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Fundamental and Computational Sciences Directorate

Staff information

Heather Brewer

Biosystms Dynamics & Simula
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-87
Richland, WA 99352

PNNL Publications


  • Dhondt I, VA Petyuk, S Bauer, HM Brewer, RD Smith, GG Depuydt, and BP Braeckman. 2017. "Changes of Protein Turnover in Aging Caenorhabditis elegans." Molecular & Cellular Proteomics. MCP 16(9):1621-1633.  doi:10.1074/mcp.RA117.000049
  • Haitjema C, SP Gilmore, JK Henske, KV Solomon, RD Groot, A Kuo, SJ Mondo, A Salamov, KM LaButti, ZJ Zhao, J Chiniquy, KW Barry, HM Brewer, SO Purvine, AT Wright, M Hainaut, B Boxma, TA Van Alen, J Hackstein, B Henrissat, SE Baker, IV Grigoriev, and MA O'Malley. 2017. "A Parts List for Fungal Cellulosomes Revealed by Comparative Genomics." Nature Microbiology 2:Article No. 17087.  doi:10.1038/nmicrobiol.2017.87
  • Ledee DR, MA Kang, M Kajimoto, SO Purvine, HM Brewer, L Pasa Tolic, and MA Portman. 2017. "Quantitative cardiac phosphoproteomics profiling during ischemia-reperfusion in an immature swine model." American Journal of Physiology. Heart and Circulatory Physiology 313(1):H125-H137.  doi:10.1152/ajpheart.00842.2016
  • Nie S, T Shi, TL Fillmore, AA Schepmoes, HM Brewer, Y Gao, E Song, H Wang, KD Rodland, W Qian, RD Smith, and T Liu. 2017. "Deep-dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues." Analytical Chemistry 89(17):9139-9146.  doi:10.1021/acs.analchem.7b01878
  • Staley C, AP Ferrieri, MM Tfaily, Y Cui, RK Chu, P Wang, JB Shaw, CK Ansong, HM Brewer, AD Norbeck, LM Markillie, FP do Amaral, T Tuleski, T Pellizzaro, BJ Agtuca, RA Ferrieri, S Tringe, L Pasa Tolic, G Stacey, and M Sadowsky. 2017. "Diurnal Cycling of Rhizosphere Bacterial Communities is Associated with Shifts in Carbon Metabolism." Microbiome 5:Article No. 65.  doi:10.1186/s40168-017-0287-1


  • Solomon KV, C Haitjema, JK Henske, SP Gilmore, D Borges-Rivera, A Lipzen, HM Brewer, SO Purvine, AT Wright, MK Theodorou, IV Grigoriev, A Regev, D Thompson, and MA O'Malley. 2016. "Early-branching Gut Fungi Possess A Large, And Comprehensive Array Of Biomass-Degrading Enzymes." Science 351(6278):1192-1195.  doi:10.1126/science.aad1431


  • Elfenbein JR, LA Knodler, ES Nakayasu, C Ansong, HM Brewer, L Bogomolnaya, LG Adams, M McClelland, JN Adkins, and HL Andrews-Polymenis. 2015. "Multicopy single-stranded DNA directs intestinal colonization of enteric pathogens." PLoS Genetics 11(9):e1005472.  doi:10.1371/journal.pgen.1005472


  • Hyung SW, PD Piehowski, RJ Moore, DJ Orton, AA Schepmoes, TRW Clauss, RK Chu, TL Fillmore, HM Brewer, T Liu, R Zhao, and RD Smith. 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(28):7117-7125.  doi:10.1007/s00216-014-8058-3
  • Brown JN, HM Brewer, CD Nicora, KK Weitz, MJ Morris, AJ Skabelund, JN Adkins, RD Smith, JH Cho, and R Gelinas. 2014. "Protein and microRNA biomarkers from lavage, urine, and serum in military personnel evaluated for dyspnea." BMC Medical Genomics 7:Article No. 58.  doi:10.1186/1755-8794-7-58
  • Depuydt GG, F Xie, VA Petyuk, A Smolders, HM Brewer, DG Camp, II, RD Smith, and BP Braeckman. 2014. "LC-MS Proteomics Analysis of the Insulin/IGF-1-Deficient Caenorhabditis elegans daf-2(e1370) Mutant Reveals Extensive Restructuring of Intermediary Metabolism." Journal of Proteome Research 13(4):1938-1956.  doi:10.1021/pr401081b
  • Hawley AK, HM Brewer, AD Norbeck, L Pasa-Tolic, and SJ Hallam. 2014. "Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes." Proceedings of the National Academy of Sciences of the United States of America 111(31):11395-11400.  doi:10.1073/pnas.1322132111
  • Mohimani H, R Kersten, W Liu, M Wang, SO Purvine, S Wu, HM Brewer, L Pasa-Tolic, N Bandeira, BS Moore, PA Pevzner, and PC Dorrestein. 2014. "Automated genome mining of ribosomal peptide natural products." ACS Chemical Biology 9(7):1545-1551.  doi:10.1021/cb500199h


