Staff information

Gordon Anderson

Bio Separations & Mass Spect
Scientist, TL
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-98
Richland, WA 99352
509/371-6582
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Biography

Mr. Gordon Anderson has more than 30 years of experience in the development of instrument control systems, high-performance data acquisition systems, and data management systems. These skills have been applied to the high-throughput proteomics research at Pacific Northwest National Laboratory (PNNL). The development of hardware and software has enabled advanced instrument control schemes for the Environmental Molecular Sciences Laboratory's (EMSL) state-of-the-art high-performance mass spectrometers. The proteomics capabilities have been enabled by Mr. Anderson's software development efforts in the area of complex spectral analysis and feature detection. Proteomics produces large volumes of multi-dimensional data that must be organized and processed using a combination of commercial software tools and custom designed tools. Mr. Anderson assembled a multi-disciplinary team and has led the development of proteomics data management and analysis efforts at PNNL.

Mr. Anderson has been issued seven U.S. patents since 1994. He currently is a Chief Engineer (Scientist & Engineer-Level V) within the Biological Sciences Division at PNNL.

Research Interests

Sensitive bimolecular detection - Design and development of specialized detection systems applied to mass spectrometry; i.e., low-noise pre-amplifiers for FTICR systems and high-performance FPGA-based detection systems for IMS-TOF.
Development of novel data analysis strategies �" Implementation of high-throughput automated data analysis pipelines to transform raw mass spectrometry data into peptide and protien quantitative information.
Analysis and control software package for advanced mass spectrometry instrumentation �" development of real-time data collection, analysis and control algorithms to enable advanced mass spectrometery measurements. This research has enabled capabilities such as individual ion detection as well as techniques applied to expanded instrument detection dynamic range.

Education and Credentials

B.S., Electrical Engineering, Washington State University, Pullman, WA, 1985
A.S., Electronics Technology, Columbia Basin College, Pasco, WA, 1975

Affiliations and Professional Service

American Society of Mass Spectrometry
Member of Joint Genome Institute's (JGI) Joint Management Board
Member of JGI’s Informatics Advisory Board

Awards and Recognitions

2005 - Pacific Northwest National Laboratory Engineering Achievement Award
2003 - INCOSE Systems Engineer of the Year Award
2003 - Pacific Northwest National Laboratory Mentor of the Year
2002 - R&D 100 Award for FT-MS Proteome Express
2001 - R&D 100 Award for Long-Range Semi-Passive Radio Frequency Identification System
1997 - PNNL Fitzner-Eberhardt Director’s Award for education
1995 - Federal Laboratory Consortium Award for Excellence in Technology Transfer

PNNL Publications

2013

Piehowski PD, VA Petyuk, JD Sandoval, KE Burnum, GR Kiebel, ME Monroe, GA Anderson, DG Camp, II, and RD Smith. 2013. "STEPS: A Grid Search Methodology for Optimized Peptide Identification Filtering of MS/MS Database Search Results." Proteomics 13(5):766-770. doi:10.1002/pmic.201200096
Lamarche BL, KL Crowell, N Jaitly, VA Petyuk, AR Shah, AD Polpitiya, JD Sandoval, GR Kiebel, ME Monroe, SJ Callister, TO Metz, GA Anderson, and RD Smith. 2013. "MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis." BMC Bioinformatics 14:Article No. 49. doi:10.1186/1471-2105-14-49
Merkley ED, ES Baker, KL Crowell, DJ Orton, T Taverner, C Ansong, YM Ibrahim, MC Burnet, JR Cort, GA Anderson, RD Smith, and JN Adkins. 2013. "Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein-Protein Interactions by Chemical Cross-Linking ." Journal of the American Society for Mass Spectrometry 24(3):444-449. doi:10.1007/s13361-012-0565-x
Shvartsburg AA, TA Seim, WF Danielson, III, RV Norheim, RJ Moore, GA Anderson, and RD Smith. 2013. "High-Definition Differential Ion Mobility Spectrometry with Resolving Power up to 500." Journal of the American Society for Mass Spectrometry 24(1):109-114. doi:10.1007/s13361-012-0517-5

