Peter A DiMaggio

Summary

Affiliation: Princeton University
Country: USA

Publications

  1. pmc Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
    Peter A DiMaggio
    Department of Chemical Engineering, Princeton University, Princeton, NJ, USA
    BMC Bioinformatics 9:458. 2008
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. doi request reprint Descriptor-free molecular discovery in large libraries by adaptive substituent reordering
    Scott R McAllister
    Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
    Bioorg Med Chem Lett 18:5967-70. 2008
  9. 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
  10. 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

Collaborators

Detail Information

Publications16

  1. pmc Biclustering via optimal re-ordering of data matrices in systems biology: rigorous methods and comparative studies
    Peter A DiMaggio
    Department of Chemical Engineering, Princeton University, Princeton, NJ, USA
    BMC Bioinformatics 9:458. 2008
    ....
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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
    ....
  7. 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...
  8. doi request reprint Descriptor-free molecular discovery in large libraries by adaptive substituent reordering
    Scott R McAllister
    Department of Chemical Engineering, Princeton University, Princeton, NJ 08544, USA
    Bioorg Med Chem Lett 18:5967-70. 2008
    ....
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. pmc A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression
    Peter A DiMaggio
    Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 5263, USA
    Toxicol Sci 118:251-65. 2010
    ....
  14. pmc Selecting high quality protein structures from diverse conformational ensembles
    Ashwin Subramani
    Department of Chemical Engineering, Princeton University, Princeton, New Jersey, USA
    Biophys J 97:1728-36. 2009
    ..In a total of 1454 proteins, with an average of 1051 conformers per protein, the conformers selected by ICON are, on an average, in the top 3.5% of the conformers in the ensemble...
  15. 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...
  16. doi request reprint A hybrid method for peptide identification using integer linear optimization, local database search, and quadrupole time-of-flight or OrbiTrap tandem mass spectrometry
    Peter A DiMaggio
    Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544 5263, USA
    J Proteome Res 7:1584-93. 2008
    ..The comparative studies demonstrate the excellent peptide identification accuracy gained from combining the strengths of our de novo method, which is based on integer linear optimization, and database driven search methods...