  • Ansong C, AC Rutledge, HD Mitchell, S Chauhan, MB Jones, YM Kim, K Mcateer, BL Deatherage, JL DuBois, HM Brewer, BC Frank, JE McDermott, TO Metz, SN Peterson, RD Smith, VL Motin, and JN Adkins. 2013. "A multi-omic systems approach to elucidating Yersinia virulence mechanisms." Molecular Biosystems 9(1):44-54.  doi:10.1039/C2MB25287B
  • Ansong C, S Wu, D Meng, X Liu, HM Brewer, BLD Kaiser, ES Nakayasu, JR Cort, PA Pevzner, RD Smith, F Heffron, JN Adkins, and L Pasa-Tolic. 2013. "Top-down proteomics reveals a unique protein S-thiolation switch in Salmonella Typimurium in response to infection-like conditions." Proceedings of the National Academy of Sciences of the United States of America 110(25):10153-10158.  doi:10.1073/pnas.1221210110
  • Depuydt GG, F Xie, VA Petyuk, N Shanmugam, A Smolders, I Dhondt, HM Brewer, DG Camp, II, RD Smith, and BP Braeckman. 2013. "Reduced insulin/Insulin-like Growth Factor-1signaling and dietary restriction inhibit translation but preserve muscle mass in Caenorhabditis elegans." Molecular and Cellular Proteomics 12(12):3624-3639.  doi:10.1074/mcp.M113.027383
  • Halim MF, F Pfeiffer, J Zou, A Frisch, DH Haft, S Wu, N Tolic, HM Brewer, SH Payne, L Pasa-Tolic, and M Pohlschroder. 2013. "Haloferax volcanii archaeosortase is required for motility, mating, and C-terminal processing of the S-layer glycoprotein." Molecular Microbiology 88(6):1164-1175.  doi: 10.1111/mmi.12248
  • Hawley AK, S Kheirandish, A Mueller, HTC Leung, AD Norbeck, HM Brewer, L Pasa-Tolic, and SJ Hallam. 2013. "Molecular Tools for Investigating Microbial Community Structure and Function in Oxygen-Deficient Marine Waters." Chapter 16 in Methods in Enzymology: Microbial Metagenomics, Metatranscriptomics, and Metaproteomics, vol. 531, ed. EF DeLong, pp. 305-329.  Academic Press, San Diego, CA. 
  • Kim YM, B Schmidt, AS Kidwai, MB Jones, BL Deatherage, HM Brewer, HD Mitchell, BO Palsson, JE McDermott, F Heffron, RD Smith, SN Peterson, C Ansong, DR Hyduke, TO Metz, and JN Adkins. 2013. "Salmonella Modulates Metabolism During Growth under Conditions that Induce Expression of Virulence Genes." Molecular Biosystems 9(6):1522-1534.  doi:10.1039/C3MB25598K


  • Andreev VP, VA Petyuk, HM Brewer, Y Karpievitch, F Xie, J Clarke, DG Camp, II, RD Smith, AP Lieberman, RL Albin, Z Nawaz, JE Hokayem, and AJ Myers. 2012. "Label-Free Quantitative LC-MS Proteomics of Alzheimer’s Disease and Normally Aged Human Brains." Journal of Proteome Research 11(6):3053-3067.  doi:10.1021/pr3001546
  • Petrus AK, KS Swithers, CR Ranjit, S Wu, HM Brewer, JP Gogarten, L Pasa-Tolic, and KM Noll. 2012. "Genes for the major structural components of Thermotogales species' togas revealed by proteomic and evolutionary analyses of OmpA and OmpB homologs." PLoS One 7(6):e40236.  doi:10.1371/journal.pone.0040236
  • Rutledge AC, MB Jones, S Chauhan, SO Purvine, J Sanford, ME Monroe, HM Brewer, SH Payne, C Ansong, BC Frank, RD Smith, S Peterson, VL Motin, and JN Adkins. 2012. "Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae." PLoS One 7(3):Article No. E33903.  doi:10.1371/journal.pone.0033903


