R L Hettich

Summary

Affiliation: Oak Ridge National Laboratory
Country: USA

Publications

  1. pmc Strategies for metagenomic-guided whole-community proteomics of complex microbial environments
    Brandi L Cantarel
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e27173. 2011
  2. pmc Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress
    Shihui Yang
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
    BMC Genomics 13:336. 2012
  3. pmc Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities
    Robert L Hettich
    Oak Ridge National Laboratory, Oak Ridge, TN 37831 6131, USA
    Anal Chem 85:4203-14. 2013
  4. doi request reprint Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities
    Robert L Hettich
    Oak Ridge National Laboratory, Oak Ridge, TN 37831 6131, USA
    Curr Opin Microbiol 15:373-80. 2012
  5. pmc Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge
    Dorothea K Thompson
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    BMC Genomics 11:311. 2010
  6. pmc A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry
    Chongle Pan
    Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
    BMC Bioinformatics 11:118. 2010
  7. ncbi request reprint Formation and characterization of iron-oligonucleotide complexes with matrix-assisted laser desorption/ionization fourier transform ion cyclotron resonance mass spectrometry
    R L Hettich
    Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Tennessee 37831 6365, USA
    J Am Soc Mass Spectrom 10:941-9. 1999
  8. ncbi request reprint 53rd American Society for Mass Spectrometry Conference. 5-9 June, 2005, Henry B Gonzalez Conference Center, San Antonio, TX, USA
    Robert L Hettich
    Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 6131, USA
    Expert Rev Proteomics 2:459-61. 2005
  9. ncbi request reprint Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach
    Michael Brad Strader
    Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, Tennessee 37831 6131, USA
    J Proteome Res 3:965-78. 2004
  10. ncbi request reprint Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics
    Chongle Pan
    Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Mol Cell Proteomics 7:938-48. 2008