2012

Baker ES, T Liu, VA Petyuk, KE Burnum-Johnson, YM Ibrahim, GA Anderson, and RD Smith. 2012. "Mass Spectrometry for Translational Proteomics: Progress and Clinical Implications." Genome Medicine 4:Article No. 63. doi:10.1186/gm364
Marginean I, SR Kronewitter, RJ Moore, GW Slysz, ME Monroe, GA Anderson, K Tang, and RD Smith. 2012. "Improving N-Glycan Coverage using HPLC-MS with Electrospray Ionization at Subambient Pressure." Analytical Chemistry 84(21):9208-9213. doi:10.1021/ac301961u
Taverner T, Y Karpievitch, AD Polpitiya, JN Brown, AR Dabney, GA Anderson, and RD Smith. 2012. "DanteR: an extensible R-based tool for quantitative analysis of -omics data." Bioinformatics 28(18):2404-2406. doi:10.1093/bioinformatics/bts449
Burnum KE, Y Hirota, ES Baker, M Yoshie, YM Ibrahim, ME Monroe, GA Anderson, RD Smith, T Daikoku, and SK Dey. 2012. "Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua." Endocrinology 153(9):4568-4579. doi:10.1210/en.2012-1335
Liu X, Y Sirotkin, Y Shen, GA Anderson, YHS Tsai, YS Ting, DR Goodlett, RD Smith, V Bafna, and PA Pevzner. 2012. "Protein Identification Using Top-Down." Molecular & Cellular Proteomics. MCP 11(6):M111.008524. doi:10.1074/mcp.M111.008524
Wang X, GA Anderson, RD Smith, and AR Dabney. 2012. "A Hybrid Approach to Protein Differential Expression in Mass Spectrometry-Based Proteomics." Bioinformatics 28(12):1586-1591. doi:10.1093/bioinformatics/bts193

2011

Shen Y, N Tolic, F Xie, R Zhao, SO Purvine, AA Schepmoes, RJ Moore, GA Anderson, and RD Smith. 2011. "Effectiveness of CID, HCD, and ETD with FT MS/MS for degradomic-peptidomic analysis: comparison of peptide identification methods." Journal of Proteome Research 10(9):3929-3943. doi:10.1021/pr200052c
Du X, SM Chowdhury, NP Manes, S Wu, MU Mayer, JN Adkins, GA Anderson, and RD Smith. 2011. "Xlink-Identifier: An Automated Data Analysis Platform for Confident Identifications of Chemically Cross-linked Peptides using Tandem Mass Spectrometry." Journal of Proteome Research 10(3):923-931. doi:10.1021/pr100848a
Frank AM, ME Monroe, AR Shah, JJ Carver, N Bandeira, RJ Moore, GA Anderson, RD Smith, and PA Pevzner. 2011. "Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra." Nature Methods 8(7):587-591. doi:10.1038/nmeth.1609
Huang X, AV Tolmachev, Y Shen, M Liu, L Huang, Z Zhang, GA Anderson, RD Smith, WC Chan, S Hinrichs, K Fu, and SJ Ding. 2011. "UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling." Journal of Proteome Research 10(3):1228-1237. doi:10.1021/pr1010058
Stanley JR, JN Adkins, GW Slysz, ME Monroe, SO Purvine, YV Karpievitch, GA Anderson, RD Smith, and AR Dabney. 2011. "A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics." Analytical Chemistry 83(16):6135-6140. doi:10.1021/ac2009806

2010

Auberry KJ, GR Kiebel, ME Monroe, JN Adkins, GA Anderson, and RD Smith. 2010. "Omics.pnl.gov: A Portal for the Distribution and Sharing of Multi-Disciplinary Pan-Omics Information." Journal of Proteomics and Bioinformatics 3(1):1-4.
Jung HJ, SO Purvine, H Kim, VA Petyuk, SW Hyung, ME Monroe, DG Mun, KC Kim, JM Park, SJ Kim, N Tolic, GW Slysz, RJ Moore, R Zhao, JN Adkins, GA Anderson, H Lee, DG Camp, II, MH Yu, RD Smith, and SW Lee. 2010. "Integrated Post-Experiment Monoisotopic Mass Refinement: An Integrated Approach to Accurately Assign Monoisotopic Precursor Masses to Tandem Mass Spectrometric Data." Analytical Chemistry 82(20):8510-8518. doi:10.1021/ac101388b
Karpievitch YV, AD Polpitiya, GA Anderson, RD Smith, and AR Dabney. 2010. "Liquid Chromatography Mass Spectrometry-Based Proteomics: Biological and Technological Aspects." The Annals of Applied Statistics 4(4):1797-1823.
Laskin J, A Laskin, PJ Roach, GW Slysz, GA Anderson, S Nizkorodov, DL Bones, and L Nguyen. 2010. "High-Resolution Desorption Electrospray Ionization Mass Spectrometry for Chemical Characterization of Organic Aerosols." Analytical Chemistry 82(5):2048-2058. doi:10.1021/ac902801f
Shah AR, K Agarwal, ES Baker, M Singhal, AM Mayampurath, YM Ibrahim, LJ Kangas, ME Monroe, R Zhao, ME Belov, GA Anderson, and RD Smith. 2010. "Machine learning based prediction for peptide drift times in ion mobility spectrometry ." Bioinformatics 26(13):1601-1607. doi:10.1093/bioinformatics/btq245
Shah AR, JL Davidson, ME Monroe, AM Mayampurath, WF Danielson, III, Y Shi, AC Robinson, BH Clowers, ME Belov, GA Anderson, and RD Smith. 2010. "An efficient data format for mass spectrometry based proteomics." Journal of the American Society for Mass Spectrometry 21(10):1784-1788. doi:10.1016/j.jasms.2010.06.014
Shah AR, N Jaitly, N Zuljevic, ME Monroe, AV Liyu, AD Polpitiya, JN Adkins, ME Belov, GA Anderson, RD Smith, and I Gorton. 2010. "An architecture for real time data acquisition and online signal processing for high throughput tandem mass spectrometry." In 5th IEEE International Conference on e-Science, pp. 88 - 93. IEEE, Piscataway, NJ. doi:10.1109/e-Science.2009.21

