University of Washington College of Engineering Center for Microbial Proteomics


Publications – Arranged by Subject

Protein and Peptide Mass Spectrometry, Microbial Proteomics, Oral Biology, Environmental and Biomedical Microbiology

Hendrickson, E. L., Beck, D. A. C., Miller, D. P., Wang, Q., Whiteley, M., Lamont, R. J., Hackett, M. "Insights into dynamic polymicrobial synergy revealed by time-coursed RNA-Seq." Frontiers in Micro., DOI: 10.3389/fmicb.2017.00261 (2017).

Kuboniwa, M., Houser, J. R., Hendrickson, E. L., Wang, Q., Alghamdi, S. A., Sakanaka, A., Miller, D. P., Hutcherson, J. A., Wang, T., Beck, D. A. C., Whiteley, M., Amano, A., Wang, H., Marcotte, E. M., Hackett, M., Lamont, R. J. "Metabolite cross-talk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection." Nat. Micro., DOI: 10.1038/s41564-017-0021-6 (2017).

Qin W., Amin, S. A., Lundeen, R. A., Heal, K. R., Martens-Habbena, W., Turkarslan, S., Urakawa, H., Costa, K. C., Hendrickson, E. L., Wang, T., et al. "Stress response of a marine ammonia-oxidizing archaeon informs physiological status of environmental populations." ISME J., in press (2017).

Wright, C. J., Xue, P., Hirano, T., Liu, C., Whitmore, S. E., Hackett, M., Lamont, R. J. "Characterization of a bacterial tyrosine kinase in Porphyromonas gingivalis involved in polymicrobial synergy." MicrobiologyOpen, 3: 383-394 (2014).

Hendrickson, E. L., Wang , T., Beck, D. A. C., Dickinson, B. C., Wright, C. J., Lamont, R. J., Hackett, M. "Proteomics of Fusobacterium nucleatum within a model developing oral microbial community." MicrobiologyOpen, DOI: 10.1002/mbo3.204 (2014).

Hirano, T., Beck, D. A. C., Wright, C. J., Demuth, D. R., Hackett, M., Lamont, R. J. "Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis." Molecular Oral Microbiology 28: 70-81 (2013).

Yoon, S. H., Turkarslan, S., Reiss, D. J., Pan, M., Burn, J. A., Costa, K. C., Lie, T. J., Slagel, J., Moritz, R. L., Hackett, M., Leigh, J. A., Baliga, N. S. "A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen." Genome Res. 23: 1839-1851 (2013).

Kuboniwa, M., Tribble, G. D., Hendrickson, E. L., Amano, A., Lamont, R. J., Hackett, M. "Insights into the virulence of oral biofilms: discoveries from proteomics." Expert Rev. Proteom. 9: 311-323 (2012)."

Hirano, T., Beck, D. A. C., Demuth, D. R., Hackett, M., Lamont, R. J. "Deep Sequencing of Porphyromonas gingivalis and comparative transcriptome analysis of a LuxS mutant." Frontiers in Cellular and Infection Microbiology 2 (79): 1-11 (2012).

Hendrickson, E. L., Wang, T., Dickinson, B. C., Whitmore, S. E., Wright, C. J., Lamont, R. J., Hackett, M. "Proteomics of Streptococcus gordonii within a model developing oral microbial community." BMC Microbiology 12: 211 (2012).

Krumholz, L. R., Wang, L., Beck, D. A., Wang, T., Hackett, M., Mooney, B., Juba, T. R., McInerney, M. J., Meyer, B., Wall, J. D., Stahl, D. A. "Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis." Microbiology 159: 2162-2168 (2013).

Costa, K. C., Wong, P. M., Wang, T., Lie, T. J., Dodsworth, J. A., Swanson, I., Burn, J. A., Hackett, M., Leigh, J. A. “Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase.” Proc Natl Acad Sci USA. 107 (24): 11050-11055 (2010).

Yoon, S. H., Reiss, D. J., Bare, J. C., Tenenbaum, D., Pan, M., Slagel, J., Moritz, R. L., Lim, S., Hackett, M., Menon, A. L., Adams, M. W. W., Barnebey, A., Yannone, S. M.,
Leigh, J. A., Baliga, N. S. "Parallel evolution of transcriptome architecture during genome reorganization." Genome Res. 21:1892-1904 (2011).

