Nathan C Verberkmoes

Summary

Affiliation: Oak Ridge National Laboratory
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. ncbi request reprint Expressed peptide tags: an additional layer of data for genome annotation
    Alon Savidor
    Graduate School of Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
    J Proteome Res 5:3048-58. 2006
  10. ncbi request reprint MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra
    David L Tabb
    Life Sciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee 37831, USA
    J Am Soc Mass Spectrom 16:1250-61. 2005

Collaborators

Detail Information

Publications28

  1. 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...
  2. 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...
  3. 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...
  4. 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
    ....
  5. 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...
  6. 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...
  7. 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...
  8. 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
    ....
  9. ncbi request reprint Expressed peptide tags: an additional layer of data for genome annotation
    Alon Savidor
    Graduate School of Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
    J Proteome Res 5:3048-58. 2006
    ..7% and 12.9% for P. ramorum and P. sojae, respectively) suggested modification to current gene calls or identified novel genes that were missed by the current genome annotation of these organisms...
  10. ncbi request reprint MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra
    David L Tabb
    Life Sciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee 37831, USA
    J Am Soc Mass Spectrom 16:1250-61. 2005
    ..This strategy is shown to be effective in reducing spectral counts by up to 20% in LC-MS/MS datasets from protein standard mixtures and proteomes, reducing database search times without a concomitant reduction in identified peptides...
  11. 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
    ....
  12. pmc Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease
    Alison R Erickson
    Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
    PLoS ONE 7:e49138. 2012
    ....
  13. 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...
  14. 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
    ....
  15. 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...
  16. ncbi request reprint Evaluation of "shotgun" proteomics for identification of biological threat agents in complex environmental matrixes: experimental simulations
    Nathan C Verberkmoes
    Graduate School of Genome Science and Technology, University of Tennessee Oak Ridge National Laboratory, 1060 Commerce Park, Oak Ridge, TN 37830 8026, USA
    Anal Chem 77:923-32. 2005
    ..This study points to the potential application of this technology for biological threat agent detection but highlights many areas of needed research before the technology will be useful in real world samples...
  17. 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...
  18. doi request reprint Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community
    Ryan S Mueller
    University of California, Berkeley, California 94720, USA
    Environ Microbiol 13:2279-92. 2011
    ..These findings provide unprecedented insight into the physiological changes that may result from competitive interactions within communities in natural environments...
  19. 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...
  20. 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...
  21. 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
    ....
  22. 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...
  23. 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
    ....
  24. 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...
  25. 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...
  26. 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...
  27. ncbi request reprint Synthesis and biophysical characterization of a multidomain peptide from a Saccharomyces cerevisiae G protein-coupled receptor
    Fred Naider
    Department of Chemistry, College of Staten Island and Institute for Macromolecular Assemblies, City University of New York, Staten Island, New York 10314, USA
    J Biol Chem 278:52537-45. 2003
    ..This study demonstrated that the tail of Ste2p can be used as a hydrophilic template to study transmembrane domain structure using techniques such as CD and NMR spectroscopy...
  28. 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...