2009

Jaitly N, AM Mayampurath, KA Littlefield, JN Adkins, GA Anderson, and RD Smith. 2009. "Decon2LS: An Open-Source Software Package for Automated Processing and Visualization of High Resolution Mass Spectrometry Data." BMC Bioinformatics 10:87. doi:10.1186/1471-2105-10-87
Kouzes RT, GA Anderson, ST Elbert, I Gorton, and DK Gracio. 2009. "The Changing Paradigm of Data Intensive Computing ." Computer 42(1):26-34.
Petyuk VA, AM Mayampurath, ME Monroe, AD Polpitiya, SO Purvine, GA Anderson, DG Camp, II, and RD Smith. 2009. "DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets." Molecular & Cellular Proteomics. MCP 9.3:486-496. doi:10.1074/mcp.M900217-MCP200
Yang F, S Wu, DL Stenoien, R Zhao, ME Monroe, MA Gritsenko, SO Purvine, AD Polpitiya, N Tolic, Q Zhang, AD Norbeck, DJ Orton, RJ Moore, K Tang, GA Anderson, L Pasa-Tolic, DG Camp, II, and RD Smith. 2009. "Combined Pulsed-Q dissociation and electron transfer dissociation for identification and quantitation of iTRAQ-labeled phosphopeptides." Analytical Chemistry 81(10):4137-4143. doi:10.1021/ac802605m
Zhang H, X Tang, GR Munske, N Tolic, GA Anderson, and JE Bruce. 2009. "Identification of Protein-Protein Interactions and Topologies in Living Cells with Chemical Cross-linking and Mass Spectrometry." Molecular & Cellular Proteomics. MCP 8(3):409-420.

2008

Shen Y, N Tolic, KK Hixson, SO Purvine, GA Anderson, and RD Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins ." Analytical Chemistry 80(20):7742-7754. doi:10.1021/ac801123p
Kaiser NK, G Skulason, CR Weisbrod, S Wu, K Zhang, DC Prior, MA Buschbach, GA Anderson, and JE Bruce. 2008. "Restrained Ion Population Transfer: A Novel Ion Transfer Method for Mass Spectrometry." Rapid Communications in Mass Spectrometry 22(12):1955-1964.
Polpitiya AD, W Qian, N Jaitly, VA Petyuk, JN Adkins, DG Camp, II, GA Anderson, and RD Smith. 2008. " DAnTE: a statistical tool for quantitative analysis of -omics data." Bioinformatics 24(13):1556-1558. doi:10.1093/bioinformatics/btn217
Tolmachev AV, ME Monroe, SO Purvine, RJ Moore, N Jaitly, JN Adkins, GA Anderson, and RD Smith. 2008. "Characterization of Strategies for Obtaining Confident Identifications in Bottom-Up Proteomics Measurements Using Hybrid FTMS instruments ." Analytical Chemistry 80(22):8514-8525. doi:10.1021/ac801376g
Zhang H, X Tang, GR Munske, N Tolic, GA Anderson, and JE Bruce. 2008. "Identification of protein-protein interaction and topologies in living cells by chemical cross-linking and mass spectrometry." Molecular & Cellular Proteomics. MCP 8(3):409-420. doi:10.1074/mcp.M800232-MCP200
Zhang H, X Tang, GR Munske, NL Zakharova, L Yang, C Zheng, MA Wolff, N Tolic, GA Anderson, L Shi, MJ Marshall, JK Fredrickson, and JE Bruce. 2008. "In Vivo Identification of the Outer Membrane Protein OmcA-MtrC Interaction Network in Shewanella oneidensis MR-1 Cells Using Novel Hydrophobic Chemical Cross-Linkers." Journal of Proteome Research 7(4):1712-1720. doi:10.1021/pr7007658

2007

Anderson GA, N Tolic, X Tang, C Zheng, and JE Bruce. 2007. "Informatics Strategies for Large-Scale Novel Cross-linking Analysis ." Journal of Proteome Research 6(9):3412-3421. doi:10.1021/pr070035z
Anderson GA, N Tolic, X Tang, C Zheng, and JE Bruce. 2007. "Informatics Strategies for Large-Scale Novel Cross-linking Analysis." Journal of Proteome Research 6(9):3412-3421. doi:10.1021/pr070035z
Chavarría-Miranda D, BH Clowers, GA Anderson, and ME Belov. 2007. "Simulating data processing for an Advanced Ion Mobility Mass Spectrometer." In Proceedings of the 1st international workshop on High-performance reconfigurable computing technology and applications (HPRCTA'07): held in conjunction with SC07, NOV 10-16, 2007, Reno Nevada, pp. 21-29. Association for Computing Machinery, New York, NY.