  • Ghazalpour A, B Bennett, VA Petyuk, L Orazco, R Hagopian, I Mungrue, CR Farber, J Sinsheimer, HM Kang, N Furlotte, C Park, PZ Wen, HM Brewer, KK Weitz, DG Camp, II, C Pan, R Yordanova, I Neuhaus, C Tilford, N Siemers, P Gargalovic, E Eskin, T Kirchgessner, DJ Smith, RD Smith, and AJ Lusis. 2011. "Comparative Analysis of Proteome and Transcriptome Variation in Mouse." PLoS Genetics 7(6):Article No. e1001393.  doi:10.1371/journal.pgen.1001393
  • Hallam SJ, AP Page, L Constan, YC Song, AD Norbeck, HM Brewer, and L Pasa-Tolic. 2011. "Molecular tools for investigating ANME community structure and function." Chapter 4 in Methods in Enzymology, Part A, vol. 494, ed. AC Rosenzweig and SW Ragsdale, pp. 75-90.  Elsevier/Academic Press, Amsterdam, Netherlands. 
  • Lin M., T Kikuchi, HM Brewer, AD Norbeck, and Y Rikihisa. 2011. "Global proteomic analysis of two tick-borne emerging zoonotic agents: Anaplasma phagocytophilum and Ehrlichia chaffeensis." Frontiers in Microbiology 2:Article No. 24.  doi:10.3389/fmicb.2011.00024
  • Niemann G, RN Brown, JK Gustin, A Stufkens, AS Shaikh-Kidwai, J Li, JE McDermott, HM Brewer, AA Schepmoes, RD Smith, JN Adkins, and F Heffron. 2011. "Discovery of Novel Secreted Virulence Factors from Salmonella enterica Serovar Typhimurium by Proteomic Analysis of Culture Supernatants." Infection and Immunity 79(1):33-43.  doi:10.1128/IAI.00771-10


  • Adkins JN, H Mottaz, TO Metz, CK Ansong, NP Manes, RD Smith, and F Heffron. 2010. "Performing Comparative Peptidomics Analyses of Salmonella from Different Growth Conditions." Chapter 2 in Peptidomics: Methods and Protocols, Methods in Molecular Biology, vol. 615, ed. Mikhail Soloviev, pp. 13-27.  Humana Press, Inc., New York, NY. 
  • Brown JN, R Estep, D Lopez-Ferrer, HM Brewer, TRW Clauss, NP Manes, M O'Connor, H Li, JN Adkins, S Wong, and RD Smith. 2010. "CHARACTERIZATION OF MACAQUE PULMONARY FLUID PROTEOME DURING MONKEYPOX INFECTION: DYNAMICS OF HOST RESPONSE." Molecular & Cellular Proteomics. MCP 9(12):2760-2771.  doi:10.1074/mcp.M110.001875


  • Ansong C, H Yoon, S Porwollik, H Mottaz-Brewer, BO Petritis, N Jaitly, JN Adkins, M Mcclelland, F Heffron, and RD Smith. 2009. "Global Systems-Level Analysis of Hfq and SmpB Deletion Mutants in Salmonella: Implications for Virulence and Global Protein Translation." PLoS One 4(3):e4809.  doi:10.1371/journal.pone.0004809
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella enterica serotype Tyhimurium Grown in Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, C Ansong, HS Smallwood, LM Rommereim, JE McDermott, HM Brewer, AD Norbeck, RC Taylor, JK Gustin, F Heffron, RD Smith, and JN Adkins. 2009. "Proteome of Salmonella Enterica SerotypeTyphimurium Grown in a Low Mg2+/pH Medium." Journal of Proteomics and Bioinformatics 2(9):388-397.  doi:10.4172/jpb.1000099
  • Shi L, SM Chowdhury, HS Smallwood, H Yoon, HM Mottaz-Brewer, AD Norbeck, JE McDermott, TRW Clauss, F Heffron, RD Smith, and JN Adkins. 2009. "Proteomic Investigation of the Time Course Responses of RAW 264.7 Macrophages to Infection with Salmonella enterica." Infection and Immunity 77(8):3227-3233.  doi:10.1128/IAI.00063-09


