Assimilation by a Cyanobacterium Under Diverse Environmental Perturbations." Molecular & Cellular Proteomics. MCP 9, no. 12:2678-89. PNNL-SA-67041. doi:10.1074/mcp.M110.000109
Yang F., K.M. Waters, J.H. Miller, M.A. Gritsenko, R. Zhao, X. Du, and E.A. Livesay, et al. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5, no. 11:e14152. PNNL-SA-73768. doi:10.1371/journal.pone.0014152
Zhang H., R.N. Brown, W. Qian, M.E. Monroe, S.O. Purvine, R.J. Moore, and M.A. Gritsenko, et al. 2010. "Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling." Journal of Proteome Research 9, no. 5:2160-2169. PNNL-SA-67314.
Zhang X., J. Zhou, M.H. Chin, A.A. Schepmoes, V.A. Petyuk, K.K. Weitz, and B.O. Petritis, et al. 2010. "Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model." Journal of Proteome Research 9, no. 3:1496-1509. PNNL-SA-67444. doi:10.1021/pr901024z
Zhang X., M.E. Monroe, B. Chen, M.H. Chin, T.H. Heibeck, A.A. Schepmoes, and F. Yang, et al. 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, no. 6:1199-1208. PNNL-SA-65899.
Zhou J., A.A. Schepmoes, X. Zhang, R.J. Moore, M.E. Monroe, J. Lee, and D.G. Camp, et al. 2010. "Improved LC-MS/MS Spectral Counting Statistics by Recovering Low Scoring Spectra Matched to Confidently Identified Peptide Sequences." Journal of Proteome Research 9, no. 11:5698-5704. PNNL-SA-74147. doi:10.1021/pr100508p

2009

Alquier T., M. Peyot, M.G. Latour, M. Kebede, C.M. Sorensen, S. Gesta, and C.R. Kahn, et al. 2009. "Deletion of GPR40 Impairs Glucose-Induced Insulin Secretion In Vivo in Mice Without Affecting Intracellular Fuel Metabolism in Islets." Diabetes 58, no. 11:2607-2615. PNNL-SA-64908.
Ansong C., H. Yoon, S. Porwollik, H. Mottaz-Brewer, B.O. Petritis, N. Jaitly, and J.N. Adkins, et al. 2009. "Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation." PLoS One 4, no. 3:e4809. PNNL-SA-63141. doi:10.1371/journal.pone.0004809
Chan E.Y., J.N. Sutton, J.M. Jacobs, A. Bondarenko, R.D. Smith, and M.G. 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, no. 18:9283-9295. PNWD-SA-8677.
Chowdhury S.M., L. Shi, H. Yoon, C. Ansong, L.M. Rommereim, A.D. Norbeck, and K.J. Auberry, et al. 2009. "A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis." Journal of Proteome Research 8, no. 3:1504-1514. PNNL-SA-58873.
Chowdhury S.M., X. Du, N. Tolic, S. Wu, R.J. Moore, M.U. Mayer, and R.D. Smith, et al. 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, no. 13:5524-5532. PNNL-SA-61747. doi:10.1021/ac900853k
Heibeck T.H., S. Ding, L.K. Opresko, R. Zhao, A.A. Schepmoes, F. Yang, and A.V. Tolmachev, et al. 2009. "An Extensive Survey of Tyrosine Phosphorylation Revealing New Sites in Human Mammary Epithelial Cells." Journal of Proteome Research 8, no. 8:3852-3861. PNNL-SA-63993.
Jaitly N., A.M. Mayampurath, K.A. Littlefield, J.N. Adkins, G.A. Anderson, and R.D. Smith. 2009. "Decon2LS: An Open-Source Software Package for Automated Processing and Visualization of High Resolution Mass Spectrometry Data." BMC Bioinformatics 10. PNNL-SA-60537. doi:10.1186/1471-2105-10-87
Karpievitch Y., J.R. Stanley, T. Taverner, J. Huang, J.N. Adkins, C. Ansong, and F. Heffron, et al. 2009. "A statistical framework for protein quantitation in bottom-up MS-based proteomics." Bioinformatics 25, no. 16:2028-2034. PNNL-SA-66740. doi:10.1093/bioinformatics/btp362
Karpievitch Y., J.R. Stanley, T. Taverner, J. Huang, J.N. Adkins, C. Ansong, and F. Heffron, et al. 2009. "A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics." Bioinformatics 25, no. 16:2028-2034. PNNL-SA-70100.
Kelly R.T., J.S. Page, I. Marginean, K. Tang, and R.D. Smith. 2009. "Dilution-Free Analysis from Picoliter Droplets by Nano-Electrospray Ionization Mass Spectrometry." Angewandte Chemie International Edition 48, no. 37:6832-6835. PNNL-SA-66743. doi:10.1002/anie.200902501
Kim B.C., D. Lopez-Ferrer, S. Lee, H. Ahn, S. Nair, S.H. Kim, and B.S. Kim, et al. 2009. "Highly Stable Trypsin-Aggregate Coatings on Polymer Nanofibers for Repeated Protein Digestion." Proteomics 9, no. 7:1893-1900. PNNL-SA-60161.
Lopez-Ferrer D., K.K. Hixson, H.S. Smallwood, T.C. Squier, K. Petritis, and R.D. Smith. 2009. "Evaluation of a High Intensity Focused Ultrasound-Immobilized Trypsin Digestion and 18 O-Labeling Method for Quantitative Proteomics." Analytical Chemistry 81, no. 15:6272-6277. PNNL-SA-63667.
Mabrouki R.B., R.T. Kelly, D.C. Prior, A.A. Shvartsburg, K. Tang, and R.D. Smith. 2009. "Improving FAIMS Sensitivity using a Planar Geometry with Slit Interfaces." Journal of the American Society for Mass Spectrometry 20, no. 9:1768-1774. PNNL-SA-65387. doi:10.1016/j.jasms.2009.05.019
Marginean I., J.S. Page, R.T. Kelly, K. Tang, and R.D. Smith. 2009. "Effect of pressure on electrospray characteristics." Applied Physics Letters 95, no. 18:Article Number: 184103. PNNL-SA-65737.
Marginean I., R.T. Kelly, R.J. Moore, D.C. Prior, B.L. Lamarche, K. Tang, and R.D. Smith. 2009. "Selection of the Optimum Electrospray Voltage for Gradient Elution LC-MS Measurements." Journal of the American Society for Mass Spectrometry 20, no. 4:682-688. PNNL-SA-62318.
Page J.S., I. Marginean, E.S. Baker, R.T. Kelly, K. Tang, and R.D. Smith. 2009. "Biases in Ion Transmission Through an Electrospray Ionization-Mass Spectrometry Capillary Inlet." Journal of the American Society for Mass Spectrometry 20, no. 12:2265-2272. PNNL-SA-66725. doi:10.1016/j.jasms.2009.08.018
Park C.C., V.A. Petyuk, W. Qian, R.D. Smith, and D.J. Smith. 2009. "Dual spatial maps of transcript and protein abundance in the mouse brain." Expert Review of Proteomics 6, no. 3:243-249. PNWD-SA-8709.
Petritis B.O., W. Qian, D.G. Camp, and R.D. Smith. 2009. "A Simple Procedure for Effective Quenching of Trypsin Activity and Prevention of 18O-Labeling Back-Exchange." Journal of Proteome Research 8, no. 5:2157-2163. PNWD-SA-8385. doi:10.1021/pr800971w
Petyuk V.A., A.M. Mayampurath, M.E. Monroe, A.D. Polpitiya, S.O. Purvine, G.A. Anderson, and D.G. Camp, et al. 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. PNNL-SA-62317. doi:10.1074/mcp.M900217-MCP200
Prasad S., K. Tang, D. Manura, D. Papanastasiou, and R.D. Smith. 2009. "Simulation of Ion Motion in FAIMS through Combined Use of SIMION and Modified SDS." Analytical Chemistry81, no. 21:8749-8757. PNNL-SA-65516. doi:10.1021/ac900880v
Qian W., T. Liu, V.A. Petyuk, M.A. Gritsenko, B.O. Petritis, A.D. Polpitiya, and A. Kaushal, et al. 2009. "Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an O-18-Labeled “Universal” Reference Sample." Journal of Proteome Research 8, no. 1:290-299. PNNL-SA-57317.
Schepmoes A.A., Q. Zhang, B.O. Petritis, W. Qian, and R.D. Smith. 2009. "N-Terminal Enrichment: Developing a Protocol to Detect Specific Proteolytic Fragments." Journal of Biomolecular Techniques:JBT 20, no. 5:263-265. PNNL-SA-75602.
Shen Y., J.S. Page, and R.D. Smith. 2009. "Advanced Capillary Liquid Chromatography-Mass Spectrometry for Proteomics." In Advances in Chromatography, edited by E Grushka and N Grinberg. 31-58. Boca Raton, Florida:CRC Press. PNNL-SA-57890.
Shi L., C. Ansong, H.S. Smallwood, L.M. Rommereim, J.E. McDermott, H.M. Brewer, and A.D. Norbeck, et al. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2, no. 9:388-397. PNNL-SA-68770. doi:10.4172/jpb.1000099
Shi L., C. Ansong, H.S. Smallwood, L.M. Rommereim, J.E. McDermott, H.M. Brewer, and A.D. Norbeck, et al. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2, no. 9:388-397. PNNL-SA-60692. doi:10.4172/jpb.1000099
Shi L., S.M. Chowdhury, H.S. Smallwood, H. Yoon, H.M. Mottaz-Brewer, A.D. Norbeck, and J.E. McDermott, et al. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77, no. 8:3227-3233. PNNL-SA-62432. doi:10.1128/IAI.00063-09
Shvartsburg A.A., K. Tang, R.D. 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, no. 19:8048-8053. PNWD-SA-8707. doi:10.1021/ac901479e
Shvartsburg A.A., R.D. 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, no. 15:6489-6495. PNWD-SA-8587. doi:10.1021/ac900892u
Shvartsburg A.A., S. Noskov, R. Purves, and R.D. 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, no. 16:6495-6500. PNNL-SA-57230.
Sowell S.M., L. Wilhelm, A.D. Norbeck, M.S. Lipton, C.D. Nicora, D.F. Barofsky, and C. carlson, et al. 2009. "Transport Functions Dominate the SAR11 Metaproteome at Low-Nutrient Extremes in the Sargasso Sea." The ISME Journal 3, no. 1:93-105. PNNL-SA-60995.
Tolmachev A.V., B.H. Clowers, M.E. Belov, and R.D. Smith. 2009. "Coulombic Effects on Ion Mobility Spectrometry." Analytical Chemistry 81, no. 12:4778-4787. PNNL-SA-64596.
Tolmachev A.V., E.W. Robinson, S. Wu, L. Pasa-Tolic, and R.D. Smith. 2009. "FT-ICR MS optimization for the analysis of intact proteins." International Journal of Mass Spectrometry287, no. 1-3 SP ISS:32-38. PNNL-SA-61301. doi:10.1016/j.ijms.2008.10.010
Weber T.J., L.K. Opresko, D.M. Waisman, G.J. Newton, R.D. Quesenberry, N. Bollinger, and R.J. Moore, et al. 2009. "Regulation of the Low Dose Radiation Paracrine-Specific Anchorage-Independent Growth Response by Annexin A2." Radiation Research 172, no. 1:96-105. PNNL-SA-56968. doi:10.1667/RR1220.1
Wu S., F. Yang, R. Zhao, N. Tolic, E.W. Robinson, D.G. Camp, and R.D. Smith, et al. 2009. "An integrated workflow for characterizing intact phosphoproteins from complex mixtures." Analytical Chemistry 81, no. 11:4210-4219. PNNL-SA-63139. doi:10.1021/ac802487q
Wu S., N.M. Lourette, N. Tolic, R. Zhao, R. Robinson, A.V. Tolmachev, and R.D. Smith, et al. 2009. "An integrated top-down and bottom-up strategy for broadly characterizing protein isoforms and modifications." Journal of Proteome Research 8, no. 3:1347-1357. PNNL-SA-58633.
Yang F., S. Wu, D.L. Stenoien, R. Zhao, M.E. Monroe, M.A. Gritsenko, and S.O. Purvine, et al. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81, no. 10:4137-4143. PNNL-SA-63701. doi:10.1021/ac802605m
Zhao R., S. Ding, Y. Shen, D.G. Camp, E.A. Livesay, H.R. Udseth, and R.D. Smith. 2009. "Automated metal-free multiple-column nanoLC for improved phosphopeptide analysis sensitivity and throughput." Journal of Chromatography B 877, no. 8-9:663-670. PNNL-SA-62634.
Zhou J., B.O. Petritis, K. Petritis, A.D. Norbeck, K.K. Weitz, R.J. Moore, and D.G. Camp, et al. 2009. "Mouse-Specific Tandem IgY7-SuperMix Immunoaffinity Separations for Improved LC-MS/MS Coverage of the Plasma Proteome." Journal of Proteome Research 8, no. 11:5387-5395. PNNL-SA-67312.

