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Fundamental and Computational Sciences Directorate

Staff information

Kim Hixson

Environmental Dynamics & Simulations
Pacific Northwest National Laboratory
PO Box 999
MSIN: J4-02
Richland, WA 99352

PNNL Publications


  • Handakumbura P, KK Hixson, SO Purvine, GC Jansson, and L Pasa Tolic. 2017. "Plant iTRAQ-based proteomics." Current Protocols in Plant Biology 2(2):158-172.  doi:10.1002/cppb.20052
  • Strand DD, AK Livingston, M Satoh-Cruz, T Koepke, HM Enlow, N Fisher, JE Froehlich, JA Cruz, D Minhas, KK Hixson, K Kohzuma, MS Lipton, A Dhingra, and D Kramer. 2017. "Defects in the Expression of Chloroplast Proteins Leads to H2O2 Accumulation and Activation of Cyclic Electron Flow around Photosystem I." Frontiers in Plant Science 7:2073.  doi:10.3389/fpls.2016.02073
  • White RA, III, A Rivas-Ubach, MI Borkum, M Koberl, A Bilbao Pena, SM Colby, DW Hoyt, AK Bingol, YM Kim, JP Wendler, KK Hixson, and GC Jansson. 2017. "The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies." Rhizosphere 3(2):212-221.  doi:10.1016/j.rhisph.2017.05.003


  • Valdes-Lopez O, JM Batek Rios, N Gomez-Hernandez, CT Nguyen, MC Isidra-Arellano, N Zhang, T Joshi, D Xu, KK Hixson, KK Weitz, JT Aldrich, L Pasa-Tolic, and G Stacey. 2016. "Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles." Frontiers in Plant Science 7:Article No. 517.  doi:10.3389/fpls.2016.00517


  • Nakayasu ES, S Wu, MA Sydor, AK Shukla, KK Weitz, RJ Moore, KK Hixson, JS Kim, VA Petyuk, ME Monroe, L Pasa-Tolic, W Qian, RD Smith, JN Adkins, and C Ansong. 2014. "A Method to determine lysine acetylation stoichiometries." International Journal of Proteomics 2014:Article No. 730725.  doi:10.1155/2014/730725


  • Nakayasu ES, RN Brown, C Ansong, MA Sydor, S Imtiaz, C Mihai, RL Sontag, KK Hixson, ME Monroe, T Sobreira, G Orr, VA Petyuk, F Yang, RD Smith, and JN Adkins. 2013. "Multi-omic data integration links Deleted in Breast Cancer 1 (DBC1) Degradation to Chromatin Remodeling in Inflammatory Response." Molecular & Cellular Proteomics. MCP 12(8):2136-2147.  doi:10.1074/mcp.M112.026138


  • Brechenmacher L, TH Nguyen, KK Hixson, M Libault, JT Aldrich, L Pasa-Tolic, and G Stacey. 2012. "Identification of soybean proteins from a single cell type: The root hair." Proteomics 12(22):3365-3373.  doi:10.1002/pmic.201200160
  • Nguyen TH, L Brechenmacher, JT Aldrich, TRW Clauss, MA Gritsenko, KK Hixson, M Libault, K Tanaka, F Yang, Q Yao, L Pasa-Tolic, D Xu, HT Nguyen, and G Stacey. 2012. "Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum." Molecular & Cellular Proteomics. MCP 11(11):1140-1155.  doi:10.1074/mcp.M112.018028


  • Lopez-Ferrer D, K Petritis, EW Robinson, KK Hixson, Z Tian, JH Lee, SW Lee, N Tolic, KK Weitz, ME Belov, RD Smith, and L Pasa-Tolic. 2011. "Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics." Molecular & Cellular Proteomics. MCP 10(2):, doi:10.1074/mcp.M110.001479
  • Lopez-Ferrer D, KK Hixson, ME Belov, and RD Smith. 2011. "Ultra-Fast Sample Preparation for High-Throughput Proteomics." Chapter 8 in Sample Preparation in Biological Mass Spectrometry, ed. AR Ivanov and AV Lazarev, pp. 125-139.  Springer, Dordrecht, Germany. 