  • Ansong C, H Yoon, AD Norbeck, JK Gustin, JE McDermott, HM Mottaz, J Rue, JN Adkins, F Heffron, and RD Smith. 2008. "Proteomics Analysis of the Causative Agent of Typhoid Fever." Journal of Proteome Research 7(2):546-557.  doi:10.1021/pr070434u
  • Brewer HM, AD Norbeck, JN Adkins, NP Manes, C Ansong, L Shi, Y Rikihisa, T Kikuchi, S Wong, RD Estep, F Heffron, L Pasa-Tolic, and RD Smith. 2008. "Optimization of proteomic sample preparation procedures for comprehensive protein characterization of pathogenic systems." Journal of Biomolecular Techniques:JBT 19(5):285-295. 
  • Elias DA, SL Tollaksen, DW Kennedy, HM Mottaz, CS Giometti, JS Mclean, EA Hill, GE Pinchuk, MS Lipton, JK Fredrickson, and YA Gorby. 2008. "The Influence of Cultivation Methods on Shewanella oneidensis Physiology and Proteome Expression ." Archives of Microbiology 189(4):313-324.  doi:10.1007/s00203-007-0321-y
  • Huang H, M. Lin, X Wang, T Kikuchi, HM Mottaz, AD Norbeck, and Y Rikihisa. 2008. "Proteomic Analysis of and Immune Responses to Ehrlichia chaffeensis Lipoproteins." Infection and Immunity 76(8):3405-3414.  doi:10.1128/IAI.00056-08
  • Kelly RT, JS Page, R Zhao, W Qian, HM Mottaz, K Tang, and RD Smith. 2008. "Capillary-Based Multi Nanoelectrospray Emitters: Improvements in Ion Transmission Efficiency and Implementation with Capillary Reversed-Phase LC-ESI-MS." Analytical Chemistry 80(1):143-149.  doi:10.1021/ac701647s
  • Manes NP, RD Estep, HM Mottaz, RJ Moore, TRW Clauss, ME Monroe, X Du, JN Adkins, S Wong, and RD Smith. 2008. "Comparative Proteomics of Human Monkeypox and Vaccinia Intracellular Mature and Extracellular Enveloped Virions." Journal of Proteome Research 3:960-8.  doi:10.1021/pr070432+
  • Qian W, DT Kaleta, BA Ogata, H Jiang, T Liu, X Zhang, HM Mottaz, SM Varnum, DG Camp, II, huang, X Fang, W Zhang, and RD Smith. 2008. "Enhanced Detection of Low Abundant Human Plasma Proteins using a Tandem IgY12-SuperMix Immunoaffinity Separation Strategy." Molecular & Cellular Proteomics. MCP 7(10):1963-1973.  doi:10.1074/mcp.M800008-MCP200
  • Shi L, S Deng, MJ Marshall, Z Wang, DW Kennedy, A Dohnalkova, HM Mottaz, EA Hill, YA Gorby, AS Beliaev, DJ Richardson, JM Zachara, and JK Fredrickson. 2008. " Direct Involvement of Type II Secretion System in Extracellular Translocation of Shewanella Oneidensis Outer Membrane Cytochromes MtrC and OmcA." Journal of Bacteriology 190(15):5512-5516.  doi:10.1128/JB.00514-08


  • Elias DA, F Yang, HM Mottaz, AS Beliaev, and MS Lipton. 2007. "Enrichment of Functional Redox Reactive Proteins and Identification by Mass Spectrometry Results in Several Terminal Fe(III)-reducing Candidate Proteins in Shewanella oneidensis MR-1." Journal of Microbiological Methods 68(2):367-375. 
  • Manes NP, JK Gustin, J Rue, HM Mottaz, SO Purvine, AD Norbeck, ME Monroe, JS Zimmer, TO Metz, JN Adkins, RD Smith, and F Heffron. 2007. "Targeted Protein Degradation by Salmonella under Phagosome-Mimicking Culture Conditions Investigated Using Comparative Peptidomics." Molecular & Cellular Proteomics. MCP 6(4):717-727.  doi:10.1074/mcp.M600282-MCP200
  • Yang F, N Jaitly, H Jayachandran, Q Lou, ME Monroe, X Du, MA Gritsenko, R Zhang, DJ Anderson, SO Purvine, JN Adkins, RJ Moore, HM Mottaz, SJ Ding, MS Lipton, DG Camp, II, HR Udseth, RD Smith, and SS Rossie. 2007. "Applying a Targeted Label-free Approach using LC-MS AMT Tags to Evaluate Changes in Protein Phosphorylation Following Phosphatase Inhibition." Journal of Proteome Research 6(11):4489-4497.  doi:10.1021/pr070068e
  • Zhang Q, N Tang, JW Brock, HM Mottaz, JM Ames, J Baynes, RD Smith, and TO Metz. 2007. "Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry." Journal of Proteome Research 6(6):2323-2330.  doi:doi:10.1021/pr070112q