2008

Ansong C., H. Yoon, A.D. Norbeck, J.K. Gustin, J.E. McDermott, H.M. Mottaz, and J. Rue, et al. 2008. "Proteomics Analysis of the Causative Agent of Typhoid Fever." Journal of Proteome Research 7, no. 2:546-557. PNNL-SA-56065. doi:10.1021/pr070434u
Ansong C., S.O. Purvine, J.N. Adkins, M.S. Lipton, and R.D. Smith. 2008. "Proteogenomics: the needs and roles to be filled by proteomics in genome annotation." Briefings in Functional Genomics and Proteomics 7, no. 1:50-62. PNNL-SA-57607.
Baker E.S., K. Tang, W.F. Danielson, D.C. Prior, and R.D. Smith. 2008. "Simultaneous Fragmentation of Multiple Ions Using IMS Drift Time Dependent Collision Energies." Journal of the American Society for Mass Spectrometry 19, no. 3:411-419. PNWD-SA-7952. doi:10.1016/j.jasms.2007.11.018
Belov M.E., B.H. Clowers, D.C. Prior, W.F. Danielson, A.V. Liyu, B.O. Petritis, and R.D. Smith. 2008. "Dynamically Multiplexed Ion Mobility Time-of-Flight Mass Spectrometry." Analytical Chemistry 80, no. 15:5873-5883. PNNL-SA-59401. doi:10.1021/ac8003665
Brewer H.M., A.D. Norbeck, J.N. Adkins, N.P. Manes, C. Ansong, L. Shi, and Y. Rikihisa, et al. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19, no. 5:285-295. PNNL-SA-60633.
Callister S.J., L.A. McCue, J.E. Turse, M.E. Monroe, K.J. Auberry, R.D. Smith, and J.N. Adkins, et al. 2008. "Comparative Bacterial Proteomics: Analysis of the Core Genome Concept." PLoS One 3, no. 2:e1542. PNNL-SA-58389. doi:10.1371/journal.pone.0001542
Chin M.H., W. Qian, H. Wang, V.A. Petyuk, J.S. Bloom, D.M. Sforza, and G. Lacan, et al. 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, no. 2:666-677. PNNL-SA-58152. doi:10.1021/pr070546l
Clowers B.H., M.E. Belov, D.C. Prior, W.F. Danielson, Y.M. Ibrahim, and R.D. Smith. 2008. "Pseudorandom Sequence Modifications for Ion Mobility Orthogonal Time-of-Flight Mass Spectrometry." Analytical Chemistry 80, no. 7:2464-2473. PNWD-SA-7989. doi:10.1021/ac7022712
Clowers B.H., Y.M. Ibrahim, D.C. Prior, W.F. Danielson, M.E. Belov, and R.D. Smith. 2008. "Enhanced Ion Utilization Efficiency Using an Electrodynamic Ion Funnel Trap as an Injection Mechanism for Ion Mobility Spectrometry." Analytical Chemistry 80, no. 3:612-623. PNWD-SA-7885. doi:10.1021/ac701648p
Ding J., C.M. Sorensen, N. Jaitly, H. Jiang, D.J. Orton, M.E. Monroe, and R.J. Moore, et al. 2008. "Application of the accurate mass and time tag approach in studies of the human blood lipidome." Journal of Chromatography B 871, no. 2:243-252. PNNL-SA-58868. doi:10.1016/j.jchromb.2008.04.040
Ding S., Y. Wang, J.M. Jacobs, W. Qian, F. Yang, A.V. Tolmachev, and X. Du, et al. 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, no. 10:4215-24. PNNL-SA-52241. doi:10.1021/pr7007785
Ding Y.R., K.K. Hixson, M. Aklujkar, M. Aklujkar, M.S. Lipton, R.D. Smith, and D.R. Lovley, et al. 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, no. 12:1935-1941. PNNL-SA-46860. doi:10.1016/j.bbapap.2008.06.011
Du X., F. Yang, N.P. Manes, D.L. Stenoien, M.E. Monroe, J.N. Adkins, and D.J. States, et al. 2008. "Linear Discriminant Analysis - Based Estimation of the False Discovery Rate for Phosphopeptide Identifications." Journal of Proteome Research 7, no. 6:2195-2203. PNNL-SA-56421. doi:10.1021/pr070510t
Du X., S.J. Callister, N.P. Manes, J.N. Adkins, R.A. Alexandridis, X. Zeng, and J. Roh, et al. 2008. "A Computational Strategy to Analyze Label-Free Temporal Bottom-up Proteomics Data." Journal of Proteome Research 7, no. 7:2595-2604. PNNL-SA-55070. doi:10.1021/pr0704837
Dumortier J., D.N. Streblow, A.V. Moses, J.M. Jacobs, C.N. Kreklywich, D.G. Camp, and R.D. Smith, et al. 2008. "Human Cytomegalovirus Secretome Contains Factors That Induce Angiogenesis and Wound Healing." Journal of Virology 82, no. 13:6524-6535. PNNL-SA-60994. doi:doi:10.1128/JVI.00502-08
Gupta N., J. Benhamida, V. Bhargava, D. Goodman, E. Kain, I. Kerman, and N. Nguyen, et al. 2008. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Research 18, no. 7:1133-1142. PNNL-SA-58924.
Ham B.M., F. Yang, H. Jayachandran, N. Jaitly, M.E. Monroe, M.A. Gritsenko, and E.A. Livesay, et al. 2008. "The Influence of Sample Preparation and Replicate Analyses on HeLa Cell Phosphoproteome Coverage." Journal of Proteome Research 7, no. 6:2215-2221. PNWD-SA-7904.
Ibrahim Y.M., M.E. Belov, A.V. Liyu, and R.D. Smith. 2008. "Automated Gain Control Ion Funnel Trap for Orthogonal Time-of-Flight Mass Spectrometry." Analytical Chemistry 80, no. 14:5367-5376. PNNL-SA-59266. doi:10.1021/ac8003488
Jacobs J.M., K.M. Waters, L.E. Kathmann, D.G. Camp, H.S. Wiley, R.D. Smith, and B.D. Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7, no. 2:558-569. PNNL-SA-56310. doi:10.1021/pr0704377
Kelly R.T., J.S. Page, I. Marginean, K. Tang, and R.D. Smith. 2008. "Nanoelectrospray Emitter Arrays Providing Interemitter Electric Field Uniformity." Analytical Chemistry 80, no. 14:5660-5665. PNNL-SA-59402. doi:10.1021/ac800508q
Kelly R.T., J.S. Page, R. Zhao, W. Qian, H.M. Mottaz, K. Tang, and R.D. Smith. 2008. "Capillary-Based Multi Nanoelectrospray Emitters: Improvements in Ion Transmission Efficiency and Implementation with Capillary Reversed-Phase LC-ESI-MS." Analytical Chemistry 80, no. 1:143-149. PNNL-SA-56420. doi:10.1021/ac701647s
Kelly R.T., K. Tang, D. Irimia, M. Toner, and R.D. Smith. 2008. "Elastomeric Microchip Electrospray Emitter for Stable Cone-Jet Mode Operation in the Nanoflow Regime." Analytical Chemistry 80, no. 10:3824-3831. PNNL-SA-58551.
Kim J., R. Zhang, E.F. Strittmatter, R.D. Smith, and R. Zand. 2008. "Post-translational Modifications of Chicken Myelin Basic Protein Charge Components." Neurochemical Research34, no. 2:360-372. PNNL-SA-64756. doi:10.1007/s11064-008-9788-4
Livesay E.A., K. Tang, B.K. Taylor, M.A. Buschbach, D.F. Hopkins, B.L. Lamarche, and R. Zhao, et al. 2008. "Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses." Analytical Chemistry 80, no. 1:294-302. PNNL-SA-56532. doi:10.1021/ac701727r
Lopez-Ferrer D., K. Petritis, K.K. Hixson, T.H. Heibeck, R.J. Moore, M.E. Belov, and D.G. Camp, et al. 2008. "Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly." Journal of Proteome Research 7, no. 8:3276-3281. PNNL-SA-60252. doi:10.1021/pr7008077
Lopez-Ferrer D., K. Petritis, N.M. Lourette, B.H. Clowers, K.K. Hixson, T.H. Heibeck, and D.C. Prior, et al. 2008. "Fast On-Line Digestion System for Protein Characterization." Analytical Chemistry 80, no. 23:8930-8936. PNWD-SA-8189. doi:10.1021/ac800927v
Lopez-Ferrer D., T.H. Heibeck, K. Petritis, K.K. Hixson, W. Qian, M.E. Monroe, and A.M. Mayampurath, et al. 2008. "Rapid Sample Processing For LC-MS Based Quantitative Proteomics Using High Intensity Focused Ultrasounds." Journal of Proteome Research 7, no. 9:3860-3867. PNNL-SA-59400. doi:10.1021/pr800161x
Manes N.P., R.D. Estep, H.M. Mottaz, R.J. Moore, T.R. Clauss, M.E. Monroe, and X. Du, et al. 2008. "Comparative Proteomics of Human Monkeypox and Vaccinia Intracellular Mature and Extracellular Enveloped Virions." Journal of Proteome Research 3. PNNL-SA-54048. doi:10.1021/pr070432+
Marginean I., R.T. Kelly, D.C. Prior, B.L. Lamarche, K. Tang, and R.D. Smith. 2008. "Analytical Characterization of the Electrospray Ion Source in the Nanoflow Regime." Analytical Chemistry 80, no. 17:6573-6579. PNNL-SA-59989. doi:10.1021/ac800683s
Mathivanan S., M. Ahmed, M. Ahmed, N.G. Ahn, H. Alexandre, H. Alexandre, and R. Amanchy, et al. 2008. "Human Proteinpedia enables sharing of human protein data." Nature Biotechnology 26, no. 2:164-167. PNNL-SA-61184.
Mayampurath A.M., N. Jaitly, S.O. Purvine, M.E. Monroe, K.J. Auberry, J.N. Adkins, and R.D. Smith. 2008. "DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra." Bioinformatics 24, no. 7:1021-1023. PNNL-SA-56275. doi:10.1093/bioinformatics/btn063
Metz T.O., J.S. Page, E.S. Baker, K. Tang, J. Ding, Y. Shen, and R.D. Smith. 2008. "High Resolution Separations and Improved Ion Production and Transmission in Metabolomics." Trends in Analytical Chemistry. TrAC 27, no. 3:205-214. PNNL-SA-56841. doi:10.1016/j.trac.2007.11.003
Metz T.O., W. Qian, J.M. Jacobs, M.A. Gritsenko, R.J. Moore, A.D. Polpitiya, and M.E. Monroe, et al. 2008. "Application of proteomics in the discovery of candidate protein biomarkers in a Diabetes Autoantibody Standardization Program sample subset." Journal of Proteome Research 7, no. 2:698-707. PNNL-SA-56533. doi:10.1021/pr700606w
Monroe M.E., J.L. Shaw, D.S. Daly, J.N. Adkins, and R.D. 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, no. 3:215-217. PNNL-SA-52621. doi:10.1016/j.compbiolchem.2008.02.006
Page J.S., K. Tang, R.T. Kelly, and R.D. Smith. 2008. "A subambient pressure ionization with nanoelectrospray (SPIN) source and interface for improved sensitivity in mass spectrometry." Analytical Chemistry 80, no. 5:1800-1805. PNNL-SA-60054. doi:10.1021/ac702354b
Page J.S., K. Tang, R.T. Kelly, and R.D. Smith. 2008. "Subambient pressure ionization with nanoelectrospray source and interface for improved sensitivity in mass spectrometry." Analytical Chemistry Vol. 80, no. 5:1800-1805. PNNL-SA-57906. doi:10.1021/ac702354b
Page J.S., R.T. Kelly, D.G. Camp, and R.D. Smith. 2008. "Improving low-level plasma protein mass spectrometry-based detection for candidate biomarker discovery and validation." ICBC Newsletter 3, no. 3. PNNL-SA-57537.
Pasa-Tolic L., J.M. Jacobs, W. Qian, and R.D. Smith. 2008. "Quantitative Proteomics using Nano-LC with High Accuracy Mass Spectrometry." In Clinical Proteomics: From Diagnosis to Therapy, edited by JE Van Eyk and MJ Dunn. 89-100. Weinheim:Wiley-VCH. PNNL-SA-51867.
Pertz O.C., Y. Wang, F. Yang, W. Wang, l.J. gay, M.A. Gritsenko, and T.R. Clauss, et al. 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, no. 6:1931-1936. PNNL-SA-58516. doi:10.1073/pnas.0706545105
Petyuk V.A., N. Jaitly, R.J. Moore, J. Ding, T.O. Metz, K. Tang, and M.E. Monroe, et al. 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, no. 3:693-706. PNNL-SA-56693. doi:10.1021/ac701863d
Petyuk V.A., W. Qian, C. Hinault, M.A. Gritsenko, M. Singhal, M.E. Monroe, and D.G. Camp, et al. 2008. "Characterization of the mouse pancreatic islet proteome and comparative analysis with other mouse tissues." Journal of Proteome Research 7, no. 8:3114-3126. PNNL-SA-58155. doi:10.1021/pr800205b
Polpitiya A.D., W. Qian, N. Jaitly, V.A. Petyuk, J.N. Adkins, D.G. Camp, and G.A. Anderson, et al. 2008. "DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24, no. 13:1556-1558. PNNL-SA-58107. doi:10.1093/bioinformatics/btn217
Pounds J.G., J.W. Flora, J.N. Adkins, K.M. Lee, G. Rana, G. Rana, and T. Sengupta, et al. 2008. "Characterization of the mouse bronchoalveolar lavage proteome by micro-capillary LC-FTICR mass spectrometry." Journal of Chromatography B 864, no. 1-2:95-101. PNNL-SA-60702.
Prichard M.N., M.N. Prichard, E. Sztul, S.L. Daily, A.L. Perry, S.L. Frederick, and R.B. Gill, et al. 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, no. 10:5054-5067. PNNL-SA-63189.
Qian W., D.T. Kaleta, B.A. Ogata, H. Jiang, T. Liu, X. Zhang, and H.M. Mottaz, et al. 2008. "Enhanced Detection of Low Abundant Human Plasma Proteins using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy." Molecular & Cellular Proteomics. MCP 7, no. 10:1963-1973. PNWD-SA-8062. doi:10.1074/mcp.M800008-MCP200
Robinson E.W., A.A. Shvartsburg, K. Tang, and R.D. Smith. 2008. "Control of Ion Distortion in Field Asymmetric Waveform Ion Mobility Spectrometry via Variation of Dispersion Field and Gas Temperature." Analytical Chemistry 80, no. 19:7508-7515. PNNL-SA-59851. doi:10.1021/ac800655d
Rodland K.D., J.N. Adkins, C. Ansong, S.M. Chowdhury, N.P. Manes, L. Shi, and H. Yoon, et al. 2008. "Use of high-throughput mass spectrometry to elucidate host pathogen interactions in Salmonella." Future Microbiology 3, no. 6:625-634. PNNL-SA-63699.
Rodland K.D., J.N. Adkins, C. Ansong, S.M. Chowdhury, N.P. Manes, L. Shi, and H. Yoon, et al. 2008. "Use of high-throughput mass spectrometry to elucidate host-pathogen interactions in Salmonella." Future Microbiology 3, no. 6:625-634. PNNL-SA-61185. doi:10.2217/17460913.3.6.625
Shen Y., K.K. Hixson, N. Tolic, D.G. Camp, S.O. Purvine, R.J. Moore, and R.D. Smith. 2008. "Mass Spectrometry Analysis of Proteome-wide Proteolytic Post-translational Degradation of Proteins." Analytical Chemistry 80, no. 15:5819-5828. PNNL-SA-58041. doi:10.1021/ac800077w
Shen Y., N. Tolic, K.K. Hixson, S.O. Purvine, G.A. Anderson, and R.D. Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins." Analytical Chemistry 80, no. 20:7742-7754. PNNL-SA-60782. doi:10.1021/ac801123p
Shen Y., N. Tolic, K.K. Hixson, S.O. Purvine, L. Pasa-Tolic, W. Qian, and J.N. Adkins, et al. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80, no. 6:1871-82. PNNL-SA-56012. doi:10.1021/ac702328x
Shvartsburg A.A., and R.D. Smith. 2008. "Fundamentals of Traveling Wave Ion Mobility Spectrometry." Analytical Chemistry 80, no. 24:9689-9699. PNWD-SA-8271. doi:10.1021/ac8016295
Shvartsburg A.A., and R.D. Smith. 2008. "Optimum Waveforms for Differential Ion Mobility Spectrometry (FAIMS)." Journal of the American Society for Mass Spectrometry 19, no. 9:1286-1295. PNNL-SA-58991.
Shvartsburg A.A., K. Tang, and R.D. Smith. 2008. "Two-Dimensional Ion Mobility Analyses of Proteins and Peptides." In Mass Spectrometry of Proteins and Peptides: Methods and Protocols, Methods in Molecular Biology, edited by MS Lipton and L Pasa-Tolic. 417-445. Totowa, New Jersey:Humana Press. PNNL-SA-53042.
Sowell S.M., A.D. Norbeck, M.S. Lipton, C.D. Nicora, S.J. Callister, R.D. Smith, and D.F. Barofsky, et al. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74, no. 13:4091-4100. PNNL-SA-114147. doi:10.1128/AEM.00599-08
Sowell S.M., A.D. Norbeck, M.S. Lipton, C.D. Nicora, S.J. Callister, R.D. Smith, and D.F. Barofsky, et al. 2008. "Proteomic Analysis of Stationary Phase in the Marine Bacterium 'Candidatus Pelagibacter ubique'." Applied and Environmental Microbiology 74, no. 13:4091-4100. PNNL-SA-59403. doi:10.1128/AEM.00599-08
Tolmachev A.V., E.W. Robinson, S. Wu, H. Kang, N.M. Lourette, L. Pasa-Tolic, and R.D. Smith. 2008. "Trapped-ion cell with improved DC potential harmonicity for FT-ICR MS." Journal of the American Society for Mass Spectrometry 19, no. 4:586 - 597. PNNL-SA-57299. doi:10.1016/j.jasms.2008.01.006
Tolmachev A.V., M.E. Monroe, S.O. Purvine, R.J. Moore, N. Jaitly, J.N. Adkins, and G.A. Anderson, et al. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments." Analytical Chemistry80, no. 22:8514-8525. PNNL-SA-61186. doi:10.1021/ac801376g
Wegener K.M., E.A. Welsh, L.E. Thornton, N.S. Keren, J.M. Jacobs, K.K. Hixson, and M.E. Monroe, et al. 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, no. 41:27829-27837. PNNL-SA-57538. doi:10.1074/jbc.M803918200
Welsh E.A., M.L. Liberton, J. Stockel, T. Loh, T.R. Elvitigala, C. Wang, and A. Wollam, et al. 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, no. 39:15094-15099. PNNL-SA-56846. doi:10.1073/pnas.0805418105
Yu R., R. Yu, O. Resnekov, A. Abola, A. Abola, S. Andrews, and S. Andrews, et al. 2008. "The Alpha Project: a model system for systems biology research." IET Systems Biology 2, no. 5:222-233. PNWD-SA-8411. doi:10.1049/iet-syb:20080127
Zhang Q., A.A. Schepmoes, J.W. Brock, S. Wu, R.J. Moore, S.O. Purvine, and J. Baynes, et al. 2008. "Improved Methods for the Enrichment and Analysis of Glycated Peptides." Analytical Chemistry 80, no. 24:9822-9829. PNNL-SA-61746. doi:10.1021/ac801704j
Zhang Q., J.M. Ames, R.D. Smith, J. Baynes, and T.O. 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, no. 2:754-769. PNNL-SA-63138.
Zhang Q., N. Tang, A.A. Schepmoes, L.S. Phillips, R.D. Smith, and T.O. Metz. 2008. "Proteomic Profiling of Nonenzymatically Glycated Proteins in Human Plasma and Erythrocyte Membrane." Journal of Proteome Research 7, no. 5:2025-2032. PNNL-SA-57905. doi:10.1021/pr700763r
Zhang Q., V.A. Petyuk, A.A. Schepmoes, D.J. Orton, M.E. Monroe, F. Yang, and R.D. Smith, et al. 2008. "Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry." Rapid Communications in Mass Spectrometry 22, no. 19:3027-3034. PNNL-SA-61116. doi:10.1002/rcm.3703