Research Grants

Collaborators

Detail Information

Publications44

  1. pmc Strategies for metagenomic-guided whole-community proteomics of complex microbial environments
    Brandi L Cantarel
    Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
    PLoS ONE 6:e27173. 2011
    ..In summary, we find that high mass accuracy peptide measurements searched against non-assembled reads from DNA sequencing of the same samples significantly increased identifiable proteins without sacrificing accuracy...
  2. pmc Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress
    Shihui Yang
    Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
    BMC Genomics 13:336. 2012
    ..thermocellum is relatively sensitive to ethanol compared to ethanologenic microorganisms such as yeast and Zymomonas mobilis that are used in industrial fermentations but do not possess native enzymes for industrial cellulose hydrolysis...
  3. pmc Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities
    Robert L Hettich
    Oak Ridge National Laboratory, Oak Ridge, TN 37831 6131, USA
    Anal Chem 85:4203-14. 2013
    ..To this end, metaproteomics exploits the power of high-performance mass spectrometry for extensive characterization of the complete suite of proteins expressed by a microbial community in an environmental sample. ..
  4. doi request reprint Microbial metaproteomics: identifying the repertoire of proteins that microorganisms use to compete and cooperate in complex environmental communities
    Robert L Hettich
    Oak Ridge National Laboratory, Oak Ridge, TN 37831 6131, USA
    Curr Opin Microbiol 15:373-80. 2012
    ..This is the realm of metaproteomics-the characterization of the complement of proteins expressed by a microbial community in an environmental sample...
  5. pmc Proteomics reveals a core molecular response of Pseudomonas putida F1 to acute chromate challenge
    Dorothea K Thompson
    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
    BMC Genomics 11:311. 2010
    ..putida strain F1 was characterized within the context of two disparate nutritional environments: rich (LB) media and minimal (M9L) media containing lactate as the sole carbon source...
  6. pmc A high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry
    Chongle Pan
    Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
    BMC Bioinformatics 11:118. 2010
    ..The improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms...
  7. ncbi request reprint Formation and characterization of iron-oligonucleotide complexes with matrix-assisted laser desorption/ionization fourier transform ion cyclotron resonance mass spectrometry
    R L Hettich
    Chemical and Analytical Sciences Division, Oak Ridge National Laboratory, Tennessee 37831 6365, USA
    J Am Soc Mass Spectrom 10:941-9. 1999
    ..These results suggest that iron may serve as a useful probe for characterizing phosphorylated biomolecules...
  8. ncbi request reprint 53rd American Society for Mass Spectrometry Conference. 5-9 June, 2005, Henry B Gonzalez Conference Center, San Antonio, TX, USA
    Robert L Hettich
    Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 6131, USA
    Expert Rev Proteomics 2:459-61. 2005
  9. ncbi request reprint Characterization of the 70S Ribosome from Rhodopseudomonas palustris using an integrated "top-down" and "bottom-up" mass spectrometric approach
    Michael Brad Strader
    Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, Tennessee 37831 6131, USA
    J Proteome Res 3:965-78. 2004
    ..To our knowledge, this is the most comprehensive protein complex analysis to date that integrates two MS techniques...
  10. ncbi request reprint Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics
    Chongle Pan
    Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Mol Cell Proteomics 7:938-48. 2008
    ..The integrated gene expression data provided strong support for the non-beta-oxidation route in R. palustris. A putative gene was proposed for every step in the non-beta-oxidation route...
  11. ncbi request reprint ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation
    Chongle Pan
    Chemical Sciences Division, Computational Biology Institute, Genome Science and Technology Graduate School, Oak Ridge National Laboratory University of Tennessee, Oak Ridge, Tennessee 37830, USA
    Anal Chem 78:7121-31. 2006
    ..The profile likelihood algorithm was integrated into a quantitative proteomics program, called ProRata, freely available at www.MSProRata.org...
  12. doi request reprint Systems biology: Functional analysis of natural microbial consortia using community proteomics
    Nathan C Verberkmoes
    Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Nat Rev Microbiol 7:196-205. 2009
    ..We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities...
  13. doi request reprint Comparative temporal proteomics of a response regulator (SO2426)-deficient strain and wild-type Shewanella oneidensis MR-1 during chromate transformation
    Karuna Chourey
    Environmental Sciences Division, Oak Ridge National Laboratory, Tennessee 37831, USA
    J Proteome Res 8:59-71. 2009
    ..In addition, the proteome data sets were mined for amino acids with potential post-translational modifications (PTMs) indicative of a level of gene expression regulation extending beyond the transcriptional control imposed by SO2426...
  14. pmc Phenotype fingerprinting suggests the involvement of single-genotype consortia in degradation of aromatic compounds by Rhodopseudomonas palustris
    Tatiana V Karpinets
    Computational Biology Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
    PLoS ONE 4:e4615. 2009
    ..This subpopulation in the consortium was confirmed in an independent experiment by consumption of dissolved nitrogen gas under the benzoate degrading conditions...
  15. ncbi request reprint Detecting differential and correlated protein expression in label-free shotgun proteomics
    Bing Zhang
    Computer Science and Mathematics Division, Computational Biology Institute, Chemical Science Division, and Life Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    J Proteome Res 5:2909-18. 2006
