Benjamin A Garcia

Summary

Affiliation: Princeton University
Country: USA

Publications

  1. pmc Proteomic interrogation of human chromatin
    Mariana P Torrente
    Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 6:e24747. 2011
  2. pmc Quantitative proteomic approaches to studying histone modifications
    Barry M Zee
    415 Schultz Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Curr Chem Genomics 5:106-14. 2011
  3. pmc Methylation of H2AR29 is a novel repressive PRMT6 target
    Tanja Waldmann
    MPI for Immunobiology and Epigenetics, Stubeweg 51, 79108 Freiburg, Germany
    Epigenetics Chromatin 4:11. 2011
  4. pmc Histone H1 variant-specific lysine methylation by G9a/KMT1C and Glp1/KMT1D
    Thomas Weiss
    MPI for Immunobiology, , 79108 Freiburg, Germany
    Epigenetics Chromatin 3:7. 2010
  5. pmc Tissue-specific expression and post-translational modification of histone H3 variants
    Benjamin A Garcia
    Institute for Genomic Biology, Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Proteome Res 7:4225-36. 2008
  6. pmc Global turnover of histone post-translational modifications and variants in human cells
    Barry M Zee
    Department of Molecular Biology, Princeton University, Princeton NJ, 08544, USA
    Epigenetics Chromatin 3:22. 2010
  7. doi request reprint What does the future hold for Top Down mass spectrometry?
    Benjamin A Garcia
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    J Am Soc Mass Spectrom 21:193-202. 2010
  8. ncbi request reprint Mass spectrometric analysis of histone variants and post-translational modifications
    Benjamin A Garcia
    Department of Molecular Biology, Princeton University, Princeton, NJ, USA
    Front Biosci (Schol Ed) 1:142-53. 2009
  9. ncbi request reprint Organismal differences in post-translational modifications in histones H3 and H4
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
    J Biol Chem 282:7641-55. 2007
  10. pmc Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a
    Nicolas L Young
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    J Am Soc Mass Spectrom 21:960-70. 2010