Mans, J. J., Hendrickson, E. L., Hackett, M. and Lamont, R. J. "Cellular and bacterial profiles associated with oral epithelium–microbiota interactions," Periodontology 2000 52: 207-217 (2009).

Xia, Q., Wang, T., Beck, D. A. C., Taub, F., Leigh, J. A. and Hackett, M. “Quantitative local false discovery rates, deep sampling and detecting protein abundance change for the model organism Methanococcus maripaludis,” BMC Microbiol, in revision.

Hendrickson, E. L., Beck, D. A. C., Wang, T., Lidstrom, M. E., Hackett, M. and Chistoserdova, L. “The expressed genome of Methylobacillus flagellatus defined through comprehensive proteomics and new insights into methylotrophy," J. Bacteriol. 192: 4859-4867(2010).

Xia, Q., Wang, T., Hendrickson, E.L., Lie, T.J., Hackett, M. and Leigh, J.A. “Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis,” BMC Microbiol. 9: 149 (2009).

Hendrickson, E. L., Xia, Q., Wang, T., Lamont, R. J., Hackett, M. “Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.” BMC Microbiol. 9:185 (2009).

Kuboniwa, M., Hendrickson, E. L., Xia, Q., Wang, T., Xie, H., Hackett, M. and Lamont, R. J. “Proteomics of Porphyromonas gingivalis within a model oral microbial community.” BMC Microbiol. 9: 98 (2009).

Kalyuhznaya, M. G., Martens-Habbena, W., Wang, T., Stolyar, S. M., Hackett, M., Stahl, D. A., Lidstrom M. E., and Chistoserdova L. “Microbial populations in freshwater lake sediment linking denitrification to methanol oxidation as assessed by stable isotope probing and pure culture analysis.” Environ. Microbiol. Rep. 1: 385-392 (2009).

Latypova, E., Yang, S., Wang, Y. S., Wang, T., Hackett, M., Schafer, H., and Kalyuzhnaya, M. G.Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5 Molec. Microbiol. 75: 426-439 (2010).

Bosch, G., Wang, T., Latypova, E., Kalyuzhnaya, M. G., Hackett, M. and Chistoserdova, L. "Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis." Microbiol. 155: 1103-1110 (2009).

Bosch, G., Skovran, E., Xia, Q., Miller, J. A., Lidstrom, M. E. and Hackett, M. “Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and non-methylotrophic conditions.” Proteomics 8: 3494-3505 (2008).

Hackett, M. “Science, marketing and wishful thinking in quantitative proteomics.” Proteomics 8: 4618-4623 (2008).

Hendrickson, E. L., Lamont, R. J. and Hackett, M. “Tools for interpreting large-scale protein profiling in microbiology.” Jour. Dent. Res. 87: 1004-1015 (2008).

Xia, Q., Wang, T., Taub. F., Park, Y., Capestanty, C. A., Lamont, R. J. and Hackett, M. “Quantitative proteomics of intracellular Porphyromonas gingivalis,” Proteomics, 7: 4323-4337 (2007).

Xia, Q., Hendrickson, E. L., Wang, T., Lamont, R. J., Leigh, J. A. and Hackett, M., “Protein abundance ratios for global studies of prokaryotes,” Proteomics, 7: 2904-2919 (2007).

Lamont, R. J., Meila, M., Xia, Q. and Hackett, M. “Mass spectrometry-based proteomics and its application to studies of Porphyromonas gingivalis invasion and pathogenicity,” Curr. Drug Targ. Infect. Disord., 6: 311-325 (2006).

Hendrickson, E. L., Xia, Q., Wang, T., Leigh, J. A. and Hackett, M. “Comparison of spectral counting and metabolic stable isotopic labeling for use with microbial proteomics,” The Analyst, 131: 1335-1341 (2006).

Xia, Q., Wang, T., Park, Y., Lamont, R. and Hackett, M “Differential quantitative proteomics of Porphyromonas gingivalis by linear ion trap mass spectrometry: non-label methods, q-values and LOWESS curve fitting,” Internat. Jour. Mass Spectrom., 259: 105-116 (2007).