2006

Wu S, K Zhang, NK Kaiser, JE Bruce, DC Prior, and GA Anderson. 2006. "Incorporation of a Flared Inlet Capillary Tube on a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer." Journal of the American Society for Mass Spectrometry 17(6):772-779.
Foster NS, GA Anderson, and AA Campbell. 2006. EMSL 2005 Annual Report. PNNL-15795, Pacific Northwest National Laboratory, Richland, WA.
Kiebel GR, KJ Auberry, N Jaitly, D Clark, ME Monroe, ES Peterson, N Tolic, GA Anderson, and RD Smith. 2006. "PRISM: A Data Management System for High-Throughput Proteomics ." Proteomics 6(6):1783-1790. doi:10.1002/pmic.200500500
Lipton MS, MF Romine, ME Monroe, DA Elias, L Pasa-Tolic, GA Anderson, DJ Anderson, JK Fredrickson, KK Hixson, CD Masselon, HM Mottaz, N Tolic, and RD Smith. 2006. "AMT Tag Approach to Proteomic Characterization of Deinococcus Radiodurans and Shewanella Oneidensis ." In Microbial Proteomics, Methods of Biochemical Analysis, vol. 49, ed. I. Humphery-Smith and M. Hecker, pp. 113-134. John Wiley & Sons, Inc., Hoboken, NJ.
Oehmen CS, TP Straatsma, GA Anderson, G Orr, BJM Webb-Robertson, RC Taylor, RW Mooney, DJ Baxter, DR Jones, and DA Dixon. 2006. "New Challenges Facing Integrative Biological Science in the Post-Genomic Era." Journal of Biological Systems 14(2):275-293.
Simpson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Mottaz, AN Vilkov, GA Anderson, MS Lipton, and RD Smith. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling." Electrophoresis 27(13):2722-2733. doi:10.1002/elps.200600037
Simson DC, S Ahn, L Pasa-Tolic, B Bogdanov, HM Brewer, AN Vilkov, GA Anderson, MS Lipton, and RD Smith. 2006. "Using size exclusion chromatography-RPLC and RPLC-CIEF as two-dimensional separation strategies for protein profiling ." Electrophoresis 27(13):2722-2733. doi:10.1002/elps.200600037

2005

Qian W, ME Monroe, T Liu, JM Jacobs, GA Anderson, Y Shen, RJ Moore, DJ Anderson, R Zhang, SE Calvano, SF Lowry, W Xiao, LL Moldawer, RW Davis, RG Tompkins, DG Camp, II, and RD Smith. 2005. "Quantitative Proteome Analysis of Human Plasma Following in vivo Lipopolysaccharide Administration using O-16/O-18 Labeling and the Accurate Mass and Time Tag Approach." Molecular & Cellular Proteomics. MCP 4(5):700-709.
Wu S, NK Kaiser, D Meng, GA Anderson, K Zhang, and JE Bruce. 2005. "Increased Protein Identification Capabilities Through Novel Tandem MS Calibration Strategies ." Journal of Proteome Research 4(4):1434-1441.
Cannon WR, KH Jarman, BJM Webb-Robertson, DJ Baxter, CS Oehmen, KD Jarman, A Heredia-Langner, KJ Auberry, and GA Anderson. 2005. "A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data." Journal of Proteome Research 4(5):1687-1698.
Elias DA, ME Monroe, MJ Marshall, MF Romine, AS Beliaev, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2005. "Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics based proteomics." Proteomics 5(12):3120-3130. doi:10.1002/pmic.200401140
Jacobs JM, ME Monroe, W Qian, Y Shen, GA Anderson, and RD Smith. 2005. "Ultra-Sensitive, High Throughput and Quantitative Proteomics Measurements." International Journal of Mass Spectrometry 240(3):195-212.
Kaiser NK, GA Anderson, and JE Bruce. 2005. "Improved Mass Accuracy for Tandem Mass Spectrometry ." Journal of the American Society for Mass Spectrometry 16(4):463-470. doi:10.1016/j.jasms.2004.12.005
Kolker E, AF Picone, MY Galperin, MF Romine, R Higdon, KS Makarova, N Kolker, GA Anderson, X Qiu, KJ Auberry, G Babnigg, AS Beliaev, P Edlefsen, DA Elias, YA Gorby, T Holzman, J Klappenbach, K Konstantinidis, ML Land, MS Lipton, LA McCue, ME Monroe, L Pasa-Tolic, GE Pinchuk, SO Purvine, M Serres, S Tsapin, BA Zakrajsek, W Zhu, J Zhou, F Larimer, C Lawrence, M Riley, FR Collart, JR Yates, III, RD Smith, CS Giometti, K Nealson, JK Fredrickson, and JM Tiedje. 2005. "Global Profiling of Shewanella oneidensis MR-1: Expression of Hypothetical Genes and Improved functional annotations." Proceedings of the National Academy of Sciences of the United States of America 102(6):2099-2104.
Masselon CD, L Pasa-Tolic, N Tolic, GA Anderson, B Bogdanov, AN Vilkov, Y Shen, R Zhao, W Qian, MS Lipton, DG Camp, II, and RD Smith. 2005. "Targeted Comparative Proteomics by Liquid Chromatography - Tandem Fourier ion cyclotron resonance Mass Spectrometry." Analytical Chemistry 77(2):400-406.
Tang K, AA Shvartsburg, HN Lee, DC Prior, MA Buschbach, F Li, AV Tolmachev, GA Anderson, and RD Smith. 2005. "High-Sensitivity Ion Mobility Spectrometry/Mass Spectrometry Using Electrodynamic Ion Funnel Interfaces ." Analytical Chemistry 77(10):3330-3339. doi:10.1021/ac048315a