2007

Baker E.S., B.H. Clowers, F. Li, K. Tang, A.V. Tolmachev, D.C. Prior, and M.E. Belov, et al. 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, no. 7:1176-1187. PNNL-SA-52620. doi:doi:10.1016/j.jasms.2007.03.031
Belov M.E., M.A. Buschbach, D.C. Prior, K. Tang, and R.D. Smith. 2007. "Multiplexed Ion Mobility Spectrometry - Orthogonal Time-Of-Flight Mass Spectrometry." Analytical Chemistry79, no. 6:2451-2462. PNNL-SA-51865. doi:10.1021/ac0617316
Chan E.Y., W. Qian, D.L. Diamond, T. Liu, M.A. Gritsenko, M.E. Monroe, and D.G. Camp, et al. 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, no. 14:7571-7583. PNWD-SA-7667.
Chin M.H., A.B. Geng, A.H. Khan, W. Qian, V.A. Petyuk, J. Boline, and S. Levy, et al. 2007. "A genome-scale map of expression for a mouse brain section obtained using voxelation." Physiological Genomics 30, no. 3:313-321. PNWD-SA-7823.
Diamond D.L., J.M. Jacobs, B. Paeper, S. Proll, M.A. Gritsenko, R.L. Carithers, Jr., and A.M. Larson, et al. 2007. "Proteomic Profiling of Human Liver Biopsies: Hepatitis C Virus-Induced Fibrosis and Mitochondrial Dysfunction." Hepatology 46, no. 3:649-657. PNWD-SA-7685. doi:10.1002/hep.21751
Ding J., C.M. Sorensen, Q. Zhang, H. Jiang, N. Jaitly, E.A. Livesay, and Y. Shen, et al. 2007. "Capillary LC Coupled with High-Mass Measurement Accuracy Mass Spectrometry for Metabolic Profiling." Analytical Chemistry 79, no. 16:6081-6093. PNNL-SA-53425. doi:10.1021/ac070064t
Ding S., W. Qian, and R.D. Smith. 2007. "Quantitative Proteomic Approaches for Studying Phosphotyrosine Signaling." Expert Review of Proteomics 4, no. 1:13-23. PNWD-SA-7569. doi:doi:10.1586/14789450.4.1.13
Gupta N., S. Tanner, N. Jaitly, J.N. Adkins, M.S. Lipton, R. Edwards, and M.F. Romine, et al. 2007. "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation." Genome Research 17, no. 9:1362-1377. PNNL-SA-52859. doi:0.1101/gr.6427907
Ibrahim Y.M., M.E. Belov, A.V. Tolmachev, D.C. Prior, and R.D. Smith. 2007. "Ion Funnel Trap Interface for Orthogonal Time-of-Flight Mass Spectrometry." Analytical Chemistry 79, no. 20:7845-7852. PNNL-SA-54591. doi:10.1021/ac071091m
Kang H., L. Pasa-Tolic, and R.D. 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, no. 7:1332-1343. PNNL-SA-54095. doi:doi:10.1016/j.jasms.2007.04.011
Kelly R.T., J.S. Page, K. Tang, and R.D. Smith. 2007. "Array of Chemically Etched Fused Silica Emitters for Improving the Sensitivity and Quantitation of Electrospray Ionization Mass Spectrometry." Analytical Chemistry 79, no. 11:4192-4198. PNNL-SA-53247. doi:10.1021/ac062417e
Kim J., K. Petritis, Y. Shen, D.G. Camp, R.J. Moore, and R.D. Smith. 2007. "Phosphopeptide elution times in reversed-phase liquid chromatography." Journal of Chromatography A 1172, no. 1:9-18. PNNL-SA-53249. doi:doi:10.1016/j.chroma.2007.09.032
Liu T., M.E. Belov, N. Jaitly, W. Qian, and R.D. Smith. 2007. "Accurate Mass Measurements in Proteomics." Chemical Reviews 107, no. 8:3621-3653. PNNL-SA-52331. doi:10.1021/cr068288j
Liu T., W. Qian, D.G. Camp, and R.D. 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. 107-24. Totowa, New Jersey:Humana Press. PNNL-SA-44833.
Luo Q., J.S. Page, K. Tang, and R.D. Smith. 2007. "MicroSPE-nanoLC-ESI-MS/MS using 10-µm-i.d. silica-based monolithic columns for proteomics." Analytical Chemistry 79, no. 2:540-545. PNNL-SA-49661.
Manes N.P., J.K. Gustin, J. Rue, H.M. Mottaz, S.O. Purvine, A.D. Norbeck, and M.E. Monroe, et al. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6, no. 4:717-727. PNNL-SA-50929. doi:10.1074/mcp.M600282-MCP200
Marginean N., R.T. Kelly, J.S. Page, K. Tang, and R.D. Smith. 2007. "Electrospray characteristic curves: in pursuit of improved performance in the nano-flow regime." Analytical Chemistry 79, no. 21:8030-8036. PNWD-SA-7791. doi:10.1021/ac070800t
Metz T.O., Q. Zhang, J.S. Page, Y. Shen, S.J. Callister, J.M. Jacobs, and R.D. Smith. 2007. "The future of liquid chromatography-mass spectrometry in metabolic profiling and metabolomic studies for biomarker discovery." Biomarkers in Medicine 1, no. 1:159-185. PNNL-SA-53806.
Monroe M.E., N. Tolic, N. Jaitly, J.L. Shaw, J.N. Adkins, and R.D. Smith. 2007. "VIPER: an advanced software package to support high-throughput LC-MS peptide identification." Bioinformatics 23, no. 15- August 2007:2021-2023. PNNL-SA-52622. doi:10.1093/bioinformatics/btm281
Page J.S., K. Tang, and R.D. 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, no. 2-3:244-250. PNNL-SA-47896. doi:10.1016/j.ijms.2007.02.032
Page J.S., R.T. Kelly, K. Tang, and R.D. Smith. 2007. "Ionization and transmission efficiency in an electrospray ionization-mass spectrometry interface." Journal of the American Society for Mass Spectrometry 18, no. 9:1582-1590. PNNL-SA-53862. doi:10.1016/j.jasms.2007.05.018
Petyuk V.A., W. Qian, M.H. Chin, H.H. Wang, E.A. Livesay, M.E. Monroe, and J.N. Adkins, et al. 2007. "Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry." Genome Research 17, no. 3:328-336. PNNL-SA-49342. doi:10.1101/gr.5799207
Sharma S., D.C. Simpson, N. Tolic, N. Jaitly, A.M. Mayampurath, R.D. 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, no. 2:602-610. PNNL-SA-50906. doi:10.1021/pr060354a
Shvartsburg A.A., and R.D. 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, no. 9:1672-1681. PNNL-SA-55353. doi:10.1016/j.jasms.2007.06.013
Shvartsburg A.A., F. Li, K. Tang, and R.D. Smith. 2007. "Distortion of Ion Structures by Field Asymmetric Waveform Ion Mobility Spectrometry." Analytical Chemistry 79, no. 4:1523-1528. PNNL-SA-50928. doi:10.1021/ac061306c
Shvartsburg A.A., S.V. Mashkevich, E.S. Baker, and R.D. Smith. 2007. "Optimization of Algorithms for Ion Mobility Calculations." Journal of Physical Chemistry A 111, no. 10:2002-2010. PNNL-SA-52282. doi:10.1021/jp066953m
Smallwood H.S., N.M. Lourette, C.B. Boschek, D.J. Bigelow, R.D. Smith, L. Pasa-Tolic, and T.C. Squier. 2007. "Identification of a Denitrase Activity Against Calmodulin in Activated Macrophages Using High-Field Liquid Chromatography - FTICR Mass Spectrometry." Biochemistry 46, no. 37:10498-10505. PNWD-SA-7801.
Smith R.D. 2007. "Forward: Jean H. Futrell." International Journal of Mass Spectrometry 265, no. 2-3:75-79. PNNL-SA-55937. doi:10.1016/j.ijms.2007.06.022
Wang Y., S. Ding, W. Wang, F. Yang, J.M. Jacobs, D.G. Camp, and R.D. Smith, et al. 2007. "Methods for Pseudopodia Purification and Proteomic Analysis." Sciences STKE Signal Transduction Knowledge Environment 2007, no. 400:p14. PNNL-SA-56168.
Wang Y., S. Ding, W. Wang, J.M. Jacobs, W. Qian, R.J. Moore, and F. Yang, et al. 2007. "Profiling Signaling Polarity in Chemotactic Cells." Proceedings of the National Academy of Sciences of the United States of America 104, no. 20:8328-8333. PNNL-SA-51866. doi:10.1073/pnas.0701103104
Whiteaker J.R., H. Zhang, J.K. Eng, R. Fang, B.D. Piening, L. Feng, and T.D. lorentzen, et al. 2007. "Head-to-Head Comparison of Serum Fractionation Techniques." Journal of Proteome Research 6, no. 2:828-836. PNWD-SA-7568. doi:10.1021/pr0604920
Yang F., D.G. Camp, M.A. Gritsenko, Q. Luo, R.T. Kelly, T.R. Clauss, and W.R. Brinkley, et al. 2007. "Identification of a novel mitotic phosphorylation motif associated with protein localization to the mitotic apparatus." Journal of Cell Science 120, no. 22:4060-70. PNNL-SA-55602. doi:10.1242/jcs.014795
Yang F., N. Jaitly, H. Jayachandran, Q. Lou, M.E. Monroe, X. Du, and M.A. Gritsenko, et al. 2007. "Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Journal of Proteome Research6, no. 11:4489-4497. PNNL-SA-52332. doi:10.1021/pr070068e
Zhang Q., A. Frolov, N. Tang, R. Hoffman, T. van der Goor, T.O. Metz, and R.D. Smith. 2007. "Application of Electron Transfer Dissociation Mass Spectrometry in Analyses of Non-enzymatically Glycated Peptides." Rapid Communications in Mass Spectrometry 21, no. 5:661-666. PNNL-SA-52281. doi:10.1002/rcm.2884
Zhang Q., N. Tang, J.W. Brock, H.M. Mottaz, J.M. Ames, J. Baynes, and R.D. Smith, et al. 2007. "Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry." Journal of Proteome Research 6, no. 6:2323-2330. PNNL-SA-53989. doi:doi:10.1021/pr070112q
Zhang Q., W. Qian, T.V. Knyushko, T.R. Clauss, S.O. Purvine, R.J. Moore, and C.A. Sacksteder, et al. 2007. "A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples." Journal of Proteome Research 6, no. 6:2257-2268. PNNL-SA-53248. doi:10.1021/pr0606934