    ....
  16. doi request reprint PTMSearchPlus: software tool for automated protein identification and post-translational modification characterization by integrating accurate intact protein mass and bottom-up mass spectrometric data searches
    Vilmos Kertesz
    Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, Tennessee 37831 6131, USA
    Anal Chem 81:8387-95. 2009
    ..Namely, AIPM data can confirm that no PTM peptides were missed in a BU search, while the BU search determines the location of the PTM. This information is not available using an AIPM search alone...
  17. ncbi request reprint DBDigger: reorganized proteomic database identification that improves flexibility and speed
    David L Tabb
    Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 6164, USA
    Anal Chem 77:2464-74. 2005
    ..We describe the implementation of these innovations in the hope that other researchers will employ them for rapid and highly flexible proteomic database search...
  18. ncbi request reprint Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states
    Nathan C Verberkmoes
    Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    J Proteome Res 5:287-98. 2006
    ..Proteins known to be associated with specialized growth states such as nitrogen fixation, photoautotrophic, or growth on benzoate, were observed to be up-regulated under those states...
  19. ncbi request reprint MASPIC: intensity-based tandem mass spectrometry scoring scheme that improves peptide identification at high confidence
    Chandrasegaran Narasimhan
    Graduate School of Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, 37830 8026, USA
    Anal Chem 77:7581-93. 2005
    ..All these investigations show MASPIC to be a versatile and reliable system for peptide tandem mass spectral identification...
  20. ncbi request reprint Molecular dynamics of the Shewanella oneidensis response to chromate stress
    Steven D Brown
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
    Mol Cell Proteomics 5:1054-71. 2006
    ....
  21. ncbi request reprint Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics
    Chongle Pan
    Computational Biology Institute, Chemical Sciences Division, Oak Ridge National Laboratory University of Tennessee, Oak Ridge, Tennessee 37830, USA
    Anal Chem 78:7110-20. 2006
    ..We demonstrate that the profile signal-to-noise ratio is inversely correlated with the variability and bias of peptide abundance ratio estimation...
  22. pmc Transcriptomic and proteomic characterization of the Fur modulon in the metal-reducing bacterium Shewanella oneidensis
    Xiu Feng Wan
    Environmental Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, TN 37831 6038, USA
    J Bacteriol 186:8385-400. 2004
    ....
  23. ncbi request reprint A computational method for assessing peptide- identification reliability in tandem mass spectrometry analysis with SEQUEST
    Jane Razumovskaya
    Life Sciences Division, Oak Ridge National Laboratory, TN, USA
    Proteomics 4:961-9. 2004
    ..This method improves the sensitivity and specificity of peptide identification compared to the standard filtering procedure used in the SEQUEST package, and provides a basis for estimating the reliability of protein identifications...
  24. doi request reprint Shotgun metaproteomics of the human distal gut microbiota
    Nathan C Verberkmoes
    Oak Ridge National Laboratory, Chemical and Life Sciences Divisions, Oak Ridge, TN, USA
    ISME J 3:179-89. 2009
    ..Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes...
  25. ncbi request reprint Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra
    David L Tabb
    Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37232 8575, USA
    J Am Soc Mass Spectrom 17:903-15. 2006
    ..The strategy outlined in this paper should be generally applicable to mass spectra obtained from any instrument capable of isotopic resolution...
  26. ncbi request reprint Characterization of pII family (GlnK1, GlnK2, and GlnB) protein uridylylation in response to nitrogen availability for Rhodopseudomonas palustris
    Heather M Connelly
    Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, TN 37831, USA
    Anal Biochem 357:93-104. 2006
    ..palustris...
  27. ncbi request reprint Integrating 'top-down" and "bottom-up" mass spectrometric approaches for proteomic analysis of Shewanella oneidensis
    Nathan C Verberkmoes
    Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, P O Box 2008, Oak Ridge, Tennessee 37831 6365, USA
    J Proteome Res 1:239-52. 2002
    ..A total of 868 proteins from virtually every functional class, including hypotheticals, were identified from this organism...
  28. doi request reprint Development of an electrochemical oxidation method for probing higher order protein structure with mass spectrometry
    Carlee McClintock
    Graduate School of Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, Tennessee 37830, USA
    Anal Chem 80:3304-17. 2008
    ..Our results indicate that electrochemical oxidation using a boron-doped diamond electrode has the potential to become a useful and easily accessible tool for conducting oxidative surface mapping experiments...
  29. ncbi request reprint Analysis of protein solvent accessible surfaces by photochemical oxidation and mass spectrometry
    Joshua S Sharp
    Graduate School of Genome Science and Technology, The University of Tennessee Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830 8026, USA
    Anal Chem 76:672-83. 2004
    ....
  30. ncbi request reprint Protein surface mapping by chemical oxidation: structural analysis by mass spectrometry
    Joshua S Sharp
    Graduate School of Genome Science and Technology, The University of Tennessee Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830 8026, USA
    Anal Biochem 313:216-25. 2003
    ..Our results indicate that all oxidized amino acids, with the exception of methionine, have highly solvent-accessible side chains, but the rate of oxidation may not be dictated solely by solvent accessibility and amino acid identity...
  31. ncbi request reprint Intact protein analysis for site-directed mutagenesis overexpression products: plasmid-encoded R67 dihydrofolate reductase