  • Bagwell CE, KK Hixson, CE Milliken, D Lopez-Ferrer, and KK Weitz. 2010. "Proteomic and Physiological Responses of Kineococcus radiotolerans to Copper." PLoS One 5(8):Article No. e12427.  doi:10.1371/journal.pone.0012427
  • DiDonato RJ, ND Young, J Butler, KJ Chin, KK Hixson, P Mouser, MS Lipton, R DeBoy, and B Methe. 2010. "Genome Sequence of the Deltaproteobacterial Strain NaphS2 and Analysis of Differential Gene Expression during Anaerobic Growth on Naphthalene." PLoS One 5(11):Article No. e14072.  doi:10.1371/journal.pone.0014072
  • Gupta N, KK Hixson, DE Culley, RD Smith, and PA Pevzner. 2010. "Analyzing Protease Specificity and Detecting in Vivo Proteolytic Events Using Tandem Mass Spectrometry." Proteomics 10(15):2833-2844. 
  • Hixson KK, D Lopez-Ferrer, EW Robinson, and L Pasa-Tolic. 2010. "Proteomics." In Encyclopedia of Spectroscopy and Spectrometry, 2nd edition, ed. J Lindon, GE Trantor, D Koppenaal, pp. 2280-2288.  Academic Press, Amsterdam, Netherlands Antilles. 
  • Lewis NE, KK Hixson, TM Conrad, JA Lerman, P Charusanti, AD Polpitiya, JN Adkins, G Schramm, SO Purvine, D Lopez-Ferrer, KK Weitz, R Eils, R Konig, RD Smith, and BO Palsson. 2010. "Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models." Molecular Systems Biology 6:Article No. 390.  doi:10.1038/msb.2010.47
  • Schutzer SE, T Liu, B Natelson, TE Angel, AA Schepmoes, SO Purvine, KK Hixson, MS Lipton, DG Camp, II, PK Coyle, RD Smith, and J Bergquist. 2010. "Establishing the Proteome of Normal Human Cerebrospinal Fluid ." PLoS One 5(6):e10980-.  doi:10.1371/journal.pone.0010980


  • Kim W, MW Silby, SO Purvine, JS Nicoll, KK Hixson, ME Monroe, CD Nicora, MS Lipton, and SB Levy. 2009. "Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1." PLoS One 4(12):Article Number: e8455.  doi:10.1371/journal.pone.0008455
  • Lopez-Ferrer D, KK Hixson, HS Smallwood, TC Squier, K Petritis, and RD Smith. 2009. "Evaluation of a High Intensity Focused Ultrasound-Immobilized Trypsin Digestion and 18 O-Labeling Method for Quantitative Proteomics." Analytical Chemistry 81(15):6272-6277. 


  • Shen Y, KK Hixson, N Tolic, DG Camp, II, SO Purvine, RJ Moore, and RD Smith. 2008. "Mass Spectrometry Analysis of Proteome-wide Proteolytic Post-translational Degradation of Proteins." Analytical Chemistry 80(15):5819-5828.  doi:10.1021/ac800077w
  • Shen Y, N Tolic, KK Hixson, SO Purvine, GA Anderson, and RD Smith. 2008. "De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins ." Analytical Chemistry 80(20):7742-7754.  doi:10.1021/ac801123p
  • Ding YHR, KK Hixson, M Aklujkar, MS Lipton, RD Smith, DR Lovley, and T Mester. 2008. "Proteome of Geobacter sulfurreducens grown with Fe(III) oxide or Fe(III) citrate as the electron acceptor." Biochimica et Biophysica Acta--Proteins and Proteomics 1784(12):1935-1941.  doi:10.1016/j.bbapap.2008.06.011
  • Lopez-Ferrer D, K Petritis, KK Hixson, TH Heibeck, RJ Moore, ME Belov, DG Camp, II, and RD Smith. 2008. "Application of pressurized solvents for ultrafast trypsin hydrolysis in proteomics: Proteomics on the fly." Journal of Proteome Research 7(8):3276-3281.  doi:10.1021/pr7008077
  • Lopez-Ferrer D, K Petritis, NM Lourette, BH Clowers, KK Hixson, TH Heibeck, DC Prior, L Pasa-Tolic, DG Camp, II, ME Belov, and RD Smith. 2008. "Fast On-Line Digestion System for Protein Characterization ." Analytical Chemistry 80(23):8930-8936.  doi:10.1021/ac800927v
  • Lopez-Ferrer D, TH Heibeck, K Petritis, KK Hixson, W Qian, ME Monroe, AM Mayampurath, RJ Moore, ME Belov, DG Camp, II, and RD Smith. 2008. "Rapid Sample Processing For LC-MS Based Quantitative Proteomics Using High Intensity Focused Ultrasounds." Journal of Proteome Research 7(9):3860-3867.  doi:10.1021/pr800161x
  • Shen Y, N Tolic, KK Hixson, SO Purvine, L Pasa-Tolic, W Qian, JN Adkins, RJ Moore, and RD Smith. 2008. "Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags." Analytical Chemistry 80(6):1871-82.  doi:10.1021/ac702328x
  • Wegener KM, EA Welsh, LE Thornton, NS Keren, JM Jacobs, KK Hixson, ME Monroe, DG Camp, II, RD Smith, and HB Pakrasi. 2008. "High Sensitivity Proteomics Assisted Discovery of a Novel Operon Involved in the Assembly of Photosystem II, a Membrane Protein Complex." Journal of Biological Chemistry 283(41):27829-27837.  doi:10.1074/jbc.M803918200