2004

Shen Y, N Tolic, CD Masselon, L Pasa-Tolic, DG Camp, II, GA Anderson, RD Smith, and MS Lipton. 2004. "Nanoscale Proteomics." Analytical and Bioanalytical Chemistry 378(4):1037-1045.
Shen Y, N Tolic, CD Masselon, L Pasa-Tolic, DG Camp, II, KK Hixson, R Zhao, GA Anderson, and RD Smith. 2004. "Ultrasensitive Proteomics using High-Efficiency on-Line Micro-SPE-NanoLC-NanoESI MS and MS/MS." Analytical Chemistry 76(1):144-154.
Belov ME, GA Anderson, MA Wingerd, HR Udseth, K Tang, DC Prior, KR Swanson, MA Buschbach, EF Strittmatter, RJ Moore, and RD Smith. 2004. "An Automated High Performance Capillary Liquid Chromatography Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for High-Throughput Proteomics." Journal of the American Society for Mass Spectrometry 15(2):212-232.
Huang Y, JM Triscari, L Pasa-Tolic, GA Anderson, MS Lipton, RD Smith, and VH Wysocki. 2004. "Dissociation Behavior of Doubly-Charged Tryptic Peptides: Correlation of Gas-Phase Cleavage Abundance with Ramachandran Plots." Journal of the American Chemical Society 126(10):3034-3035.
Liu T, W Qian, EF Strittmatter, DG Camp, II, GA Anderson, BD Thrall, and RD Smith. 2004. "High throughput comparative proteome analysis using a quantitative cysteinyl-peptide enrichment technology." Analytical Chemistry 76(18):5345-5353.
Romine MF, DA Elias, ME Monroe, KJ Auberry, R Fang, JK Fredrickson, GA Anderson, RD Smith, and MS Lipton. 2004. "Validation of Shewanella oneidensis MR-1 Small Proteins by AMT Tag-based Proteome Analysis." OMICS. A Journal of Integrative Biology 8(3):239-254.
Strittmatter EF, LJ Kangas, K Petritis, HM Mottaz, GA Anderson, Y Shen, JM Jacobs, DG Camp, II, and RD Smith. 2004. "Application of Peptide LC Retention Time Information in a Discriminant Function for Peptide Identification by Tandem Mass Spectrometry." Journal of Proteome Research 3(4):760-769.
Vilkov AN, B Bogdanov, L Pasa-Tolic, DC Prior, GA Anderson, CD Masselon, RJ Moore, and RD Smith. 2004. "Tailored Noise Waveform/ Collision-Induced Dissociation of Ions Stored in a Linear Ion Trap Combined with Liquid Chromatography/Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Rapid Communications in Mass Spectrometry 18(22):2682-2690.

2003

Petritis K, LJ Kangas, PL Ferguson, GA Anderson, L Pasa-Tolic, MS Lipton, KJ Auberry, EF Strittmatter, Y Shen, R Zhao, and RD Smith. 2003. "Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses." Analytical Chemistry 75(5):1039-1048.
Belov ME, VS Rakov, EN Nikolaev, MB Goshe, GA Anderson, and RD Smith. 2003. "Initial Implementation of external accumulation liquid chromatography/electrospray ionization Fourier transform ion cyclotron resonance with automated gain control." Rapid Communications in Mass Spectrometry 17(7):627-636.
Masselon CD, L Pasa-Tolic, SW Lee, L Li, GA Anderson, R Harkewicz, and RD Smith. 2003. "Identification of Tryptic Peptides from Large Databases using Multiplexed Tandem Mass Spectrometry: Simulations and Experimental Results." Proteomics 3(7):1279-1286.