2006

Adkins J.N., H.M. Mottaz, A.D. Norbeck, J.K. Gustin, J. Rue, T.R. Clauss, and S.O. Purvine, et al. 2006. "Analysis of the Salmonella typhimurium Proteome through Environmental Response toward Infectious Conditions." Molecular & Cellular Proteomics. MCP 5, no. 8:1450-1461. PNNL-SA-46556. doi:10.1074/mcp.M600139-MCP200
Baas T., C.R. Baskin, D.L. Diamond, A. Garcia-Sastre, H. Bielefeldt-Ohmann, T.M. Tumpey, and M.J. Thomas, et al. 2006. "Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics." Journal of Virology 80, no. 21:10813 (16 pages). PNWD-SA-7379. doi:10.1128/JVI.00851-06
Callister S.J., C.D. Nicora, X. Zeng, J. Roh, M. Dominguez, C. Tavano, and M.E. Monroe, et al. 2006. "Comparison of aerobic and photosynthetic Rhodobacter sphaeroides 2.4.1 proteomes." Journal of Microbiological Methods 67, no. 3:424-436. PNNL-SA-46423. doi:10.1016/j.mimet.2006.04.021
Callister S.J., M. Dominguez, C.D. Nicora, X. Zeng, C. Tavano, S. Kaplan, and T. Donohue, et al. 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, no. 8:1940-1947. PNNL-SA-48567.
Callister S.J., R.C. Barry, J.N. Adkins, E.T. Johnson, W. Qian, B.M. Webb-Robertson, and R.D. Smith, et al. 2006. "Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics." Journal of Proteome Research 5, no. 2:277-286. PNNL-SA-46453. doi:10.1021/pr050300l
Diamond D.L., S. Proll, J.M. Jacobs, E.Y. Chan, D.G. Camp, R.D. Smith, and M.G. Katze. 2006. "HepatoProteomics: Applying Proteomic Technologies to the Study of Liver Function and Disease." Hepatology 44, no. 2:299-308. PNWD-SA-7378.
Ding Y.R., K.K. Hixson, C.S. Giometti, A. Stanley, A. Esteve-Nunez, T. Khare, and S.L. Tollaksen, et al. 2006. "The Proteome of Dissimilatory Metal-reducing Microorganism Geobacter Sulfurreducens under Various Growth Conditions." Biochimica et Biophysica Acta--Proteins and Proteomics 1764, no. 7:1198-1206. PNNL-SA-47069. doi:10.1016/j.bbapap.2006.04.017
Elias D.A., M.E. Monroe, R.D. Smith, J.K. Fredrickson, and M.S. Lipton. 2006. "Confirmation of the Expression of a Large Set of Conserved Hypothetical Proteins in Shewanella oneidensis MR-1." Journal of Microbiological Methods 66, no. 2:223-233. PNNL-SA-45416.
Elshafey A., N. Tolic, M.M. Young, K.L. Sale, R.D. Smith, and V. Kery. 2006. "“Zero-length” Cross-linking in Solid State as an Approach for Analysis of Protein -Protein Interactions." Protein Science 15, no. 3:429-440. PNNL-SA-46071.
Fang R., D.A. Elias, M.E. Monroe, Y. Shen, M. McIntosh, P. Wang, and C.D. Goddard, et al. 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, no. 4:714-725. PNNL-SA-47983. doi:10.1074/mcp.M500301-MCP200
Hixson K.K., J.N. Adkins, S.E. Baker, R.J. Moore, R.D. Smith, S.L. McCutchen-Maloney, and M.S. Lipton. 2006. "Biomarker Candidate Identification in Yersinia Pestis Using Organism-Wide Semiquantitative Proteomics." Journal of Proteome Research 5, no. 11:3008-3017. PNNL-SA-49565.
Ibrahim Y.M., K. Tang, A.V. Tolmachev, A.A. Shvartsburg, and R.D. Smith. 2006. "Improving Mass Spectrometer Sensitivity Using a High-Pressure Electrodynamic Ion Funnel Interface." Journal of the American Society for Mass Spectrometry 17, no. 9:1299-1305. PNNL-SA-49272. doi:10.1016/j.jasms.2006.06.005
Jacobs J.M., and R.D. Smith. 2006. "Proteomic Analyses Using High-Efficiency Separations and Accurate Mass Measurements." In Separation Methods in Proteomics, edited by GB Smejkal and A Lazareu. 363-385. Boca Raton, Florida:CRC Taylor & Francis. PNNL-SA-42439.
Jacobs J.M., and R.D. Smith. 2006. "Proteomic Analyses using High-Efficiency Separations and Accurate Mass Measurements." In Separations in Proteomics, edited by Smejkal, GB and A Lazareu. 363-385. New York, New York:CRC Taylor and Francis Group. PNNL-SA-43219.
Jaitly N., M.E. Monroe, V.A. Petyuk, T.R. Clauss, J.N. Adkins, and R.D. 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, no. 21:7397-7409. PNNL-SA-48693.
Kelly R.T., J.S. Page, Q. Luo, R.J. Moore, D.J. Orton, K. Tang, and R.D. Smith. 2006. "Chemically Etched Open Tubular and Monolithic Emitters for Nanoelectrospray Ionization Mass Spectrometry." Analytical Chemistry 78, no. 22:7796-7801. PNNL-SA-50640.
Kiebel G.R., K.J. Auberry, N. Jaitly, D. Clark, M.E. Monroe, E.S. Peterson, and N. Tolic, et al. 2006. "PRISM: A Data Management System for High-Throughput Proteomics." Proteomics 6, no. 6:1783-1790. PNNL-SA-45753. doi:10.1002/pmic.200500500
Koeniger S.L., S.I. Merenbloom, S.J. Valentine, M.F. Jarrold, H.R. Udseth, R.D. Smith, and D.E. Clemmer. 2006. "An IMS-IMS Analogue of MS-MS." Analytical Chemistry 78, no. 12:4161-4174. PNNL-SA-50434.
Lipton M.S., M.F. Romine, M.E. Monroe, D.A. Elias, L. Pasa-Tolic, G.A. Anderson, and D.J. Anderson, et al. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis." In Microbial Proteomics, Methods of Biochemical Analysis, edited by I. Humphery-Smith and M. Hecker. 113-134. Hoboken, New Jersey:John Wiley & Sons, Inc. PNNL-SA-42692.
Liu T., W. Qian, H.M. Mottaz, M.A. Gritsenko, A.D. Norbeck, R.J. Moore, and S.O. Purvine, et al. 2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry." Molecular & Cellular Proteomics. MCP 5, no. 11:2167-2174. PNWD-SA-7363.
Liu T., W. Qian, M.A. Gritsenko, W. Xiao, L.L. Moldawer, A. Kaushal, and M.E. Monroe, et al. 2006. "High Dynamic Range Characterization of the Trauma Patient Plasma Proteome." Molecular & Cellular Proteomics. MCP 5, no. 10:1899-1913. PNWD-SA-7271. doi:10.1074/mcp.M600068-MCP200
Luo Q., K. Tang, F. Yang, A. Elias, Y. Shen, R.J. Moore, and R. Zhao, et al. 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, no. 5:1091-1097. PNNL-SA-47984.
Metz T.O., J.M. Jacobs, M.A. Gritsenko, G. Fontes, W. Qian, D.G. Camp, and V.J. Poitout, et al. 2006. "Characterization of the Human Pancreatic Islet Proteome by Two-Dimensional LC/MS/MS." Journal of Proteome Research 5, no. 12:3345-3354. PNNL-SA-49730. doi:10.1021/pr060322n
Norbeck A.D., S.J. Callister, M.E. Monroe, N. Jaitly, D.A. Elias, M.S. Lipton, and R.D. Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods67, no. 3:473-486. PNNL-SA-46770. doi:10.1016/j.mimet.2006.04.024
Norbeck A.D., S.J. Callister, M.E. Monroe, N. Jaitly, D.A. Elias, M.S. Lipton, and R.D. Smith. 2006. "Proteomic approaches to bacterial differentiation." Journal of Microbiological Methods67, no. 3:473-486. PNNL-SA-47555.
Page J.S., A.V. Tolmachev, K. Tang, and R.D. 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, no. 4:586-592. PNNL-SA-47277.
Patwardhan A.j., E.F. Strittmatter, D.G. Camp, R.D. 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, no. 9:2903-2915. PNNL-SA-46350. doi:10.1002/pmic200500582
Petritis K., L.J. Kangas, B. Yan, M.E. Monroe, E.F. Strittmatter, W. Qian, and J.N. Adkins, et al. 2006. "Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information." Analytical Chemistry 78, no. 14:5026-5039. PNNL-SA-50263. doi:10.1021/ac060143p
Qian W., J.M. Jacobs, T. Liu, D.G. Camp, and R.D. Smith. 2006. "Advances and Challenges in Liquid Chromatography-Mass Spectrometry-Based Proteomics Profiling for Clinical Applications." Molecular & Cellular Proteomics. MCP 5, no. 10:1727-1744. PNWD-SA-7399. doi:10.1074/mcp.M600162-MCP200
Sacksteder C.A., W. Qian, T.V. Knyushko, H.H. Wang, M.H. Chin, G. Lacan, and W.P. Melega, et al. 2006. "Endogenously Nitrated Proteins in Mouse Brain: Links To Neurodegenerative Disease." Biochemistry 45, no. 26:8009-8022. PNNL-SA-47471. doi:10.1021/bi060474w
Shi L., J.N. Adkins, J.R. Coleman, A.A. Schepmoes, A. Dohnalkova, H.M. Mottaz, and A.D. Norbeck, et al. 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. PNNL-SA-51416. doi:10.1074/jbc.M604640200
Shvartsburg A.A., F. Li, K. Tang, and R.D. Smith. 2006. "Characterizing the Structures and Folding of Free Proteins Using 2-D Gas-Phase Separations: Observation of Multiple Unfolded Conformers." Analytical Chemistry 78, no. 10:3304-3315. PNNL-SA-46452. doi:10.1021/ac060283z
Shvartsburg A.A., F. Li, K. Tang, and R.D. Smith. 2006. "High-Resolution Field Asymmetric Waveform Ion Mobility Spectrometry Using New Planar Geometry Analyzers." Analytical Chemistry 78, no. 11:3706-3714. PNNL-SA-47897. doi:10.1021/ac052020v
Shvartsburg A.A., S.V. Mashkevich, and R.D. Smith. 2006. "Feasibility of Higher-Order Differential Ion Mobility Separations Using New Asymmetric Waveforms." Journal of Physical Chemistry A 110, no. 8:2663-2673. PNNL-SA-45720. doi:10.1021/jp055349t
Shvartsburg A.A., T. Bryskiewicz, R. Purves, K. Tang, R. Guevremont, and R.D. Smith. 2006. "Field Asymmetric Waveform Ion Mobility Spectrometry Studies of Proteins: Dipole Alignment in Ion Mobility Spectrometry?." Journal of Physical Chemistry B 110, no. 43:21966-21980. PNNL-SA-49341. doi:10.1021/jp062573p
Simpson D.C., S. Ahn, L. Pasa-Tolic, B. Bogdanov, H.M. Mottaz, A.N. Vilkov, and G.A. Anderson, et al. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling." Electrophoresis 27, no. 13:2722-2733. PNNL-SA-46424. doi:10.1002/elps.200600037
Simson D.C., S. Ahn, L. Pasa-Tolic, B. Bogdanov, H.M. Brewer, A.N. Vilkov, and G.A. Anderson, et al. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling." Electrophoresis 27, no. 13:2722-2733. PNNL-SA-49244. doi:10.1002/elps.200600037
Smith R.D. 2006. "Future directions for electrospray ionization for biological analysis using mass spectrometry." BioTechniques 41, no. 2:147-148. PNNL-SA-50264.
Smith R.D., K. Tang, and Y. Shen. 2006. "Ultra-sensitive and quantitative characterization of proteomes." Molecular Biosystems 2, no. 5:221-230. PNNL-SA-48286. doi:10.1039/b601468b
Streblow D.N., S.M. Varnum, R.D. Smith, and J. Nelson. 2006. "A Proteomics Analysis of Human Cytomegalovirus Particles." In Cytomegaloviruses: Molecular Biology and Immunology, edited by Matthias J. Reddehase. 91-110. Hethersett:Caister Academic Press. PNNL-SA-48348.
Tolmachev A.V., M.E. Monroe, N. Jaitly, V.A. Petyuk, J.N. Adkins, and R.D. Smith. 2006. "Mass Measurement Accuracy In Analyses Of Highly Complex Mixtures Based Upon Multidimensional Recalibration." Analytical Chemistry 78, no. 24:8374-8385. PNNL-SA-49340. doi:10.1021/ac0606251
Valentine S.J., M.D. Plasencia, X. Liu, M. Krishnan, S. Naylor, H.R. Udseth, and R.D. Smith, et al. 2006. "Toward Plasma Proteome Profiling with Ion Mobility-Mass Spectrometry." Journal of Proteome Research 5, no. 11:2977-2984. PNNL-SA-52232. doi:10.1021/pr060232i
Wang H.H., W. Qian, M.H. Chin, V.A. Petyuk, R.C. Barry, T. Liu, and M.A. Gritsenko, et al. 2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5, no. 2:361-369. PNNL-SA-46752.
Yang F., D.L. Stenoien, E.F. Strittmatter, J. Wang, L. Ding, M.S. Lipton, and M.E. Monroe, et al. 2006. "Phosphoproteome Profiling of Human Skin Fibroplast Cells in Response to Low- and High-Dose Irradiation." Journal of Proteome Research 5, no. 5:1252-1260. PNNL-SA-46275.
Zhang H., P. Loriaux, J.K. Eng, D. Campbell, A. Keller, P. Moss, and R.A. Bonneau, et al. 2006. "UniPep-A database for human N-linked glycosites: a resource for biomarker discovery." Genome Biology 7, no. 8:Article No. R73. PNNL-SA-48562. doi:10.1186/gb-2006-7-8-r73
Zhang W., D.E. Culley, M.A. Gritsenko, R.J. Moore, L. Nie, J.C. Scholten, and K. Petritis, et al. 2006. "LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris." Biochemical and Biophysical Research Communications 349, no. 4:1412-1419. PNNL-SA-45667. doi:10.1016/j.bbrc.2006.09.019
Zhang W., D.E. Culley, M.A. Gritsenko, R.J. Moore, L. Nie, J.C. Scholten, and K. Petritis, et al. 2006. "LC-MS/MS Based Proteomic Analysis and Functional Inference of Hypothetical Proteins in Desulfovibrio Vulgaris." Biochemical and Biophysical Research Communications349, no. 4:1412-1419. PNNL-SA-51397. doi:10.1016/j.bbrc.2006.09.019
Zhang W., M.A. Gritsenko, R.J. Moore, D.E. Culley, L. Nie, K. Petritis, and E.F. Strittmatter, et al. 2006. "A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry." Proteomics 6, no. 15:4286-4299. PNNL-SA-45506. doi:10.1002/pmic.200500930
Zimmer J.S., M.E. Monroe, W. Qian, and R.D. Smith. 2006. "Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach." Mass Spectrometry Reviews 25, no. 3:450-482. PNNL-SA-43136.