  • Adkins JN, HM Mottaz, AD Norbeck, JK Gustin, J Rue, TRW Clauss, SO Purvine, KD Rodland, F Heffron, and RD Smith. 2006. "Analysis of the Salmonella typhimurium Proteome through Environmental Response toward Infectious Conditions." Molecular & Cellular Proteomics. MCP 5(8):1450-1461.  doi:10.1074/mcp.M600139-MCP200
  • Liu T, W Qian, HM Mottaz, MA Gritsenko, AD Norbeck, RJ Moore, SO Purvine, DG Camp, II, and RD Smith. 2006. "Evaluation of Multi-Protein Immunoaffinity Subtraction for Plasma Proteomics and Candidate Biomarker Discovery Using Mass Spectrometry ." Molecular & Cellular Proteomics. MCP 5(11):2167-2174. 
  • 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. 
  • Shi L, B Chen, Z Wang, DA Elias, MU Mayer, YA Gorby, S Ni, BH Lower, DW Kennedy, DS Wunschel, HM Mottaz, MJ Marshall, EA Hill, AS Beliaev, JM Zachara, JK Fredrickson, and TC Squier. 2006. "Isolation of a High-Affinity Functional Protein Complex between OmcA and MtrC: Two Outer Membrane Decaheme c-type Cytochromes of Shewanella oneidensis MR-1 ." Journal of Bacteriology 188(13):4705-4714.  doi:10.1128/JB.01966-05
  • Shi L, JN Adkins, JR Coleman, AA Schepmoes, A Dohnalkova, HM Mottaz, AD Norbeck, SO Purvine, NP Manes, HS Smallwood, HH Wang, J Forbes, P Gros, S Uzzau, KD Rodland, F Heffron, RD Smith, and TC Squier. 2006. "Proteomic Analysis of Salmonella enterica Serovar Typhimurium Isolated from RAW 264.7 Macrophages: identification of a novel protein that contributes to the replication of serovar Typhimurium inside macrophages." Journal of Biological Chemistry 281:29131-29140.  doi:10.1074/jbc.M604640200
  • 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
  • Wang HH, W Qian, MH Chin, VA Petyuk, RC Barry, T Liu, MA Gritsenko, HM Mottaz, RJ Moore, DG Camp, II, AH Khan, D Smith, and RD Smith. 2006. "Characterization of the Mouse Brain Proteome Using Global Proteomic Analysis Complemented with Cysteinyl-Peptide Enrichment." Journal of Proteome Research 5(2):361-369. 


  • 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. 
  • Schmid AK, MS Lipton, HM Mottaz, ME Monroe, RD Smith, and ME Lidstrom. 2005. "Global whole-cell FTICR mass spectrometric proteomics analysis of the heat shock response in the radioresistant bacterium Deinococcus radiodurans." Journal of Proteome Research 4(3):709-718. 
  • Wang HH, W Qian, HM Mottaz, TRW Clauss, DJ Anderson, RJ Moore, DG Camp, II, AH Khan, DM Sforza, M Pallavicini, DJ Smith, and RD Smith. 2005. "Development and Evaluation of a Micro- and Nanoscale Proteomic Sample Preparation Method." Journal of Proteome Research 4(6):2397-2403.  doi:10.1021/pr050160f


  • Jacobs JM, HM Mottaz, LR Yu, DJ Anderson, RJ Moore, WNU Chen, KJ Auberry, EF Strittmatter, ME Monroe, BD Thrall, DG Camp, II, and RD Smith. 2004. "Multidimensional Proteome Analysis of Human Mammary Epithelial Cells." Journal of Proteome Research 3(1):68-75. 
  • 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. 
  • 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. 

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