2002

Belov ME, GA Anderson, and RD Smith. 2002. "Higher-Resolution Data-Dependent Selective External Ion Accumulation for Capillary LC-FTICR." International Journal of Mass Spectrometry 218(3):265-279.
Belov ME, GA Anderson, and RD Smith. 2002. "Higher-Resolution Data-Dependent Selective External ION Accumulation for Capillary LC-FTICR." International Journal of Mass Spectrometry 218(3):265-279.
Disselkamp RS, JF Kelly, RL Sams, and GA Anderson. 2002. "Signal-to-Noise Enhancement Techniques for Quantum Cascade Absorption Spectrometers Employing Optimal Filtering and Other Approaches." Applied Physics B. Lasers and Optics 75(2-3):359-366.
Shen Y, R Zhao, SJ Berger, GA Anderson, N Rodriguez, and RD Smith. 2002. "High-Efficiency Nanoscale Liquid Chromatography Coupled On-Line with Mass Spectrometry using Nanoelectrospray Ionization for Proteomics." Analytical Chemistry 74:4235-4249.
Tolmachev AV, CD Masselon, GA Anderson, HR Udseth, and RD Smith. 2002. "Frequency Shifts Due to the Interference of Resolved Peaks in Magnitude-Mode Fourier-Transform Ion Cyclotron Resonance Mass Spectra." Journal of the American Society for Mass Spectrometry 13(4):387-401.
Berger SJ, SW Lee, GA Anderson, L Pasa-Tolic, N Tolic, Y Shen, R Zhao, and RD Smith. 2002. "High-Throughput Global Peptide Proteomic Analysis by Combining Stable Isotope Amino Acid Labeling and Data-Dependent Multiplexed-MS/MS." Analytical Chemistry 74(19):4994-5000.
Harkewicz R, ME Belov, GA Anderson, L Pasa-Tolic, CD Masselon, DC Prior, HR Udseth, and RD Smith. 2002. "ESI-FTICR Mass Spectrometry Employing Data-Dependent External Ion Selection and Accumulation." Journal of the American Society for Mass Spectrometry 13(2):144-154.
Lee SW, SJ Berger, S Martinovic, L Pasa-Tolic, GA Anderson, Y Shen, R Zhao, and RD Smith. 2002. "Direct Mass Spectrometric Analysis of Intact Proteins of the Yeast Large Ribosomal Subunit using Capillary LC/FTICR." Proceedings of the National Academy of Sciences of the United States of America 99(9):5942-5947.
Lipton MS, L Pasa-Tolic, GA Anderson, DJ Anderson, DL Auberry, JR Battista, MJ Daly, JK Fredrickson, KK Hixson, HM Kostandarithes, CD Masselon, LM Markillie, RJ Moore, MF Romine, Y Shen, EF Strittmatter, N Tolic, HR Udseth, A Venkateswaran, KK Wong, R Zhao, and RD Smith. 2002. "Global Analysis of Deinococcus Radiodurans Proteome by Csing Accurate Mass Tags." Proceedings of the National Academy of Sciences of the United States of America 99(17):11049-11054.
Martinovic S, TD Veenstra, GA Anderson, L Pasa-Tolic, and RD Smith. 2002. "Selective Incorporation Acids for Identification Proteome-wide Level." Journal of Mass Spectrometry 37(1):99-107.
Masselon CD, AV Tolmachev, GA Anderson, R Harkewicz, and RD Smith. 2002. "Mass Measurement Errors Caused by "Local" Frequency Perturbations in FTICR Mass Spectrometry"." Journal of the American Society for Mass Spectrometry 13:99-106.
Pasa-Tolic L, MS Lipton, CD Masselon, GA Anderson, Y Shen, N Tolic, and RD Smith. 2002. "Gene expression profiling using advanced mass spectrometric approaches." Journal of Mass Spectrometry 37(12):1185-1198.
Pasa-Tolic L, R Harkewicz, GA Anderson, N Tolic, Y Shen, R Zhao, BD Thrall, CD Masselon, and RD Smith. 2002. "Increased Proteome Coverage for Quantitative Peptide Abundance Measurements Based upon High Performance Separations and DREAMS FTICR Mass Spectrometry." Journal of the American Society for Mass Spectrometry 13(8):954-963.
Smith RD, GA Anderson, MS Lipton, CD Masselon, L Pasa-Tolic, Y Shen, and HR Udseth. 2002. "The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics." OMICS. A Journal of Integrative Biology 6(1):61-90.
Smith RD, GA Anderson, MS Lipton, L Pasa-Tolic, Y Shen, TP Conrads, TD Veenstra, and HR Udseth. 2002. "An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements." Proteomics 2:513-523.
Smith RD, GA Anderson, TP Conrads, CD Masselon, MS Lipton, L Pasa-Tolic, and TD Veenstra. 2002. "Advanced Mass Spectrometric Approaches for Rapid and Quantitative Proteomics." Chapter 8 in Applied Electrospray Mass Spectrometry, ed. BN Pramanik,, AK Ganguly & ML Gross, pp. 307-360. Marcel Dekker, New York, NY.