2005

Adkins J.N., M.E. Monroe, K.J. Auberry, Y. Shen, J.M. Jacobs, D.G. Camp, and F. Vitzthum, et al. 2005. "A Proteomic Study of the HUPO Plasma Proteome Project's Pilot Samples using an Accurate Mass and Time Tag Strategy." Proteomics 5, no. 13:3454-3466. PNWD-SA-6982. doi:10.1002/pmic.200401333
Aebersold R., L.N. Anderson, R.M. Caprioli, B. Druker, L.D. Hartwell, and R.D. Smith. 2005. "Perspective: A Program to Improve Protein Biomarker Discovery for Cancer." Journal of Proteome Research 4, no. 4:1104-1109. PNWD-SA-6953.
Aebersold R., L.N. Anderson, R.M. Caprioli, B. Druker, L.D. Hartwell, and R.D. Smith. 2005. "Perspective: A Program to Improve Protein Biomarker Discovery for Cancer." Journal of Proteome Research 4, no. 4:1104-1109. PNWD-SA-7013.
Bogdanov B., and R.D. Smith. 2005. "Proteomics by FTICR Mass Spectrometry: Top Down and Bottom Up." Mass Spectrometry Reviews 24, no. 2:168-200. PNNL-SA-39961.
Elias D.A., M.E. Monroe, M.J. Marshall, M.F. Romine, A.S. Beliaev, J.K. Fredrickson, and G.A. Anderson, et al. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics5, no. 12:3120-3130. PNNL-SA-42041. doi:10.1002/pmic.200401140
Huang Y., J.M. Triscari, G.C. Tseng, L. Pasa-Tolic, M.S. Lipton, R.D. Smith, and V.H. Wysocki. 2005. "Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns." Analytical Chemistry 77, no. 18:5800-5813. PNNL-SA-45900.
Jacobs J.M., D.L. Diamond, E.Y. Chan, M.A. Gritsenko, W. Qian, M. Stastna, and T. Baas, et al. 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, no. 12:7558-7569. PNWD-SA-6678.
Jacobs J.M., J.N. Adkins, W. Qian, T. Liu, Y. Shen, D.G. Camp, and R.D. Smith. 2005. "Utilizing human blood plasma for proteomic biomarker discovery." Journal of Proteome Research 4, no. 4:1073-1085. PNWD-SA-6880. doi:10.1021/pr0500657
Jacobs J.M., M.E. Monroe, W. Qian, Y. Shen, G.A. Anderson, and R.D. Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240, no. 3:195-212. PNNL-SA-42919.
Jacobs J.M., X. Yang, B.J. Luft, J.J. Dunn, D.G. Camp, and R.D. Smith. 2005. "Proteomic Analysis of Lyme Disease: Global Protein Comparison of Three Strains of Borrelia burgdorferi." Proteomics 5, no. 5:1446-1453. PNNL-SA-42921.
Kolker E., A.F. Picone, M.Y. Galperin, M.F. Romine, R. Higdon, K.S. Makarova, and N. Kolker, et al. 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, no. 6:2099-2104. PNNL-SA-43139.
Liu T., W. Qian, M.A. Gritsenko, D.G. Camp, M.E. Monroe, R.J. Moore, and R.D. Smith. 2005. "Human Plasma N-Glycoproteome Analysis by Immunoaffinity Subtraction, Hydrazide Chemistry, and Mass Spectrometry." Journal of Proteome Research 4, no. 6:2070-2080. PNNL-SA-44967.
Liu T., W. Qian, W.U. Chen, J.M. Jacobs, R.J. Moore, D.J. Anderson, and M.A. Gritsenko, et al. 2005. "Improved Proteome Coverage by Using High Efficiency Cysteinyl-peptide Enrichment: The Human Mammary Epithelial Cell Proteome." Proteomics 5, no. 5:1263-1273. PNNL-SA-42468.
Luo Q., Y. Shen, K.K. Hixson, R. Zhao, F. Yang, R.J. Moore, and H.M. Mottaz, et al. 2005. "Preparation of 20-µm-i.d. Silica-based Monolithic Columns and Application for Proteomic Analysis." Analytical Chemistry 77, no. 15:5028-5035. PNNL-SA-44543.
Masselon C.D., L. Pasa-Tolic, N. Tolic, G.A. Anderson, B. Bogdanov, A.N. Vilkov, and Y. Shen, et al. 2005. "Targeted Comparative Proteomics by Liquid Chromatography - Tandem Fourier ion cyclotron resonance Mass Spectrometry." Analytical Chemistry 77, no. 2:400-406. PNNL-SA-42470.
Norbeck A.D., M.E. Monroe, J.N. Adkins, K.K. Anderson, D.S. Daly, and R.D. 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, no. 8:1239-1249. PNNL-SA-44395.
Page J.S., A.V. Tolmachev, K. Tang, and R.D. Smith. 2005. "Variable low-mass filtering using an electrodynamic ion funnel." Journal of Mass Spectrometry 40, no. 9:1215-1222. PNNL-SA-44831. doi:10.1002/jms.900
Page J.S., B. Bogdanov, A.N. Vilkov, D.C. Prior, M.A. Buschbach, K. Tang, and R.D. 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, no. 2:244-253. PNNL-SA-42436.
Patwardhan A.J., E.F. Strittmatter, D.G. Camp, R.D. Smith, and M. Pallavicini. 2005. "Comparison of Normal and Breast Cancer Cell lines using Proteome, Genome and Interactome data." Journal of Proteome Research 4, no. 6:1952-1960. PNNL-SA-46284.
Qian W., J.M. Jacobs, D.G. Camp, M.E. Monroe, R.J. Moore, M.A. Gritsenko, and S.E. Calvano, et al. 2005. "Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry." Proteomics 5, no. 2:572-584. PNNL-SA-40692. doi:10.1002/pmic.200400942
Qian W., J.M. Jacobs, D.G. Camp, M.E. Monroe, R.J. Moore, M.A. Gritsenko, and S.E. Calvano, et al. 2005. "Comparative Proteome Analyses of Human Plasma Following in vivo Lipopolysaccharide Administration Using Multidimensional Separations Coupled with Tandem Mass Spectrometry." Proteomics 5, no. 2:572-584. PNNL-SA-41257.
Qian W., M.E. Monroe, T. Liu, J.M. Jacobs, G.A. Anderson, Y. Shen, and R.J. Moore, et al. 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, no. 5:700-709. PNNL-SA-44302.
Qian W., T. Liu, M.E. Monroe, E.F. Strittmatter, J.M. Jacobs, L.J. Kangas, and K. Petritis, et al. 2005. "Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome." Journal of Proteome Research4, no. 1:53-62. PNNL-SA-42815.
Schad M., M.S. Lipton, P. Giavalisco, R.D. 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, no. 14:2729-2738. PNNL-SA-46425.
Schmid A.K., M.S. Lipton, H.M. Mottaz, M.E. Monroe, R.D. Smith, and M.E. 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, no. 3:709-718. PNNL-SA-44177.
Shen Y., and R.D. Smith. 2005. "Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics." Expert Review of Proteomics 2, no. 3:431-447. PNNL-SA-44169.
Shen Y., E.F. Strittmatter, R. Zhang, T.O. Metz, R.J. Moore, F. Li, and H.R. Udseth, et al. 2005. "Making broad proteome protein measurements in 1-5 min using high-speed RPLC separations and high-accuracy mass measurments." Analytical Chemistry 77, no. 23:7763-7773. PNNL-SA-45881. doi:10.1021/ac051257o
Shen Y., J. Kim, E.F. Strittmatter, J.M. Jacobs, D.G. Camp, R. Fang, and N. Tolic, et al. 2005. "Characterization of the human blood plasma proteome." Proteomics 5, no. 15:4034-4045. PNWD-SA-6708.
Shen Y., R. Zhang, R.J. Moore, J. Kim, T.O. Metz, K.K. Hixson, and R. Zhao, et al. 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, no. 10:3090-3100. PNNL-SA-43807.
Shvartsburg A.A., K. Tang, and R.D. 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, no. 9:1447-1455. PNNL-SA-44306. doi:10.1016/j.jasms.2005.04.003
Shvartsburg A.A., K. Tang, and R.D. Smith. 2005. "Optimization of the Design and Operation of FAIMS Analyzers." Journal of the American Society for Mass Spectrometry 16, no. 1:2-12. PNNL-SA-42469.
Simpson D.C., and R.D. Smith. 2005. "Combining Capillary Electrophoresis with Mass Spectrometry for Applications in Proteomics." Electrophoresis 26, no. 7-8:1291-1305. PNNL-SA-42467.
Tang K., A.A. Shvartsburg, H. Lee, D.C. Prior, M.A. Buschbach, F. Li, and A.V. Tolmachev, et al. 2005. "High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces." Analytical Chemistry 77, no. 10:3330-3339. PNNL-SA-43713. doi:10.1021/ac048315a
Tang K., F. Li, A.A. Shvartsburg, E.F. Strittmatter, and R.D. Smith. 2005. "Two-Dimensional Gas-Phase Separations Coupled to Mass Spectrometry for Analysis of Complex Mixtures." Analytical Chemistry 77, no. 19:6381-6388. PNNL-SA-43809.
Wang H.H., W. Qian, H.M. Mottaz, T.R. Clauss, D.J. Anderson, R.J. Moore, and D.G. Camp, et al. 2005. "Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method." Journal of Proteome Research 4, no. 6:2397-2403. PNNL-SA-45347. doi:10.1021/pr050160f
Yang F., B. Bogdanov, E.F. Strittmatter, A.N. Vilkov, M.A. Gritsenko, L. Shi, and D.A. Elias, et al. 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, no. 3:846-854. PNNL-SA-43808. doi:10.1021/pr0497475
Zhang H., E.C. Yi, X. Li, P. Mallick, K.S. Kelly-Spratt, C.D. Masselon, and D.G. Camp, et al. 2005. "High Throughput Quantitative Analysis of Serum Proteins using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry." Molecular & Cellular Proteomics. MCP 4, no. 2:144-155. PNNL-SA-44544.
Zhang H., E.C. Yi, X. Li, P. Mallick, K.S. Kelly-Spratt, C.D. Masselon, and D.G. Camp, et al. 2005. "High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry." Molecular & Cellular Proteomics. MCP 4. PNNL-SA-47067.