Collaborators

Detail Information

Publications50

  1. pmc Proteomic interrogation of human chromatin
    Mariana P Torrente
    Department of Chemistry, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 6:e24747. 2011
    ....
  2. pmc Quantitative proteomic approaches to studying histone modifications
    Barry M Zee
    415 Schultz Laboratory, Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Curr Chem Genomics 5:106-14. 2011
    ..This review covers the latest developments in mass spectrometry for the analysis of histone PTMs, with the hope of inspiring the continued integration of proteomic, genomic and epigenetic research...
  3. pmc Methylation of H2AR29 is a novel repressive PRMT6 target
    Tanja Waldmann
    MPI for Immunobiology and Epigenetics, Stubeweg 51, 79108 Freiburg, Germany
    Epigenetics Chromatin 4:11. 2011
    ..abstract:..
  4. pmc Histone H1 variant-specific lysine methylation by G9a/KMT1C and Glp1/KMT1D
    Thomas Weiss
    MPI for Immunobiology, , 79108 Freiburg, Germany
    Epigenetics Chromatin 3:7. 2010
    ..To our knowledge, this is the first demonstration of variant-specific histone methylation by the same methyltransferases, but with differing downstream readers, thereby supporting the hypothesis of H1 variants having specific functions...
  5. pmc Tissue-specific expression and post-translational modification of histone H3 variants
    Benjamin A Garcia
    Institute for Genomic Biology, Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    J Proteome Res 7:4225-36. 2008
    ..H3.3 was hypermodified compared to H3.2 in some, but not all tissues. In addition, a novel rat testes-specific H3 protein was identified with this approach...
  6. pmc Global turnover of histone post-translational modifications and variants in human cells
    Barry M Zee
    Department of Molecular Biology, Princeton University, Princeton NJ, 08544, USA
    Epigenetics Chromatin 3:22. 2010
    ..Understanding turnover in the context of histone modifications and sequence variants could provide valuable additional insight into the function of histone replacement...
  7. doi request reprint What does the future hold for Top Down mass spectrometry?
    Benjamin A Garcia
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    J Am Soc Mass Spectrom 21:193-202. 2010
    ....
  8. ncbi request reprint Mass spectrometric analysis of histone variants and post-translational modifications
    Benjamin A Garcia
    Department of Molecular Biology, Princeton University, Princeton, NJ, USA
    Front Biosci (Schol Ed) 1:142-53. 2009
    ..Here the recent mass spectrometry based studies of histone variants and the characterization of their modifications is reviewed...
  9. ncbi request reprint Organismal differences in post-translational modifications in histones H3 and H4
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, USA
    J Biol Chem 282:7641-55. 2007
    ..Additionally, modification profiles of H4 acetylation were very similar among the organisms examined...
  10. pmc Collective mass spectrometry approaches reveal broad and combinatorial modification of high mobility group protein A1a
    Nicolas L Young
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    J Am Soc Mass Spectrom 21:960-70. 2010
    ..This report presents one of the most detailed analyses of HMGA1a to date and illustrates the strength of using a combined MS effort...
  11. pmc A novel approach for untargeted post-translational modification identification using integer linear optimization and tandem mass spectrometry
    Richard C Baliban
    Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544, USA
    Mol Cell Proteomics 9:764-79. 2010
    ..A protocol is finally developed for the analysis of a complete LC-MS/MS scan using template sequences generated from SEQUEST and is demonstrated on over 270,000 MS/MS spectra collected from a total chromatin digest...
  12. pmc In vivo residue-specific histone methylation dynamics
    Barry M Zee
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    J Biol Chem 285:3341-50. 2010
    ..Here we show that quantitative proteomic approaches such as this can determine the dynamics of multiple methylated residues, an understudied portion of histone biology...
  13. ncbi request reprint Modifications of human histone H3 variants during mitosis
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
    Biochemistry 44:13202-13. 2005
    ....
  14. ncbi request reprint Comprehensive phosphoprotein analysis of linker histone H1 from Tetrahymena thermophila
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
    Mol Cell Proteomics 5:1593-609. 2006
    ..Relative levels of site-specific phosphorylation on H1 isolated from growing and starved Tetrahymena were obtained using a combination of stable isotopic labeling, IMAC, and tandem mass spectrometry...
  15. pmc One-pot shotgun quantitative mass spectrometry characterization of histones
    Mariana D Plazas-Mayorca
    Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
    J Proteome Res 8:5367-74. 2009
    ..Our protocol significantly streamlines the analysis of histone PTMs and will allow for studies of differentially expressed PTMs between multiple samples during biologically relevant processes in a rapid and quantitative fashion...
  16. pmc Heterochromatin protein 1 is extensively decorated with histone code-like post-translational modifications
    Gary LeRoy
    Department Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Mol Cell Proteomics 8:2432-42. 2009
    ....
  17. pmc H4K20 methylation regulates quiescence and chromatin compaction
    Adam G Evertts
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544 Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129 Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104 Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, and Department of Biological Chemistry, David Geffen School of Medicine, Los Angeles, CA 90095