Xia, Q., Hendrickson, E. L., Zhang, Y., Wang,, T., Taub, F., Moore,, B. C., Porat, , I., Whitman,, W. B., Hackett, M. and Leigh,, J. A. “Quantitative proteomics of the Archaeon Methanococcus maripaludis validated by microarray analysis and real time PCR,” Molec. Cell Proteom., 5: 868-881 (2006).

Li, Q., Xia, Q., Wang, T., Meila, M. and Hackett, M. “Analysis of the stochastic variation in LTQ single scan Mass spectra,” Rapid Commun. Mass Spectrom., 20: 1551-1557 (2006).

Porat, I., Kim, W., Hendrickson, E. L., Xia, Q., Zhang, Y., Wang, T., Taub, F., Moore, B. C., Anderson, I. J., Hackett, M., Leigh, J. A. and Whitman, W. B. “Disruption of the operaon encoding Ehb hydrogenase limits anabolic CO2 assimilation in the Archaeon Methanococcus maripaludis,” Jour. Bacteriol., 188: 1373-1380 (2006).

Zhang, Y., Wang, T., Chen, W., Yilmaz, O., Park, Y., Jung, I. L., Lamont, R. J., and Hackett, M. “Differential protein expression by the oral pathogen Porphyromonas gingivalis in response to secreted epithelial cell components,” Proteomics, 5: 198-211 (2005).

Park, Y., Simionato, M. R., Sekiya, K., Murakami, D. J., Chen, W., Hackett, M., Yoshimura, F., Demuth, D. M., and Lamont, R. J. “The short fimbriae of Porphyromonas gingivalis and their role in coadhesion with Streptococcus gordonii,” Infect. Immunn., 73: 3983-3989 (2005).

E. L. Hendrickson, R. Kaul, Y. Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J. Dodsworth, W. Gillett, D. E. Graham, M. Hackett, A. K. Haydock, A. Kang, M. L. Land, R. Levy, T. J. Lie, T. A. Major, B. Moore, I. Porat, R. Overbeek, A. Palmeiri, G. Rouse, C. Saenphimmachak, D. Söll, T. Wang, W. B. Whitman, Q. Xia1, Y. Zhang, F. W. Larimer, M. V. Olson, and J. A. Leigh “Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis,J. Bacteriol., 186: 6956-6969 (2004).

Wang, T., Zhang, Y., Chen, W., Park, Y., Lamont, R. J. and Hackett, M. “Reconstructed protein arrays from 3D HPLC/tandem mass spectrometry and 2D gels: complementary approaches to Porphyromonas gingivalis protein expression,” The Analyst 127: 1450-1456 (2002).

Chen, W., Laidig, K. E., Park, Y., Park, K., Yates, J. R. III, Lamont, R. J. and Hackett, M. "Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra," The Analyst 126: 52-57(2001).

Sigle, R., Hackett, M. and Aird, S. D. "Primary structures of four trypsin inhibitor E homologs from venom of Dendroaspis angusticeps, structure-function comparisons with other dendrotoxin homologs," Toxicon. 40: 297-308 (2002).

Lim, K. B., Bazemore Walker, C. R., Guo, L., Pellett, S., Shabanowitz, J., Hunt, D. F., Hewlett, E. L., Ludwig, A., Goebel, W., Welch, R. A. and Hackett, M. "Escherichia coli a-Hemolysin (HlyA) is Heterogeneously Acylated in vivo With 14, 15 and 17 Carbon Fatty Acids," J. Biol. Chem. 275: 36698-36702 (2000).

Basar, T., Havlicek, V., Bezouskova, S., Hackett, M., and Sebo, P. “Acylation of lysine 983 is sufficient for toxin activity of Bordetella pertussis adenylate cyclase: substitutions of alanine 140 modulate acylation site selectivity of the toxin acyltransferase CyaC,” J. Biol. Chem. 276: 348-354 (2001).

Guina, T., Yi, E. C., Wang, H, Hackett, M., and Miller, S. I. "A PhoP-regulated outer-membrane protease of Salmonella typhimurium promotes resistance to alpha-helical antimicrobial peptides,"J. Bacteriol. 182:4077-4086 (2000).

Havlícek, V., Higgins, L., Chen, W., Halada, P., Sebo, P., Sakamoto, H., and Hackett, M. "Mass Spectrometric Analysis of Recombinant Adenylate Cyclase Toxin from Bordetella pertussis strain 18323/pHSP9" J. Mass Spectrom. 36: 384-391 (2001).