2004

Belov M.E., G.A. Anderson, M.A. Wingerd, H.R. Udseth, K. Tang, D.C. Prior, and K.R. Swanson, et al. 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, no. 2:212-232. PNNL-SA-38749.
Blonder J., M.B. Goshe, W. Xiao, D.G. Camp, M.A. Wingerd, R.W. Davis, and R.D. Smith. 2004. "Global Analysis of the Membrane Subproteome of Pseudomonas aeruginosa using Liquid Chromatography-Tandem Mass Spectrometry." Journal of Proteome Research 3, no. 3:434-444. PNNL-SA-39660.
Camp D.G., and R.D. Smith. 2004. "The Use of Accurate Mass Tags based upon High-Throughput Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Global Proteomic Characterization." In Proteome Analysis: Interpreting the Genome, edited by David W Speicher. 183-224. Amsterdam:Elsevier. PNWD-SA-5751.
Gorshkov M.V., C.D. Masselon, E.N. Nikolaev, H.R. Udseth, L. Pasa-Tolic, and R.D. Smith. 2004. "Consideration for Electron Capture Dissociation Efficiency in FTICR Mass Spectrometry." International Journal of Mass Spectrometry 234, no. 1-3:131-136. PNNL-SA-39793.
Huang Y., J.M. Triscari, L. Pasa-Tolic, G.A. Anderson, M.S. Lipton, R.D. Smith, and V.H. 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, no. 10:3034-3035. PNNL-SA-43138.
Jacobs J.M., H.M. Mottaz, L. Yu, D.J. Anderson, R.J. Moore, W.U. Chen, and K.J. Auberry, et al. 2004. "Multidimensional Proteome Analysis of Human Mammary Epithelial Cells." Journal of Proteome Research 3, no. 1:68-75. PNWD-SA-6087.
Kim J., D.G. Camp, and R.D. Smith. 2004. "Improved detection of multi-phosphorylated peptides in the presence of phosphoric acid in liquid chromatography/mass spectrometry." Journal of Mass Spectrometry 39, no. 2:206-215. PNNL-SA-39083.
Liu T., W. Qian, E.F. Strittmatter, D.G. Camp, G.A. Anderson, B.D. Thrall, and R.D. Smith. 2004. "High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Analytical Chemistry 76, no. 18:5345-5353. PNWD-SA-6477.
Martinovic S., L. Pasa-Tolic, and R.D. Smith. 2004. "Capillary Isoelectric Focusing-Mass Spectrometry of Proteins and Protein Complexes." In Capillary Electrophoresis of Proteins and Peptides: Methods in Molecular Biology, edited by MA Strege and AL Lagu. 291-304. Totowa, New Jersey:Human Press. PNNL-SA-37970.
Page J.S., C.D. Masselon, and R.D. Smith. 2004. "FTICR Mass Spectrometry for Qualitative and Quantitative Bioanalyses." Current Opinion in Biotechnology 15, no. 1:3-11. PNNL-SA-39615.
Pasa-Tolic L., C.D. Masselon, R.C. Barry, Y. Shen, and R.D. Smith. 2004. "Proteomic Analyses using an Accurate Mass and Time Tag Strategy." BioTechniques 37, no. 4:621-636. PNNL-SA-42437.
Pedrioli P.G., J.K. Eng, R. Hubley, M. Vogelzang, E.W. Deutsch, B. Raught, and B. Pratt, et al. 2004. "A common open representation of mass spectrometry data and its application to proteomics research." Nature Biotechnology 22, no. 11:1459-1466. PNWD-SA-6864.
Prokisch H., C.M. Scharfe, D.G. Camp, W. Xiao, L. David, C. Andreoli, and M.E. Monroe, et al. 2004. "Integrative Analysis of the Mitochondrial Proteome in Yeast." PLoS Biology 2, no. 6:0795-0804. PNWD-SA-6619.
Qian W., D.G. Camp, and R.D. Smith. 2004. "High Throughput Proteomics Using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Expert Review of Proteomics 1, no. 1:87-95. PNNL-SA-41680.
Romine M.F., D.A. Elias, M.E. Monroe, K.J. Auberry, R. Fang, J.K. Fredrickson, and G.A. Anderson, et al. 2004. "Validation of Shewanella oneidensis MR-1 Small Proteins by AMT Tag-based Proteome Analysis." OMICS. A Journal of Integrative Biology 8, no. 3:239-254. PNNL-SA-42691.
Shen Y., J.M. Jacobs, D.G. Camp, R. Fang, R.J. Moore, R.D. Smith, and W. Xiao, et al. 2004. "Ultra-High-Efficiency Strong Cation Exchange LC/RPLC/MS/MS for High Dynamic Range Characterization of the Human Plasma Proteome." Analytical Chemistry 76, no. 4:1134-1144. PNNL-SA-39155.
Shen Y., N. Tolic, C.D. Masselon, L. Pasa-Tolic, D.G. Camp, G.A. Anderson, and R.D. Smith, et al. 2004. "Nanoscale Proteomics." Analytical and Bioanalytical Chemistry 378, no. 4:1037-1045. PNNL-SA-39154.
Shen Y., N. Tolic, C.D. Masselon, L. Pasa-Tolic, D.G. Camp, K.K. Hixson, and R. Zhao, et al. 2004. "Ultrasensitive Proteomics using High-Efficiency on-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS." Analytical Chemistry 76, no. 1:144-154. PNNL-SA-38244.
Shvartsburg A.A., K. Tang, and R.D. Smith. 2004. "Modeling the Resolution and Sensitivity of FAIMS analyses." Journal of the American Society for Mass Spectrometry 15, no. 10:1487-98. PNNL-SA-41703.
Shvartsburg A.A., K. Tang, and R.D. Smith. 2004. "Understanding and Designing Field Asymmetric Waveform Ion Mobility Spectrometry Separations in Gas Mixtures." Analytical Chemistry 76, no. 24:7366-7374. PNNL-SA-42277. doi:10.1021/ac049299k
Smith R.D., 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, no. 4:269-278. PNNL-SA-39791.
Strittmatter E.F., L.J. Kangas, K. Petritis, H.M. Mottaz, G.A. Anderson, Y. Shen, and J.M. Jacobs, et al. 2004. "Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry." Journal of Proteome Research 3, no. 4:760-769. PNNL-SA-40693.
Tang K., J.S. Page, and R.D. 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, no. 10:1416-1423. PNNL-SA-41627.
Tolmachev A.V., A.N. Vilkov, B. Bogdanov, L. Pasa-Tolic, C.D. Masselon, and R.D. 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, no. 11:1616-1628. PNNL-SA-41836.
Varnum S.M., D.N. Streblow, M.E. Monroe, P. Smith, K.J. Auberry, L. Pasa-Tolic, and D. Wang, et al. 2004. "Identification of Proteins in Human Cytomegalovirus (HCMV) Particles: the HCMV Proteome." Journal of Virology 78, no. 20:10960-10966. PNNL-SA-43398.
Vilkov A.N., B. Bogdanov, L. Pasa-Tolic, D.C. Prior, G.A. Anderson, C.D. Masselon, and R.J. Moore, et al. 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, no. 22:2682-2690. PNNL-SA-42697.
Wunschel D.S., C.D. Masselon, B. Feng, and R.D. Smith. 2004. "Proofreading activity of Pfu thermostable DNA polymerase on a 6-O-Methylguanine Containing Template Monitored by ESI-FTICR Mass Spectrometry." Chembiochem 5, no. 7:1012-1015. PNNL-SA-40946.
Zangar R.C., S.M. Varnum, C.Y. Covington, and R.D. Smith. 2004. "A rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and ELISA microarrays." Disease Markers 20, no. 3:135-148. PNNL-SA-42179.

2003

Belov M.E., R. Zhang, E.F. Strittmatter, D.C. Prior, K. Tang, and R.D. 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, no. 16:4195-4205. PNNL-SA-37925.
Belov M.E., V.S. Rakov, E.N. Nikolaev, M.B. Goshe, G.A. Anderson, and R.D. 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, no. 7:627-636. PNNL-SA-37927.
Chen W.U., L. Yu, E.F. Strittmatter, B.D. Thrall, D.G. Camp, and R.D. 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, no. 8:1647-1651. PNWD-SA-5957.
Ferguson P.L., and R.D. Smith. 2003. "Proteome Analysis by Mass Spectrometry." In Annual Review in Biophysics and Biomolecular Structure, edited by Robert M. Stroud. 399-424. Palo Alto, California:Annual Reviews. PNNL-SA-37868.
Goshe M.B., and R.D. Smith. 2003. "Stable Isotope-Coded Proteomic Mass Spectrometry." Current Opinion in Biotechnology 14, no. 1:101-109. PNNL-SA-37308.
Goshe M.B., J. Blonder, and R.D. Smith. 2003. "Affinity Labeling of Highly Hydrophobic Integral Membrane Proteins for Proteome-Wide Analysis." Journal of Proteome Research 2, no. 2:153-161. PNNL-SA-37545.
Masselon C.D., L. Pasa-Tolic, S. Lee, L. Li, G.A. Anderson, R. Harkewicz, and R.D. Smith. 2003. "Identification of Tryptic Peptides from Large Databases using Multiplexed Tandem Mass Spectrometry: Simulations and Experimental Results." Proteomics 3, no. 7:1279-1286. PNWD-SA-5898.
Mohan D., L. Pasa-Tolic, C.D. Masselon, N. Tolic, B. Bogdanov, K.K. Hixson, and R.D. Smith, et al. 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, no. 17:4432-4440. PNNL-SA-39340.
Petritis K., L.J. Kangas, P.L. Ferguson, G.A. Anderson, L. Pasa-Tolic, M.S. Lipton, and K.J. Auberry, et al. 2003. "Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses." Analytical Chemistry 75, no. 5:1039-1048. PNNL-SA-37767.
Qian W., M.B. Goshe, D.G. Camp, L. Yu, K. Tang, and R.D. Smith. 2003. "Phosphoprotein Isotope-Coded Solid-Phase Tag Approach for Enrichment and Quantitative Analysis of Phosphopeptides from Complex Mixtures." Analytical Chemistry 75, no. 20:5441-5450. PNNL-SA-38312.
Shen Y., R.J. Moore, R. Zhao, J. Blonder, D.L. Auberry, C.D. Masselon, and L. Pasa-Tolic, et al. 2003. "High-Efficiency On-Line Solid-Phase Extraction Coupling to 15-150 um I.D. Column Liquid Chromatography for Proteomic Analysis." Analytical Chemistry 75, no. 14:3596-3605. PNNL-SA-38207.
Strittmatter E.F., N. Rodriguez, and R.D. 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, no. 3:460-468. PNNL-SA-37114.
Strittmatter E.F., P.L. Ferguson, K. Tang, and R.D. 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, no. 9:980-991. PNNL-SA-38208.
Tolmachev A.V., A.N. Vilkov, L. Pasa-Tolic, H.R. Udseth, and R.D. 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, no. 11:1229-1235. PNNL-SA-38354.
Tolmachev A.V., H.R. Udseth, and R.D. Smith. 2003. "Modeling the ion density distribution in collisional cooling RF multipole ion guides." International Journal of Mass Spectrometry 222, no. 1-3:155-174. PNNL-SA-37086.
Varnum S.M., C.C. Covington, R.L. Woodbury, K. Petritis, L.J. Kangas, M.S. Abdullah, and J.G. Pounds, et al. 2003. "Proteomic Characterization of Nipple Aspirate Fluid: Identification of Potential Biomarkers of Breast Cancer." Breast Cancer Research and Treatment 80, no. 1:87-97. PNWD-SA-5788.
Varnum S.M., C.C. Covington, R.L. Woodbury, K. Petritis, L.J. Kangas, M.S. Abdullah, and J.G. Pounds, et al. 2003. "Proteomic Characterization of Nipple Aspirate Fluid: Identification of Potential Biomarkers of Breast Cancer." Breast Cancer Research and Treatment 80, no. 1:87-97. PNWD-SA-5810.
Varnum S.M., C.C. Covington, R.L. Woodbury, K. Petritis, L.J. Kangas, M.S. Abdullah, and J.G. Pounds, et al. 2003. "Proteomic characterization of nipple aspirate fluid: Identification of potential biomarkers of breast cancer." Breast Cancer Research and Treatment 80, no. 1:87-97. PNNL-SA-39981. doi:10.1023/A:1024479106887
Yang X., S. Martinovic, R.D. Smith, and B. Gong. 2003. "Duplex Foldamers from Assembly Induced Folding." Journal of the American Chemical Society 125, no. 33:9932-9933. PNNL-SA-39336.
Zeng H., X. Yang, A.L. Brown, S. Martinovic, R.D. Smith, and B. Gong. 2003. "An extremely stable, self-complementary hydrogen-bonded duplex." Chemical Communications 13. PNNL-SA-39038.