2001

Belov ME, EN Nikolaev, GA Anderson, HR Udseth, TP Conrads, TD Veenstra, CD Masselon, MV Gorshkov, and RD Smith. 2001. "Design and Performance of an ESI Interface for Selective External Ion Accumulation Coupled to a Fourier Transform Ion Cyclotron Mass Spectrometer." Analytical Chemistry 73(2):253-261.
Belov ME, EN Nikolaev, GA Anderson, KJ Auberry, R Harkewicz, and RD Smith. 2001. "Electrospray Ionization - Fourier Transform Ion Cyclotron Mass Spectrometry Using Ion Preselection and External Accumulation for Ultrahigh Sensitivity." Journal of the American Society for Mass Spectrometry 12(1):38-48.
Shen Y, N Tolic, R Zhao, L Pasa-Tolic, L Li, SJ Berger, R Harkewicz, GA Anderson, ME Belov, and RD Smith. 2001. "High-Throughput Proteomics Using High Efficiency Multiple-Capillary Liquid Chromatography With On-Line High-Performance ESI FTICR Mass Spectrometry." Analytical Chemistry 73(13):3011-3021.
Shen Y, R Zhao, ME Belov, TP Conrads, GA Anderson, K Tang, L Pasa-Tolic, TD Veenstra, MS Lipton, HR Udseth, and RD Smith. 2001. "Packed Capillary Reversed-Phase Liquid Chromatography with High Performance Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics ." Analytical Chemistry 73(8):1766-1775.
Belov ME, GA Anderson, NH Angell, Y Shen, N Tolic, HR Udseth, and RD Smith. 2001. "Dynamic Range Expansion Applied to Mass Spectrometry (DREAMS) Based on Data-Dependent Selective Ion Ejection in Capillary Liquid Chromatography Fourier Transform Ion Cyclotron Resonance for Enhanced Proteome Characterization." Analytical Chemistry 73(21):5052-5060.
Conrads TP, K Alving, TD Veenstra, ME Belov, GA Anderson, DJ Anderson, MS Lipton, L Pasa-Tolic, HR Udseth, WB Chrisler, BD Thrall, and RD Smith. 2001. "Quantitative Analysis of Bacterial and Mammalian Proteomes using a Combination of Cysteine Affinity Tags and 15N-Metabolic Labeling." Analytical Chemistry 73(9):2132-2139.
Gorshkov MV, CD Masselon, GA Anderson, HR Udseth, and RD Smith. 2001. "Dynamically Assisted Gated Trapping for Fourier Transform Ion Cyclotron Mass Spectrometry." Rapid Communications in Mass Spectrometry 15(17):1558-1561.
Gorshkov MV, CD Masselon, GA Anderson, HR Udseth, R Harkewicz, and RD Smith. 2001. "A Dynamic Ion Cooling Technique for FTICR Mass Spectrometry." Journal of the American Society for Mass Spectrometry 12(11):1169-1173.
Li L, CD Masselon, GA Anderson, L Pasa-Tolic, SW Lee, Y Shen, R Zhao, MS Lipton, TP Conrads, N Tolic, and RD Smith. 2001. "High-Throughput Peptide Identification from Protein Digests Using Data-Dependent Multiplexed Tandem FTICR Mass Spectrometry Coupled with Capillary Liquid Chromatography." Analytical Chemistry 73(14):3312-3322.
Smith RD, L Pasa-Tolic, MS Lipton, PK Jensen, GA Anderson, Y Shen, TP Conrads, HR Udseth, R Harkewicz, ME Belov, CD Masselon, and TD Veenstra. 2001. "Rapid quantitative measurements of proteomes by Fourier transform ion cyclotron resonance mass spectrometry." Electrophoresis 22:1652-1668.