    Nathan C Verberkmoes
    Organic and Biological Mass Spectrometry Group, Oak Ridge National Laboratory, Building 5510, Oak Ridge, TN 37831 6365, USA
    Anal Biochem 305:68-81. 2002
    ..The ion/ion reaction approach achieved the same results as the proteolytic-digestion-based methodology in a much shorter analysis time...
  32. pmc Global molecular and morphological effects of 24-hour chromium(VI) exposure on Shewanella oneidensis MR-1
    Karuna Chourey
    Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
    Appl Environ Microbiol 72:6331-44. 2006
    ....
  33. ncbi request reprint Multipole-storage-assisted dissociation for the characterization of large proteins and simple protein mixtures by ESI-FTICR-MS
    Chongle Pan
    Genome Science and Technology Graduate School, Oak Ridge National Laboratory University of Tennessee, Oak Ridge, Tennessee 37831 6131, USA
    Anal Chem 77:3072-82. 2005
    ..This presents a novel way to interrogate the identities of these fragment ions as well as obtain amino acid sequence tag information that can be used to identify proteins from mixtures...
  34. ncbi request reprint A graph-theoretic approach for the separation of b and y ions in tandem mass spectra
    Bo Yan
    Computational Systems Biology Laboratory, Department of Biochemical and Molecular Biology, University of Georgia, Athens, GA 30602, USA
    Bioinformatics 21:563-74. 2005
    ....
  35. ncbi request reprint Mass spectrometric approaches for characterizing bacterial proteomes
    Nathan C Verberkmoes
    Genome Science and Technology Graduate School, University of Tennessee, Knoxville, TN 37996, USA
    Expert Rev Proteomics 1:433-47. 2004
    ..This level of global protein information about an organism such as a bacterium can be combined with genomic and metabolomic data to enable a systems biology approach for understanding how these organisms live and function...
  36. ncbi request reprint Community proteomics of a natural microbial biofilm
    Rachna J Ram
    Department of Environmental Science, Policy, and Management, University of California at Berkeley, Berkeley, CA 94720, USA
    Science 308:1915-20. 2005
    ..We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation...
  37. doi request reprint Systematic assessment of the benefits and caveats in mining microbial post-translational modifications from shotgun proteomic data: the response of Shewanella oneidensis to chromate exposure
    Melissa R Thompson
    Graduate School of Genome Science and Technology, Oak Ridge National Laboratory and University of Tennessee, Knoxville, Tennessee 37830, USA
    J Proteome Res 7:648-58. 2008
    ..As a demonstration of this approach, a number of S. oneidensis chemotaxis proteins as well as low-abundance signal transduction proteins were identified as being post-translationally modified in response to chromate challenge...
  38. ncbi request reprint Implications of strain- and species-level sequence divergence for community and isolate shotgun proteomic analysis
    Vincent J Denef
    Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
    J Proteome Res 6:3152-61. 2007
    ..4% reduction of the initial protein coverage per 1% amino acid divergence and total identification loss at 86% AAI. Consequently, shotgun proteomics is capable of cross-strain identifications but avoids most cross-species false positives...
  39. ncbi request reprint Dosage-dependent proteome response of Shewanella oneidensis MR-1 to acute chromate challenge
    Melissa R Thompson
    Graduate School of Genome Science and Technology, Oak Ridge National Laboratory University of Tennessee Knoxville, Tennessee 37830, USA
    J Proteome Res 6:1745-57. 2007
    ..The results presented in this work demonstrate the dynamic dosage response of S. oneidensis to sub-toxic levels of chromate...
  40. ncbi request reprint Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
    Ian Lo
    University of California, Berkeley, California 94720, USA
    Nature 446:537-41. 2007
    ....
  41. doi request reprint Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal
    Paul Wilmes
    Department of Earth and Planetary Sciences, University of California at Berkeley, Berkeley, CA 94720, USA
    ISME J 2:853-64. 2008
    ....
  42. doi request reprint Cytochrome 572 is a conspicuous membrane protein with iron oxidation activity purified directly from a natural acidophilic microbial community
    Chris Jeans
    Chemistry Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
    ISME J 2:542-50. 2008
    ..Due to its abundance, cellular location and Fe(2+) oxidation activity at very low pH, we propose that Cyt(572) provides a critical function for fitness within the ecological niche of these acidophilic microbial communities...
  43. ncbi request reprint Comparison of sustained off-resonance irradiation collisionally activated dissociation and multipole storage-assisted dissociation for top-down protein analysis
    Karin M Keller
    Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin Texas 78712 0165, USA
    J Mass Spectrom 39:402-11. 2004
    ..e. those occurring at D and P residues) just as well as SORI, which implies that MSAD data may be somewhat more compatible with search algorithms that utilize unprocessed fragment ion masses...
  44. ncbi request reprint Proteogenomic approaches for the molecular characterization of natural microbial communities
    Jillian F Banfield
    Department of Earth and Planetary Science, and Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
    OMICS 9:301-33. 2005
    ....

Research Grants4

  1. Protein Surface Mapping: Experimentation and Computation
    Robert Hettich; Fiscal Year: 2005
    ..At present, this experimental capability is non-existent. ..
  2. Protein Surface Mapping: Experimentation and Computation
    Robert Hettich; Fiscal Year: 2007
    ..At present, this experimental capability is non-existent. ..
  3. Protein Surface Mapping: Experimentation and Computation
    Robert Hettich; Fiscal Year: 2006
    ..At present, this experimental capability is non-existent. ..