2002

Adkins J.N., S.M. Varnum, K.J. Auberry, R.J. Moore, N. Angell, R.D. Smith, and D.L. Springer, et al. 2002. "Toward a Human Blood Serum Proteome: Analysis by Multidimensional Separation Coupled with Mass Spectrometry." Molecular & Cellular Proteomics. MCP 1, no. 12:947-955. PNWD-SA-5845.
Belov M.E., G.A. Anderson, and R.D. Smith. 2002. "Higher-Resolution Data-Dependent Selective External Ion Accumulation for Capillary LC-FTICR." International Journal of Mass Spectrometry 218, no. 3:265-279. PNNL-SA-36692.
Belov M.E., G.A. Anderson, and R.D. Smith. 2002. "Higher-Resolution Data-Dependent Selective External ION Accumulation for Capillary LC-FTICR." International Journal of Mass Spectrometry 218, no. 3:265-279. PNNL-SA-38002.
Berger S.J., S. Lee, G.A. Anderson, L. Pasa-Tolic, N. Tolic, Y. Shen, and R. Zhao, et al. 2002. "High-Throughput Global Peptide Proteomic Analysis by Combining Stable Isotope Amino Acid Labeling and Data-Dependent Multiplexed-MS/MS." Analytical Chemistry 74, no. 19:4994-5000. PNNL-SA-39339.
Blonder J., M.B. Goshe, R.J. Moore, L. Pasa-Tolic, C.D. Masselon, M.S. Lipton, and R.D. Smith. 2002. "Enrichment of Integral Membrane Proteins for Proteomic Analysis Using Liquid Chromatography-Tandem Mass Spectrometry." Journal of Proteome Research 1, no. 4:351-360. PNNL-SA-36193.
Borisov O.V., M.B. Goshe, T.P. Conrads, V.S. Rakov, T.D. Veenstra, and R.D. Smith. 2002. "Low-Energy Collision-Induced Dissociation Fragmentation Analysis of Cysteinyl-Modified Peptides." Analytical Chemistry 74. PNWD-SA-5627.
Buchanan M.V., F. Larimer, H.S. Wiley, S.J. Kennel, T.C. Squier, J.M. Ramsey, and K.D. Rodland, et al. 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, no. 4:287-303. PNWD-SA-6390.
Chen J., C.S. Lee, Y. Shen, R.D. Smith, and E. Baehrecke. 2002. "Integration of capillary isoelectric focusing with capillary reversed-phase liquid chromatography for two-dimensional proteomics separation." Electrophoresis 23. PNNL-SA-39341.
Gong B., H. Zeng, J. Zhu, L. Yuan, Y. Han, S. Cheng, and M. Furukawa, et al. 2002. "Creating nanocavities of tunable sizes: Hollow helices." Proceedings of the National Academy of Sciences of the United States of America 99, no. 18:11583-88. PNNL-SA-39654.
Goshe M., T.D. Veenstra, E.A. Panisko, T.P. Conrads, N.H. Angell, and R.D. Smith. 2002. "Phosphoprotein Isotope-coded Affinity Tags: Application to the Enrichment and Identification of Low-Abundance Phosphoproteins." Analytical Chemistry 74, no. 3:607-616. PNWD-SA-5412.
Harkewicz R., M.E. Belov, G.A. Anderson, L. Pasa-Tolic, C.D. Masselon, D.C. Prior, and H.R. Udseth, et al. 2002. "ESI-FTICR Mass Spectrometry Employing Data-Dependent External Ion Selection and Accumulation." Journal of the American Society for Mass Spectrometry 13, no. 2:144-154. PNNL-SA-34711.
Hixson K.K., N. Rodriguez, D.G. Camp, E.F. Strittmatter, M.S. Lipton, and R.D. Smith. 2002. "Evaluation of Enzymatic Digestion and Liquid Chromatography-Mass Spectrometry Peptide Mapping of the Integral Membrane Protein Bacteriorhodopsin." Electrophoresis 23, no. 18:3224-3232. PNNL-SA-39337.
Lee S., S.J. Berger, S. Martinovic, L. Pasa-Tolic, G.A. Anderson, Y. Shen, and R. Zhao, et al. 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, no. 9:5942-5947. PNWD-SA-5450.
Lin Y., K. Tang, and R.D. Smith. 2002. "Laser-Machined Microdevices for Mass Spectrometry." In Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research, edited by J. Silberring and R. Ekman. 171-192. Wiley Interscience, New York:John Wiley & Sons. PNNL-SA-35813.
Lipton M.S., L. Pasa-Tolic, G.A. Anderson, D.J. Anderson, D.L. Auberry, J.R. Battista, and M.J. Daly, et al. 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, no. 17:11049-11054. PNNL-SA-35211.
Luo H., M.S. Lipton, and R.D. Smith. 2002. "Charge Effects for Differentiation of Oligodeoxynucleotide Isomers Containing 8-oxo-dG Residues." Journal of the American Society for Mass Spectrometry 13. PNNL-SA-35202.
Martinovic S., T.D. Veenstra, G.A. Anderson, L. Pasa-Tolic, and R.D. Smith. 2002. "Selective Incorporation Acids for Identification Proteome-wide Level." Journal of Mass Spectrometry 37, no. 1:99-107. PNWD-SA-5482.
Masselon C.D., A.V. Tolmachev, G.A. Anderson, R. Harkewicz, and R.D. Smith. 2002. "Mass Measurement Errors Caused by "Local" Frequency Perturbations in FTICR Mass Spectrometry"." Journal of the American Society for Mass Spectrometry 13. PNWD-SA-5458.
Pasa-Tolic L., M.S. Lipton, C.D. Masselon, G.A. Anderson, Y. Shen, N. Tolic, and R.D. Smith. 2002. "Gene expression profiling using advanced mass spectrometric approaches." Journal of Mass Spectrometry 37, no. 12:1185-1198. PNWD-SA-5864.
Pasa-Tolic L., R. Harkewicz, G.A. Anderson, N. Tolic, Y. Shen, R. Zhao, and B.D. Thrall, et al. 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, no. 8:954-963. PNNL-SA-35815.
Ramelot T.A., J.R. Cort, A. Yee, F. Liu, M.B. Goshe, A.M. Edwards, and R.D. Smith, et al. 2002. "Myxoma Virus Immunomodulatory Protein M156R is a Structural Mimic of Eukaryotic Translation Initiation Factor eIF2 alpha." Journal of Molecular Biology 322, no. 5:943-954. PNWD-SA-5541.
Shen Y., and R.D. Smith. 2002. "Proteomics Based on High-Efficiency Capillary Separations." Electrophoresis 23. PNNL-SA-39344.
Shen Y., R. Zhao, S.J. Berger, G.A. Anderson, N. Rodriguez, and R.D. Smith. 2002. "High-Efficiency Nanoscale Liquid Chromatography Coupled On-Line with Mass Spectrometry using Nanoelectrospray Ionization for Proteomics." Analytical Chemistry 74. PNNL-SA-39338.
Smith R.D. 2002. "Advanced Mass Spectrometric Methods for the Rapid and Quantitative Characterization of Proteomes." Journal of Structural and Functional Genomics 3, no. 2:143-150. PNNL-SA-35907.
Smith R.D. 2002. "Trends in mass spectrometry instrumentation for proteomics." Trends in Biotechnology 20, no. 12:S3-S7. PNNL-SA-36817.
Smith R.D., G.A. Anderson, M.S. Lipton, C.D. Masselon, L. Pasa-Tolic, Y. Shen, and H.R. Udseth. 2002. "The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics." OMICS. A Journal of Integrative Biology 6, no. 1:61-90. PNNL-SA-36632.
Smith R.D., G.A. Anderson, M.S. Lipton, L. Pasa-Tolic, Y. Shen, T.P. Conrads, and T.D. Veenstra, et al. 2002. "An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements." Proteomics 2. PNNL-SA-34714.
Smith R.D., G.A. Anderson, T.P. Conrads, C.D. Masselon, M.S. Lipton, L. Pasa-Tolic, and T.D. Veenstra. 2002. "Advanced Mass Spectrometric Approaches for Rapid and Quantitative Proteomics." In Applied Electrospray Mass Spectrometry, edited by BN Pramanik,, AK Ganguly & ML Gross. 307-360. New York, New York:Marcel Dekker. PNNL-SA-33075.
Tang K., A.V. Tolmachev, E.N. Nikolaev, R. Zhang, M.E. Belov, H.R. Udseth, and R.D. Smith. 2002. "Independent Control of Ion Transmission in a Jet Disrupter Dual-Channel Ion Funnel Electrospray Ionization MS Interface." Analytical Chemistry 74, no. 20:5431-5437. PNNL-SA-41476.
Tolmachev A.V., C.D. Masselon, G.A. Anderson, H.R. Udseth, and R.D. 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, no. 4:387-401. PNNL-SA-35834.
Yu L., M. Johnson, T.P. Conrads, R.D. Smith, R.S. Morrison, and T.D. Veenstra. 2002. "Proteome Analysis of Camptothecin-Treated Cortical Neurons using Isotope-Coded Affinity Tags." Electrophoresis 23. PNNL-SA-39342.

2001

Belov M.E., E.N. Nikolaev, G.A. Anderson, H.R. Udseth, T.P. Conrads, T.D. Veenstra, and C.D. Masselon, et al. 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, no. 2:253-261. PNNL-SA-33327.
Belov M.E., E.N. Nikolaev, G.A. Anderson, K.J. Auberry, R. Harkewicz, and R.D. 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, no. 1:38-48. PNNL-SA-33645.
Belov M.E., E.N. Nikolaev, K. Alving, and R.D. 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, no. 14:1172-1180. PNWD-SA-5483.
Belov M.E., E.N. Nikolaev, R. Harkewicz, C.D. Masselon, K. Alving, and R.D. 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, no. 1-3:205-225. PNNL-SA-33786.
Belov M.E., G.A. Anderson, N.H. Angell, Y. Shen, N. Tolic, H.R. Udseth, and R.D. 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, no. 21:5052-5060. PNNL-SA-35028.
Belov M.E., M.V. Gorshkov, H.R. Udseth, and R.D. 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, no. 12:1312-1319. PNWD-SA-5481.
Belov M.E., M.V. Gorshkov, K. Alving, and R.D. 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, no. 21:1988-1996. PNWD-SA-5453.
Conrads T.P., K. Alving, T.D. Veenstra, M.E. Belov, G.A. Anderson, D.J. Anderson, and M.S. Lipton, et al. 2001. "Quantitative Analysis of Bacterial and Mammalian Proteomes using a Combination of Cysteine Affinity Tags and 15N-Metabolic Labeling." Analytical Chemistry 73, no. 9:2132-2139. PNNL-SA-34135.
Gorshkov M.V., C.D. Masselon, G.A. Anderson, H.R. Udseth, and R.D. Smith. 2001. "Dynamically Assisted Gated Trapping for Fourier Transform Ion Cyclotron Mass Spectrometry." Rapid Communications in Mass Spectrometry 15, no. 17:1558-1561. PNNL-SA-34974.
Gorshkov M.V., C.D. Masselon, G.A. Anderson, H.R. Udseth, R. Harkewicz, and R.D. Smith. 2001. "A Dynamic Ion Cooling Technique for FTICR Mass Spectrometry." Journal of the American Society for Mass Spectrometry 12, no. 11:1169-1173. PNNL-SA-35081.
Goshe M.B., T.P. Conrads, E.A. Panisko, N.H. Angell, T.D. Veenstra, and R.D. Smith. 2001. "Phosphoprotein Isotope-coded Affinity Tag (PhIAT) Approach for Isolating and Quantitating Phosphopeptides in Proteome-wide Analyses." Analytical Chemistry 73, no. 11:2578-2586. PNNL-SA-34061.
Iakoucheva L.M., A.L. Kimzey, C.D. Masselon, J.E. Bruce, E.C. Garner, C.J. Brown, and A.K. Dunker, et al. 2001. "Identification of Intrinsic Order and Disorder in the DNA Repair Protein XPA." Protein Science 10, no. 3:560-571. PNNL-SA-33033. doi:10.1110/ps.29401
Iakoucheva L.M., A.L. Kimzey, C.D. Masselon, J.E. Bruce, E.C. Garner, C.J. Brown, and A.K. Dunker, et al. 2001. "Identification of intrinsic order and disorder in the DNA repair protein XPA." Protein Science 10, no. 3:560-571. PNWD-SA-5368.
Iakoucheva L.M., A.L. Kimzey, C.D. Masselon, R.D. Smith, A.K. Dunker, and E.J. Ackerman. 2001. "Aberrant mobility phenomena of the DNA repair protein XPA." Protein Science 10, no. 7:1353-1362. PNWD-SA-5300.
Kane R.S., P.T. Glink, R.G. Chapman, J.C. Mcdonald, P.K. Jensen, H. Gao, and L. Pasa-Tolic, et al. 2001. "Basicity of the Amino Groups of the Aminoglycoside Amikacin Using Capillary Electrophoresis and coupled CE-MS-MS techniques." Analytical Chemistry 73, no. 16:4028-4036. PNNL-SA-34179.
Kim T., K. Tang, H.R. Udseth, and R.D. Smith. 2001. "A Multi-capillary Inlet Jet Disruption Electrodynamic Ion Funnel Interface for Improved Sensitivity Using Atmospheric Pressure Ion Sources." Analytical Chemistry 73, no. 17:4162-4170. PNNL-SA-34944.
Koppenaal D.W., P.D. Ellis, and R.D. Smith. 2001. Annual Report 2000 Macromolecular Structure and Dynamics. PNNL-13626. Richland, WA: Pacific Northwest National Laboratory.
Li L., C.D. Masselon, G.A. Anderson, L. Pasa-Tolic, S. Lee, Y. Shen, and R. Zhao, et al. 2001. "High-Throughput Peptide Identification from Protein Digests Using Data-Dependent Multiplexed Tandem FTICR Mass Spectrometry Coupled with Capillary Liquid Chromatography." Analytical Chemistry 73, no. 14:3312-3322. PNWD-SA-5251.
Shen Y., N. Tolic, R. Zhao, L. Pasa-Tolic, L. Li, S.J. Berger, and R. Harkewicz, et al. 2001. "High-Throughput Proteomics Using High Efficiency Multiple-Capillary Liquid Chromatography With On-Line High-Performance ESI FTICR Mass Spectrometry." Analytical Chemistry 73, no. 13:3011-3021. PNNL-SA-33921.
Shen Y., R. Zhao, M.E. Belov, T.P. Conrads, G.A. Anderson, K. Tang, and L. Pasa-Tolic, et al. 2001. "Packed Capillary Reversed-Phase Liquid Chromatography with High Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics." Analytical Chemistry 73, no. 8:1766-1775. PNNL-SA-34100.
Shen Y., S.J. Berger, and R.D. Smith. 2001. "High-Efficiency Capillary Isoelectric Focusing of Protein Complexes from Escherichia coli Cytosolic Extracts." Journal of Chromatography A914, no. 1-2:257-264. PNNL-SA-33069.
Smith R.D., L. Pasa-Tolic, M.S. Lipton, P.K. Jensen, G.A. Anderson, Y. Shen, and T.P. Conrads, et al. 2001. "Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry." Electrophoresis 22. PNNL-SA-35082.
Tang K., and R.D. Smith. 2001. "Physical/Chemical Separations in the Break-up of Highly Charged Droplets from Electrosprays." Journal of the American Society for Mass Spectrometry12, no. 3:343-347. PNNL-SA-33927.
Tang K., and R.D. 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, no. 1-3:69-76. PNNL-SA-27816.
Tang K., Y. Lin, D.W. Matson, T. Kim, and R.D. Smith. 2001. "Generation of Multiple Electrosprays Using Microfabricated Emitter Arrays for Improved Mass Spectrometric Sensitivity." Analytical Chemistry 73, no. 8:1658-1663. PNNL-SA-34087.