2000

Belov ME, MV Gorshkov, HR Udseth, GA Anderson, and RD Smith. 2000. "Zeptomole-Sensitivity Electrospray Ionization - Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Proteins." Analytical Chemistry 72(10):2271-2279.
Belov ME, MV Gorshkov, HR Udseth, GA Anderson, AV Tolmachev, DC Prior, R Harkewicz, and RD Smith. 2000. "Initial Implementation of an Electrodynamic Ion Funnel with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Journal of the American Society for Mass Spectrometry 11(1):19-23.
Shen Y, SJ Berger, GA Anderson, and RD Smith. 2000. "High-Efficiency Capillary Isoelectric Focusing of Peptides." Analytical Chemistry 72(9):2154-2159.
Bruce JE, GA Anderson, CY Lin, MV Gorshkov, AL Rockwood, and RD Smith. 2000. "A Novel High Performance Fourier Transform Ion Cyclotron Resonance Cell for Improved Biopolymer Characterization ." Journal of Mass Spectrometry 35(1):85-94.
Bruce JE, GA Anderson, MD Brands, L Pasa-Tolic, and RD Smith. 2000. "Obtaining More Accurate Fourier Transform Ion Cyclotron Resonance Mass Measurements Without Internal Standards Using Multiply Charged Ions." Journal of the American Society for Mass Spectrometry 11(5):416-421.
Conrads TP, GA Anderson, TD Veenstra, L Pasa-Tolic, and RD Smith. 2000. "Utility of Accurate Mass Tags for Proteome-Wide Protein Identification." Analytical Chemistry 72(14):3349-3354.
Gao H, Y Shen, TD Veenstra, R Harkewicz, GA Anderson, JE Bruce, L Pasa-Tolic, and RD Smith. 2000. "Two Dimensional Electrophoretic/Chromatographic Separations Combined with Electrospray Ionization FTICR Mass Spectrometry for High Throughput Proteome Analysis." Journal of Microcolumn Separations 12(7):383-390.
Goodlet DR, JE Bruce, GA Anderson, B Rist, L Pasa-Tolic, ON Fiehn, RD Smith, and R Aebersold. 2000. "Protein Identification with a Single Accurate Mass of a Cysteine-Containing Peptide and Constrained Database Searching." Analytical Chemistry 72(6):1112-1118.
Jensen PK, L Pasa-Tolic, KK Peden, S Martinovic, MS Lipton, GA Anderson, N Tolic, KK Wong, and RD Smith. 2000. "Mass Spectrometric Detection for Capillary Isoelectric Focusing Separations of Complex Protein Mixtures." Electrophoresis 21(7):1372-1380.
Kim TM, AV Tolmachev, R Harkewicz, DC Prior, GA Anderson, HR Udseth, RD Smith, TH Bailey, VS Rakov, and JH Futrell. 2000. "Design and Implementation of a New Electrodynamic Ion Funnel." Analytical Chemistry 72:2247-2255.
Masselon CD, GA Anderson, R Harkewicz, JE Bruce, L Pasa-Tolic, and RD Smith. 2000. "Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures." Analytical Chemistry 72(8):1918-1924.
Veenstra TD, S Martinovic, GA Anderson, L Pasa-Tolic, and RD Smith. 2000. "Proteome Analysis using Selective Incorporation of Isotopically Labeled Amino Acids." Journal of the American Society for Mass Spectrometry 11(1):78-82.
Xiang F, GA Anderson, TD Veenstra, MS Lipton, and RD Smith. 2000. "Characterization of Microorganisms and Biomarker Development from Global ESI-MS/MS Analyses of Cell Lysates." Analytical Chemistry 72(11):2475-2481.
Zhang CX, F Xiang, L Pasa-Tolic, GA Anderson, TD Veenstra, and RD Smith. 2000. "Stepwise Mobilization of Focused Proteins in Capillary Isoelectric Focusing Mass Spectrometry." Analytical Chemistry 72(7):1462-1468.

1999

Pasa-Tolic L, PK Jensen, GA Anderson, MS Lipton, KK Peden, S Martinovic, N Tolic, JE Bruce, and RD Smith. 1999. "High Throughput Proteome-Wide Precision Measurements of Protein Expression using Mass Spectrometry." Journal of the American Chemical Society 121(34):7949-7950.
Bruce JE, GA Anderson, JY Wen, R Harkewicz, and RD Smith. 1999. "High Mass Measurement Accuracy 100% Sequence Coverage of Enzymatically Digested Bovine Serum Albumin from a Single ESI-FTICR Mass Spectrum." Analytical Chemistry 71(14):2595-2599.
Jensen PK, L Pasa-Tolic, GA Anderson, JA Horner, MS Lipton, JE Bruce, and RD Smith. 1999. "Probing Proteomes Using Capillary Isoelectric Focusing-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry." Analytical Chemistry 71(11):2076-2084.
Shaffer SA, AV Tolmachev, DC Prior, GA Anderson, HR Udseth, and RD Smith. 1999. "Characterization of an Improved Electrodynamic Ion Funnel Interface for Electrospray Ionization Mass Spectrometry." Analytical Chemistry 71(15):2957-2964.

1998

Shaffer SA, DC Prior, GA Anderson, HR Udseth, and RD Smith. 1998. "An Ion Funnel Interface for Improved Ion Focusing and Sensitivity Using Electrospray Ionization Mass Spectometry." Analytical Chemistry 70(19):4111-4119.