    Mol Biol Cell 24:3025-37. 2013
    ..The results suggest that the same lysine on H4K20 may, in its different methylation states, facilitate mitotic functions in M phase and promote chromatin compaction and cell cycle exit in quiescent cells...
  18. pmc A mixed integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed electron transfer dissociation tandem mass spectrometry
    Peter A DiMaggio
    Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544 5263, USA
    Mol Cell Proteomics 8:2527-43. 2009
    ..This new computational method will facilitate the unprecedented LC-MS/MS ETD analysis of many hypermodified proteins and offer novel biological insight into these previously understudied systems...
  19. pmc Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization
    Richard C Baliban
    Department of Chemical and Biological Engineering, Princeton University, Princeton, USA
    J Clin Periodontol 40:131-9. 2013
    ....
  20. pmc PILOT_PROTEIN: identification of unmodified and modified proteins via high-resolution mass spectrometry and mixed-integer linear optimization
    Richard C Baliban
    Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
    J Proteome Res 11:4615-29. 2012
    ..The algorithm demonstrates superior protein identification accuracy with a lower false positive rate. All materials are freely available to the scientific community at http://pumpd.princeton.edu...
  21. pmc High throughput characterization of combinatorial histone codes
    Nicolas L Young
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Mol Cell Proteomics 8:2266-84. 2009
    ....
  22. pmc Tandem mass spectrometry with ultrahigh mass accuracy clarifies peptide identification by database retrieval
    Michael T Boyne
    Department of Chemistry, University of Illinois at Urbana Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
    J Proteome Res 8:374-9. 2009
    ....
  23. ncbi request reprint Mild performic acid oxidation enhances chromatographic and top down mass spectrometric analyses of histones
    James J Pesavento
    Center for Biophysics and Computational Biology, Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Mol Cell Proteomics 6:1510-26. 2007
    ....
  24. pmc Revealing histone variant induced changes via quantitative proteomics
    Anna M Arnaudo
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Crit Rev Biochem Mol Biol 46:284-94. 2011
    ..In this review, we discuss the biology of histone variants and methods to characterize them using mass spectrometry-based proteomics...
  25. pmc Quantitative proteomics reveals direct and indirect alterations in the histone code following methyltransferase knockdown
    Mariana D Plazas-Mayorca
    Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
    Mol Biosyst 6:1719-29. 2010
    ..Our results provide new insights into the intra- and inter- histone cross-regulation of histone K9 methylation and its potential downstream gene targets...
  26. ncbi request reprint Characterization of histones and their post-translational modifications by mass spectrometry
    Benjamin A Garcia
    Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Curr Opin Chem Biol 11:66-73. 2007
    ..As chromatin biology demands, mass spectrometry has adapted and continues as a key technology for the analysis of gene regulation networks involving histone modifications...
  27. pmc Quantitative dynamics of the link between cellular metabolism and histone acetylation
    Adam G Evertts
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    J Biol Chem 288:12142-51. 2013
    ..The methods we describe can be broadly applied to defining the turnover of histone acetylation in other cell states such as during cellular reprogramming and to quantify non-histone protein acetylation dynamics...
  28. pmc Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples
    Richard C Baliban
    Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
    J Clin Periodontol 39:203-12. 2012
    ..To identify possible novel biomarkers in gingival crevicular fluid (GCF) samples from chronic periodontitis (CP) and periodontally healthy individuals using high-throughput proteomic analysis...
  29. ncbi request reprint Resetting the epigenetic histone code in the MRL-lpr/lpr mouse model of lupus by histone deacetylase inhibition
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
    J Proteome Res 4:2032-42. 2005
    ..These aberrant post-translational histone modifications can therefore be reset with histone deacetylase inhibition in vivo...
  30. ncbi request reprint Heavy methyl-SILAC labeling coupled with liquid chromatography and high-resolution mass spectrometry to study the dynamics of site-specific histone methylation
    Xing Jun Cao
    Department of Molecular Biology, Princeton University, Princeton, NJ, USA
    Methods Mol Biol 977:299-313. 2013
    ..In this chapter, we comprehensively describe the experimental strategy to determine the dynamics of multiple histone methylated residues including SILAC labeling, histone extraction/purification and mass spectrometry analysis...
  31. pmc Validation of protein acetylation by mass spectrometry
    Barry M Zee
    Department of Molecular Biology, Princeton University, Princeton, NJ, USA
    Methods Mol Biol 981:1-11. 2013
    ..Here we detail experimental and analytical procedures for the characterization of lysine acetylation on proteins in general and on histones in particular, which are among the most highly modified proteins in eukaryotic cells...
  32. pmc Global secretome analysis identifies novel mediators of bone metastasis
    Mario Andres Blanco
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Cell Res 22:1339-55. 2012
    ..Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets...
  33. pmc Origins and formation of histone methylation across the human cell cycle
    Barry M Zee
    Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
    Mol Cell Biol 32:2503-14. 2012
    ..In short, we have systematically characterized the temporal origins and methylation pathways for histone posttranslational modifications during the cell cycle...
  34. pmc Breaking the histone code with quantitative mass spectrometry
    Laura Mae P Britton
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Expert Rev Proteomics 8:631-43. 2011
    ..Here, we review the accomplishments of mass spectrometry in the histone field, and outline the future roadblocks that must be overcome for mass spectrometry-based proteomics to become the method of choice for chromatin biologists...
  35. doi request reprint The significance, development and progress of high-throughput combinatorial histone code analysis
    Nicolas L Young
    Department of Molecular Biology, Princeton University, 415 Schultz Laboratory, Princeton, NJ 08544, USA
    Cell Mol Life Sci 67:3983-4000. 2010
    ..Recently, progress has been made in determining such information quickly, quantitatively and sensitively. Here we review both the historical and recent progress toward routine and rapid combinatorial histone code analysis...
  36. ncbi request reprint The platelet microparticle proteome
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
    J Proteome Res 4:1516-21. 2005
    ....
  37. pmc Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation
    Yun Wu
    Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
    J Proteome Res 12:316-27. 2013
    ..Our findings provide new targets in a key telomerase regulatory protein for modulation of telomere dynamics...
  38. ncbi request reprint Pervasive combinatorial modification of histone H3 in human cells
    Benjamin A Garcia
    Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Nat Methods 4:487-9. 2007
    ....
  39. ncbi request reprint Chemical derivatization of histones for facilitated analysis by mass spectrometry
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
    Nat Protoc 2:933-8. 2007
    ..The protocol should take approximately 15-19 h to complete, including all chemical reactions, enzymatic digestion and mass spectrometry experiments...
  40. ncbi request reprint Analysis of protein phosphorylation by mass spectrometry
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
    Methods 35:256-64. 2005
    ..These strategies hold the potential for rapid and sensitive profiling of phosphoproteins from a variety of sources and cellular conditions...
  41. doi request reprint Systems-wide proteomic characterization of combinatorial post-translational modification patterns
    Nicolas L Young
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Expert Rev Proteomics 7:79-92. 2010
    ..This review will outline combinatorial PTM examples in biology, and the mass spectrometry-based techniques and applications utilized in the investigations of these combinatorial PTMs...
  42. ncbi request reprint Characterization of phosphorylation sites on histone H1 isoforms by tandem mass spectrometry
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
    J Proteome Res 3:1219-27. 2004
    ..The adjacent lysine residue to the phosphoserine was also shown to be methylated. This finding raises the question of whether the hypothesized "methyl/phos" switch could be extended to linker histones, and not exclusive to core histones...
  43. pmc Protein quantification across hundreds of experimental conditions
    Zia Khan
    Department of Computer Science, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
    Proc Natl Acad Sci U S A 106:15544-8. 2009
    ..We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates...
  44. ncbi request reprint Protein profile of osteoarthritic human articular cartilage using tandem mass spectrometry
    Benjamin A Garcia
    Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
    Rapid Commun Mass Spectrom 20:2999-3006. 2006
    ..It is believed that this type of proteomic analysis will aid future work centered on investigating the pathology of this and other related joint diseases...
  45. ncbi request reprint Discovery of lysine post-translational modifications through mass spectrometric detection
    Barry M Zee
    Department of Molecular Biology, Princeton University, Princeton, NJ 08540, U S A
    Essays Biochem 52:147-63. 2012
    ..This chapter provides a succinct overview of such methods for the characterization of protein lysine modifications as broadly classified, such as methylation and ubiquitination...
  46. pmc Modern approaches for investigating epigenetic signaling pathways
    Adam G Evertts
    Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    J Appl Physiol (1985) 109:927-33. 2010
    ....
  47. pmc Stable Isotope Labeling of Phosphoproteins for Large-scale Phosphorylation Rate Determination
    Rosalynn C Molden
    Department of Chemistry, Frick Laboratory, Princeton University, Princeton, New Jersey 08544
    Mol Cell Proteomics 13:1106-18. 2014
    ..The data have been deposited to the ProteomeXchange with the identifier PXD000680. ..
  48. pmc De novo peptide design and experimental validation of histone methyltransferase inhibitors
    James Smadbeck
    Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
    PLoS ONE 9:e90095. 2014
    ..The validated peptides are the first computationally designed peptides that directly inhibit EZH2. These inhibitors should prove useful for further chromatin biology investigations. ..
  49. pmc Branched tricarboxylic acid metabolism in Plasmodium falciparum
    Kellen L Olszewski
    Department of Molecular Biology and Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
    Nature 466:774-8. 2010
    ..These results significantly clarify our understanding of the Plasmodium metabolic network and highlight the ability of altered variants of central carbon metabolism to arise in response to unique environments...