2000

Belov M.E., M.V. Gorshkov, H.R. Udseth, G.A. Anderson, A.V. Tolmachev, D.C. Prior, and R. Harkewicz, et al. 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, no. 1:19-23. PNNL-SA-31459.
Belov M.E., M.V. Gorshkov, H.R. Udseth, G.A. Anderson, and R.D. Smith. 2000. "Zeptomole-Sensitivity Electrospray Ionization - Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Proteins." Analytical Chemistry 72, no. 10:2271-2279. PNNL-SA-32455.
Bruce J.E., G.A. Anderson, C. Lin, M.V. Gorshkov, A.L. Rockwood, and R.D. Smith. 2000. "A Novel High Performance Fourier Transform Ion Cyclotron Resonance Cell for Improved Biopolymer Characterization." Journal of Mass Spectrometry 35, no. 1:85-94. PNNL-SA-29190.
Bruce J.E., G.A. Anderson, M.D. Brands, L. Pasa-Tolic, and R.D. 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, no. 5:416-421. PNNL-SA-32245.
Conrads T.P., G.A. Anderson, T.D. Veenstra, L. Pasa-Tolic, and R.D. Smith. 2000. "Utility of Accurate Mass Tags for Proteome-Wide Protein Identification." Analytical Chemistry 72, no. 14:3349-3354. PNNL-SA-32770.
Feng B., and R.D. 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, no. 1:94-99. PNNL-SA-31135.
Gao H., Y. Shen, T.D. Veenstra, R. Harkewicz, G.A. Anderson, J.E. Bruce, and L. Pasa-Tolic, et al. 2000. "Two Dimensional Electrophoretic/Chromatographic Separations Combined with Electrospray Ionization FTICR Mass Spectrometry for High Throughput Proteome Analysis." Journal of Microcolumn Separations 12, no. 7:383-390. PNNL-SA-32592.
Goodlet D.R., J.E. Bruce, G.A. Anderson, B. Rist, L. Pasa-Tolic, O.N. Fiehn, and R.D. Smith, et al. 2000. "Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching." Analytical Chemistry 72, no. 6:1112-1118. PNNL-SA-32976.
Jensen P.K., L. Pasa-Tolic, K.K. Peden, S. Martinovic, M.S. Lipton, G.A. Anderson, and N. Tolic, et al. 2000. "Mass Spectrometric Detection for Capillary Isoelectric Focusing Separations of Complex Protein Mixtures." Electrophoresis 21, no. 7:1372-1380. PNNL-SA-32088.
Kim T., A.V. Tolmachev, R. Harkewicz, D.C. Prior, G.A. Anderson, H.R. Udseth, and R.D. Smith, et al. 2000. "Design and Implementation of a New Electrodynamic Ion Funnel." Analytical Chemistry 72. PNNL-SA-33501.
Kim T., H.R. Udseth, and R.D. Smith. 2000. "Improved Ion Transmission from Atmospheric Pressure to High Vacuum using a Multi-Capillary Inlet and Electrodynamic Ion Funnel Interface." Analytical Chemistry 72, no. 20:5014-5019. PNNL-SA-32916.
Krahmer M.T., J.J. Walters, K.F. Fox, A. Fox, K.E. Creek, L. Pirisi, and D.S. Wunschel, et al. 2000. "MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR Products." Analytical Chemistry 72, no. 17:4033-4040. PNNL-SA-33561.
Lin Y., D.W. Matson, D.E. Kurath, J.Y. Wen, F. Xiang, W.D. Bennett, and P.M. Martin, et al. 2000. "Microfluidic Devices on Polymer Substrates for Bioanalytical Applications." In 3rd International Conference on Microreaction Technology; Microreaction Technology: Industrial Prospects IMRET 3, April 1999., 451-460. New York, New York:Springer. PNNL-SA-31717.
Maier C., X. Yan, M.E. Harder, M.I. Schimerlik, L. Pasa-Tolic, and R.D. 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, no. 3:237-243. PNNL-SA-34431.
Martinovic S., L. Pasa-Tolic, C.D. Masselon, P.K. Jensen, C.L. Stone, and R.D. Smith. 2000. "Characterization of Human Alcohol Dehydrogenase Isoenzymes by Capillary Isoelectric Focusing-Mass Spectrometry." Electrophoresis 21, no. 12:2368-2375. PNNL-SA-32630.
Martinovic S., S.J. Berger, L. Pasa-Tolic, and R.D. Smith. 2000. "Separation and Detection of Intact Noncovalent Protein Complexes from Mixtures by On-Line Capillary Isoelectric Focusing-Mass Spectrometry." Analytical Chemistry 72, no. 21:5356-5360. PNNL-SA-33036.
Masselon C.D., G.A. Anderson, R. Harkewicz, J.E. Bruce, L. Pasa-Tolic, and R.D. Smith. 2000. "Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures." Analytical Chemistry 72, no. 8:1918-1924. PNNL-SA-32241.
Shen Y., and R.D. Smith. 2000. "High-Resolution Capillary Isoelectric Focusing of Proteins Using Highly Hydrophilic-Substituted Cellulose-Coated Capillaries." Journal of Microcolumn Separations 12, no. 3:135-141. PNNL-SA-32141.
Shen Y., S.J. Berger, G.A. Anderson, and R.D. Smith. 2000. "High-Efficiency Capillary Isoelectric Focusing of Peptides." Analytical Chemistry 72, no. 9:2154-2159. PNNL-SA-32454.
Smith R.D. 2000. "Evolution of ESI-Mass Spectrometry and Fourier Transform Ion Cyclotron Resonance for Proteomics and Other Biological Applications." International Journal of Mass Spectrometry 200. PNNL-SA-33630.
Smith R.D. 2000. "Probing Proteomes-Seeing the Whole Picture?." Nature Biotechnology 18, no. 10:1041-1042. PNNL-SA-33644.
Tolmachev A.V., H.R. Udseth, and R.D. 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, no. 5:970-978. PNNL-SA-31460.
Tolmachev A.V., H.R. Udseth, and R.D. 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, no. 20:1907-1913. PNNL-SA-33560.
Tolmachev A.V., T. Kim, H.R. Udseth, R.D. Smith, T.H. Bailey, and J.H. Futrell. 2000. "Simulation-Based Optimization of the Electrodynamic Ion Funnel for High Sensitivity Electrospray Ionization-Mass Spectrometry." International Journal of Mass Spectrometry 203, no. 1-3:31-47. PNNL-SA-32246.
Veenstra T.D., S. Martinovic, G.A. Anderson, L. Pasa-Tolic, and R.D. Smith. 2000. "Proteome Analysis using Selective Incorporation of Isotopically Labeled Amino Acids." Journal of the American Society for Mass Spectrometry 11, no. 1:78-82. PNNL-SA-32093.
Wen J.Y., Y. Lin, F. Xiang, D.W. Matson, H.R. Udseth, and R.D. Smith. 2000. "Microfabricated Isoelectric Focusing Devices for Direct Electrospray Ionization-Mass Spectrometry." Electrophoresis 21, no. 1:191-197. PNNL-SA-31322.
Wunschel D.S., L. Pasa-Tolic, B. Feng, and R.D. 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, no. 4:333-337. PNNL-SA-33317.
Xiang F., G.A. Anderson, T.D. Veenstra, M.S. Lipton, and R.D. Smith. 2000. "Characterization of Microorganisms and Biomarker Development from Global ESI-MS/MS Analyses of Cell Lysates." Analytical Chemistry 72, no. 11:2475-2481. PNNL-SA-32597.
Zhang C., F. Xiang, L. Pasa-Tolic, G.A. Anderson, T.D. Veenstra, and R.D. Smith. 2000. "Stepwise Mobilization of Focused Proteins in Capillary Isoelectric Focusing Mass Spectrometry." Analytical Chemistry 72, no. 7:1462-1468. PNNL-SA-31558.

1999

Bruce J.E., G.A. Anderson, J.Y. Wen, R. Harkewicz, and R.D. 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, no. 14:2595-2599. PNNL-SA-31044.
Feng B., D.S. Wunschel, C.D. Masselon, L. Pasa-Tolic, and R.D. Smith. 1999. "Retrieval of DNA using Soft-Landing after Mass Analysis by ESI-FTICR for Enzymatic Manipulation." Journal of the American Chemical Society 121, no. 38:8961-8962. PNNL-SA-32087.
Gao J., Q. Wu, J. Carbeck, Q.P. Lei, R.D. Smith, and G.M. Whitesides. 1999. "Probing the Energetics of Dissociation of Carbonic Anhydrase-Ligand Complexes in the Gas Phase." Biophysical Journal 76, no. 6:3253-3260. PNNL-SA-30555.
Gorshkov M.V., L. Pasa-Tolic, and R.D. 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. PNWD-SA-30523.
Jensen P.K., L. Pasa-Tolic, G.A. Anderson, J.A. Horner, M.S. Lipton, J.E. Bruce, and R.D. Smith. 1999. "Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 71, no. 11:2076-2084. PNNL-SA-30888.
Li L., R.W. Garden, P.D. Floyd, T.P. Moroz, J.M. Gleeson, J.V. Sweedler, and L. Pasa-Tolic, et al. 1999. "Egg-Laying Hormone Peptides in the Aplysiidae Family." Journal of Experimental Biology 202. PNWD-SA-5269.
Lin Y., J.Y. Wen, X. Fan, D.W. Matson, and R.D. 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, edited by C.H. Ahn and A.B. Frazier, 3877, 28-35. Bellingham, Washington:SPIE. PNNL-SA-31483.
Pasa-Tolic L., P.K. Jensen, G.A. Anderson, M.S. Lipton, K.K. Peden, S. Martinovic, and N. Tolic, et al. 1999. "High Throughput Proteome-Wide Precision Measurements of Protein Expression using Mass Spectrometry." Journal of the American Chemical Society 121, no. 34:7949-7950. PNNL-SA-31133.
Shaffer S.A., A.V. Tolmachev, D.C. Prior, G.A. Anderson, H.R. Udseth, and R.D. Smith. 1999. "Characterization of an Improved Electrodynamic Ion Funnel Interface for Electrospray Ionization Mass Spectrometry." Analytical Chemistry 71, no. 15:2957-2964. PNNL-SA-32090.
Shen Y., F. Xiang, T.D. Veenstra, N. Fung, and R.D. Smith. 1999. "High-Resolution Capillary Isoelectric Focusing of Complex Protein Mixtures from Lysates of Microogranisms." Analytical Chemistry 71. PNNL-SA-31273.
Tang K., and R.D. Smith. 1999. "Theoretical Prediction of Charged Droplet Evaporation and Fission in Electrospray Ionization." International Journal of Mass Spectrometry 185/186/187. PNNL-SA-30023.
Xiang F., Y. Lin, J.Y. Wen, D.W. Matson, and R.D. 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, no. 8:1485-1490. PNNL-SA-30690.
Xu N., L. Pasa-Tolic, R.D. Smith, S. Ni, and B.D. Thrall. 1999. "Electrospray Ionization-Mass Spectrometry Study of the Interaction of Cisplatin-Adducted Oligonucleotides with Human XPA Minimal Binding Domain Protein." Analytical Biochemistry 272, no. 1:26-33. PNNL-SA-30454.

1998

Lin Y., N. Xu, J.Y. Wen, D.W. Matson, and R.D. 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, edited by D.J. Harrison and A.V. den Berg, 343-346. Boston, Massachusetts:Kluwer Academic Publishers. PNNL-SA-32258.
Shaffer S.A., D.C. Prior, G.A. Anderson, H.R. Udseth, and R.D. Smith. 1998. "An Ion Funnel Interface for Improved Ion Focusing and Sensitivity Using Electrospray Ionization Mass Spectometry." Analytical Chemistry 70, no. 19:4111-4119. PNNL-SA-29752.
Yang L., C.S. Lee, S.A. Hofstadler, and R.D. Smith. 1998. "Characterization of Microdialysis Acidification for Capillary Isoelectric Focusing Microelectrospray Ionization Mass Spectrometry." Analytical Chemistry 70, no. 23:4945-4950. PNNL-SA-29819.