  • Fried M, KK Hixson, L Anderson, Y Ogata, TK Mutabingwa, and PE Duffy. 2007. "The distinct proteome of placental malaria parasites." Molecular and Biochemical Parasitology 155(1):57-65.  doi:10.1016/j.molbiopara.2007.05.010
  • Resch W, KK Hixson, RJ Moore, MS Lipton, and B Moss. 2007. "Protein Composition of the Vaccinia Virus Mature Virion." Virology 358(1):233-247. 


  • Ding YHR, KK Hixson, CS Giometti, A Stanley, A Esteve-Nunez, T Khare, SL Tollaksen, W Zhu, JN Adkins, MS Lipton, RD Smith, T Mester, and DR Lovley. 2006. "The Proteome of Dissimilatory Metal-reducing Microorganism Geobacter Sulfurreducens under Various Growth Conditions." Biochimica et Biophysica Acta--Proteins and Proteomics 1764(7):1198-1206.  doi:10.1016/j.bbapap.2006.04.017
  • Hixson KK, JN Adkins, SE Baker, RJ Moore, RD Smith, SL McCutchen-Maloney, and MS Lipton. 2006. "Biomarker Candidate Identification in Yersinia Pestis Using Organism-Wide Semiquantitative Proteomics ." Journal of Proteome Research 5(11):3008-3017. 
  • 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. 
  • Luo Q, K Tang, F Yang, A Elias, Y Shen, RJ Moore, R Zhao, KK Hixson, SS Rossie, and RD Smith. 2006. "More sensitive and quantitative proteomic measurements using very low flow rate porous silica monolithic LC columns with electrospray ionization-mass spectrometry ." Journal of Proteome Research 5(5):1091-1097. 


  • Shen Y, R Zhang, RJ Moore, J Kim, TO Metz, KK Hixson, R Zhao, EA Livesay, HR Udseth, and RD Smith. 2005. "Automated 20 kpsi RPLC-MS and MS/MS with chromatographic peak capacities of 1000-1500 and capabilities in proteomics and metabolomics ." Analytical Chemistry 77(10):3090-3100. 
  • Luo Q, Y Shen, KK Hixson, R Zhao, F Yang, RJ Moore, HM Mottaz, and RD Smith. 2005. "Preparation of 20-µm-i.d. Silica-based Monolithic Columns and Application for Proteomic Analysis." Analytical Chemistry 77(15):5028-5035. 


  • 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. 
  • Prokisch H, CM Scharfe, DG Camp, II, W Xiao, L David, C Andreoli, ME Monroe, RJ Moore, MA Gritsenko, C Kozany, KK Hixson, HM Mottaz, H Zischka, M Ueffing, ZS Herman, RW Davis, T Meitinger, P Oefner, RD Smith, and LM Steinmetz. 2004. "Integrative Analysis of the Mitochondrial Proteome in Yeast." PloS Biology 2(6):0795-0804. 


  • Shen Y, RJ Moore, R Zhao, J Blonder, DL Auberry, CD Masselon, L Pasa-Tolic, KK Hixson, KJ Auberry, and RD Smith. 2003. "High-Efficiency On-Line Solid-Phase Extraction Coupling to 15-150 um I.D. Column Liquid Chromatography for Proteomic Analysis." Analytical Chemistry 75(14):3596-3605. 
  • Mohan D, L Pasa-Tolic, CD Masselon, N Tolic, B Bogdanov, KK Hixson, RD Smith, and CS Lee. 2003. "Integration of Electrokinetic-Based Multidimensional Separations/Concentration Platform with electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry for Proteome Analysis of Shewanella Oneidensis." Analytical Chemistry 75(17):4432-4440. 


  • Hixson KK, N Rodriguez, DG Camp, II, EF Strittmatter, MS Lipton, and RD Smith. 2002. "Evaluation of Enzymatic Digestion and Liquid Chromatography-Mass Spectrometry Peptide Mapping of the Integral Membrane Protein Bacteriorhodopsin." Electrophoresis 23(18):3224-3232. 
  • 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. 


  • 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. 

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