Basar, T., Havlicek, V., Bezouskova, S., Halada, P., Hackett, M., and Sebo, P. “The conserved lysine 860 in the additional fatty-acylation site of Bordetella pertussis adenylate cyclase is crucial for the toxin function independently of its acylation status,” J. Biol. Chem. 274: 10777-10783 (1999).

Furuya, K., Hackett, M., Cirelli, M. A. Schegg, K. M., Wang, H., Shabanowitz, J., Hunt, D. F., and Schooley, D. A. “A cardioactive peptide from the southern armyworm, Spodoptera eridania,” Peptides, 20: 53-61 (1999).

Wang, H., Lim, K. B., Lawrence, R. F, Howald, W. N., Taylor, J. A., Ericsson, L. H., Walsh, K. A., and Hackett, M. "Stability enhancement for peptide analysis by electrospray using the triple quadrupole mass spectrometer," Anal. Biochem. 250: 162-168 (1997).

Hackett, M., Walker, C. B., Guo, L., Gray, M. C., Van Cuyk, S., Shabanowitz, J., Hunt, D. F., Ullmann, A., Hewlett, E. L. and Sebo, P. “Hemolytic, but not cell-invasive activity, of adenylate cyclase toxin is selectively affected by differential fatty-acylation in E. coli.” J. Biol. Chem. 270: 20250-20253 (1995).

Hackett, M., Guo, L., Shabanowitz, J., Hunt, D. F., and Hewlett, E. L. “Internal lysine palmitoylation inadenylate cyclase toxin from Bordetella pertussis.” Science 266: 433-435 (1994).

Gulden, P. H., Hackett, M., Addona, T., Guo, L., Walker, C. B., Sherman, N. E., Shabanowitz, J., Hewlett, E. L., and Hunt, D. F. “Mass spectrometric methods for peptide sequence analysis: applications to immunology and protein acylation,” in Mass Spectrometry in the Biological Sciences, Burlingame, A. L., Carr, S. A., eds. Humana: Clifton, New Jersey pp. 281-306 (1995).

Hjelmqvist, L., Hackett, M., Shafqat, J., Danielsson, O., Iida, J., Hendrickson, Ronald C., Michel, H., Shabanowitz, J., Hunt, D. F. and Jornvall, H. “Multiplicity of N-terminal structures of medium-chain alcohol dehydrogenases.” FEBS Letters 367: 237-240 (1995).

Furuya, K., Liao, S., Reynolds, S. E., Ota, R., Hackett, M., and Schooley, D.A. “Isolation and identification of a cardioactive peptide from Tenebrio molitor and Spodoptera eridania.Biol. Chem. Hoppe-Seyler 374: 1065-1074 (1993).


Lipids, Glycolipids and Related

Stonehouse, M. J., Cota-Gomez, A., Parker, S. K., Martin, W. E., Hankin, J. A., Murphy, R. C., Chen, W., Hackett, M., Vasil, A. I., and Vasil, M. L. "A novel class of phosphatidylcholine-specific phospholipases C," Mol. MicroBiol.46: 661-676(2002).

Yi, E. C. and Hackett, M. "Rapid isolation method for lipopolysaccharide and lipid A from Gram-negative bacteria," The Analyst 125: 651-656 (2000).

Ernst, R. K., Yi, Eugene C, Guo, L., Lim, K. B., Burns, J. L., Hackett, M. and Miller, S. I. "Specific lipopolysaccharide found in cystic fibrosis airway Pseudomonas aeruginosa," Science 286:1561-1565 (1999).

Guo, L., Lim, K. B., Poduje, C. M., Daniel, M., Gunn, J. S., Hackett, M., and Miller, S. I. “Lipid A acylation and bacterial resistance and vertebrate antimicrobial peptides,” Cell, 95: 189-198 (1998).

Guo, L., Lim, K. B., Gunn, J. S., Bainbridge, B., Darveau, R., Hackett, M., and Miller, S. I. "Regulation of Lipid A Modifications by Salmonella typhimurium Virulence Genes phoP-phoQ," Science 276: 250-253 (1997).

