Skip to main content

Kenneth Auberry
Senior Research Scientist

Ken Auberry is the team leader for Research Software Engineering and Data Science team. Initially coming to PNNL to do mass spectrometry research, Ken Auberry found that his talents were much more effective when applied to software and database designs that allowed scientists to better help themselves analyze and interpret their data. By helping bridge the cultural and language gap between laboratory research scientists and software engineers, he helped streamline the process of data management.

Auberry now serves as the primary data architect for the NEXUS User Portal workflow management system currently under development. Over the last 20 years, he has helped design and implement many of the systems that have been the foundation for this type of data management strategy. He was one of the original architects for the Proteomics Research Information Storage and Management (PRISM) system, which is used by PNNL researchers to control, manage, and process the flow of information from an array of mass spectrometers into usable research data. Later, he developed the original prototype system that would eventually evolve into the MyEMSL data management system and helped pave the way for the NEXUS system.

Research Interests

  • Data management
  • Database design


  • PhD in Analytical Chemistry, Purdue University, 1999
  • BS in Chemistry, University of Tennessee, 1993

Awards and Recognition

  • Team Innovation Of The Year contributions to the DataHub Project, Communications/IT Directorate, PNNL (2019)
  • Achievement Award for the HRMAC 21T Mass Spectrometer Development Effort, U.S. Department of Energy (2016)
  • Staff Recognition Award for Developing World-class Capabilities for the HRMAC Project, Earth and Biological Sciences Directorate, PNNL (2015)
  • Director’s Award for Collaboration Enhancement Through the MyEMSL Data Management Project, EMSL (2011)
  • Invited Speaker, Department of Pharmaceutical Chemistry, University of Kansas (2008)
  • Outstanding Performance Award, Fundamental Science Directorate, PNNL (2007)
  • Invited Speaker, University of Virginia Medical School (2006)
  • Inaugural Candidate, Scientist and Engineer Development Program, PNNL ( 2004–2006)
  • Outstanding Performance Award, Fundamental Science Directorate, PNNL (2003)
  • Outstanding Performance Award, Fundamental Science Directorate, PNNL (2002)


Anderson, G. A., Auberry, K. J., Kangas, L. J., Smith, R. D. 2006. “Method for enhanced accuracy in predicting the elution times of peptides using liquid separations or chromatography.” United States Patent 7,136,759.



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


Ahring B.K., N.S. Baliga, J.R. Frederickson, S. Kaplan, H.B. Pakrasi, J.G. Pounds, and I. shah, et al. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP). PNNL-20717. Richland, WA: Pacific Northwest National Laboratory. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP)


Auberry K.J., G.R. Kiebel, M.E. Monroe, J.N. Adkins, G.A. Anderson, and R.D. Smith. 2010. " 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.


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.

Taylor R.C., M. Singhal, D.S. Daly, J.M. Gilmore, W.R. Cannon, K.O. Domico, and A.M. White, et al. 2009. "An analysis pipeline for the inference of protein-protein interaction networks." International Journal of Data Mining and Bioinformatics 3, no. 4) (Sp. Iss. SI:409-430. PNNL-SA-59756. doi:10.1504/IJDMB.2009.029204


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

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

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


Taylor R.C., M. Singhal, D.S. Daly, K.O. Domico, A.M. White, D.L. Auberry, and K.J. Auberry, et al. 2007. "SEBINI-CABIN: An Analysis Pipeline for Biological Network Inference, with a Case Study in Protein-Protein Interaction Network Reconstruction." In Sixth International Conference on Machine Learning and Applications, (ICMLA 2007), 587-593. Washington Dc:IEEE Computer Society. PNNL-SA-55941. doi:10.1109/ICMLA.2007.63


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


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

Cannon W.R., K.H. Jarman, B.M. Webb-Robertson, D.J. Baxter, C.S. Oehmen, K.D. Jarman, and A. Heredia-Langner, et al. 2005. "A Comparison of Probability and Likelihood Models for Peptide Identification from Tandem Mass Spectrometry Data." Journal of Proteome Research 4, no. 5:1687-1698. PNNL-SA-45622.

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.


Havre S.L., M. Singhal, B. Gopalan, D.A. Payne, K.R. Klicker, G.R. Kiebel, and K.J. Auberry, et al. 2004. "Integrating Evolving Tools for Proteomics Research." In Proceedings of The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, edited by Valafar, Faramarz and Homayoun Valafar, 2004, 307-313. Las Vegas, Nevada:CSREA Press. PNNL-SA-40933.

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.

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.

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.


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.

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.


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., 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.


Auberry, K. J., Y. G. Byun, D. B. Jacobson, and B. S. Freiser. 1999. “Kinetics of Metallocarbohedrenes: An FT-ICR Mass Spectrometry Study of the Association Reactions of Ti8C12+ with Polar and Nonpolar Molecules.” Journal of Physical Chemistry A 103 (45): 9029-9035.


Chen, Q., K. J. Auberry, and B. S. Freiser. 1998. “Reactions of FeCF2+ and CoCF2+ with Simple Alkanes and Olefins in the Gas Phase: An FTICR and Density Functional Study.” International Journal of Mass Spectrometry and Ion Processes 175 (1-2): 1-14.