Gunn, J.S., Lim, K. B., Krueger, J., Kim, K., Guo, L., Hackett, M and Miller, S. “PmrA-PmrB-regulated genes necessary for 4-aminoarabinose lipid A modification and polymixin resistance,” Mol. Microbiol. 27: 1171-1182 (1998).

Moore, B. D., Hackett, M., and Seemann, J. R. “Hamamelitol purification, identification by electrospray ionization mass spectrometry, and quantitation in plant leaves.” Planta 195: 418-425 (1995).

Hong, L., Wang, H., Hackett, M. and Schooley, D. A. "The structure of dolichols isolated from Manduca sexta larvae." Insect Biochem. Molec. Biol. 25: 1019-1026 (1995).


Small Molecule Analytical Chemistry and Organic Mass spectrometry

Wang, H., Yi, E. C., Ibarra, C. A. and Hackett, M. "A remote flow cell for UV absorbance detection with capillary HPLC based on a single strand fiber optic," The Analyst 125: 1061-1064 (2000).

Upthagrove, A. L., Hackett, M. and Nelson, W. L. “Fragmentation pathways of selectively labeled propranolol using electrospray ionization on an ion trap mass spectrometer and comparison with ions formed by electron impact,” Rapid Commun. Mass Spectrom. 13: 534-541 (1999).

Upthagrove, A. L., Hackett, M. and Nelson, W. L. "Mass spectral fragmentation pathways of propranolol related beta-fluorinated amines studied by electrospray and electron impact ionization," Rapid Commun. Mass Spectrom. 13: 1671-1679 (1999).

Wang, H. and Hackett, M. "Ionization Within a cylindrical capacitor: electrospray without an externally applied high voltage," Anal. Chem. 70: 205-212 (1998).

Lofthagen, M., Seigel, J. S., Hackett, M. “Synthesis of metallomacrocyclophanes--deduction of structure from electrospray ionization mass spectroscopy and molecular mechanics computations.” Tetrahedron 51(22): 6195-6208 (1995).

Hackett, M., Wang, H., Miller, G. C., and Bornhop, D. J. “Ultraviolet-visible detection for capillary gas chromatography and combined ultraviolet-mass spectrometry using a remote flow cell.” J. Chromatogr. A, 695 (2): 243-257 (1995).

Bornhop, D.J., Hlousek, L., Hackett, M., Wang, H. and Miller, G.C. “Remote scanning ultraviolet detection for capillary gas chromatography.” Rev. Sci. Instrum. 63(1): 191-201 (1992).

Wilt, M. C., Miller, G. C., Hackett, M., and Everett, R. L. “Monoterpene concentrations in fresh, senescent and decaying foliage of singleleaf pinyon (Pinus monophylla) from the western great basin.” Jour. Chem. Ecol. 19(2): 185-194 (1993).

Kerkvliet, N. I., Wagner, S. L., Schmotzer, W. B., Hackett, M. Schrader, W. K. and Hultgren, B. “Dioxin intoxication from chronic exposure of horses to pentachlorophenol-contaminated wood shavings.” J. Am. Vet. Med. Assoc. 201(2): 296-302 (1992).

Pruell, R. J., Norwood, C. B., Bowen R. D., Boothman, W. S., Rogerson, P. F, Hackett, M., Butterworth, B. C. “Geochemical study of sediment contamination in New Bedford Harbor, Massachusetts.” Marine Environ. Res. 29(2): 77-101 (1990).

Marquis, P. J., Hackett, M., Holland L. G., Larsen M. L., Butterworth, B., Kuehl, D. W. “Analytical methods for a national study of chemical residues in fish .1. polychlorinated dibenzo-p-dioxins dibenzofurans.” Chemosphere 29: 495-508 (1994).

Kieatiwong, S., Nguyen, L. V., Hebert, V. R., Hackett, M., Miller, G. C., Miille M. J., Mitzel, R. “Photolysis of chlorinated dioxins in organic-solvents and on soils.” Environ. Sci. Technol. 24 (10): 1575-1580 (1990).

Norwood, C. B., Hackett, M., Pruell, R. J., Butterworth, B. C., Williamson, K. J., Naumann, S. M. “Polychlorinated dibenzo-para-dioxins and dibenzofurans in selected estuarine sediments.” Chemosphere 18: 553-560 (1989).