Namrata D Udeshi

Summary

Publications

  1. doi request reprint Large-scale identification of ubiquitination sites by mass spectrometry
    Namrata D Udeshi
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 8:1950-60. 2013
  2. pmc Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments
    Namrata D Udeshi
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Mol Cell Proteomics 12:825-31. 2013
  3. pmc iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics
    Philipp Mertins
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Mol Cell Proteomics 11:M111.014423. 2012
  4. pmc Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition
    Namrata D Udeshi
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Mol Cell Proteomics 11:148-59. 2012
  5. pmc Integrated proteomic analysis of post-translational modifications by serial enrichment
    Philipp Mertins
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 10:634-7. 2013
  6. doi request reprint Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging
    Victoria Hung
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 55:332-41. 2014
  7. pmc An unbiased approach to identify endogenous substrates of "histone" deacetylase 8
    David E Olson
    Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the Science of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
    ACS Chem Biol 9:2210-6. 2014
  8. pmc Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry
    Amanda L Creech
    The Broad Institute of MIT and Harvard University, 415 Main St, Cambridge, MA 02142, United States
    Methods 72:57-64. 2015
  9. pmc Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming
    Amit Choudhary
    Society of Fellows, Harvard University, Cambridge, Massachusetts, United States of America Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS ONE 9:e95194. 2014
  10. pmc Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging
    Hyun Woo Rhee
    Department of Chemistry, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 339:1328-31. 2013

Collaborators

  • Philipp Mertins
  • Paul A Clemons
  • Shao En Ong
  • Mark A Rubin
  • Steven A Carr
  • Tanya Svinkina
  • Jacob D Jaffe
  • Hyun Woo Rhee
  • Sally E Peach
  • Amanda L Creech
  • Victoria Hung
  • David E Olson
  • Amit Choudhary
  • Jean Philippe P Theurillat
  • Peng Zou
  • Vamsi K Mootha
  • Alice Y Ting
  • Verena K Maier
  • Caitlin M Feeney
  • Jordan E Taylor
  • Xiaoyun Wu
  • Jeannie T Lee
  • Jesse S Boehm
  • Aravind Subramanian
  • Bridget K Wagner
  • Joshiawa Paulk
  • Marius Pop
  • Gilbert G Prive
  • Kaihui Hu He
  • Anna C Groner
  • Peter J Wild
  • Eleanor Howe
  • Levi A Garraway
  • Stuart L Schreiber
  • Doug Barker
  • Ted Natoli
  • Mirjam Blattner
  • Edward B Holson
  • Patrick McCarren
  • Florence F Wagner
  • Yan Ling Zhang
  • Carol A Fierke
  • Eric D Sullivan
  • Xiaodong Lu
  • Valentin Cracan
  • Holger Moch
  • Vlado Dancik
  • Jennifer P Gale
  • Stefan Kubicek
  • Carol Ann Pitcairn
  • Dina Fomina-Yadlin
  • Sylvan C Baca
  • Noah A Wolfson
  • Fanny Lazzaro
  • Wesley J Errington
  • Jeffrey D Martell
  • Emily L Rudomin

Detail Information

Publications12

  1. doi request reprint Large-scale identification of ubiquitination sites by mass spectrometry
    Namrata D Udeshi
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 8:1950-60. 2013
    ..After cell or tissue samples have been prepared for lysis, the described protocol can be completed in ∼5 d. ..
  2. pmc Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments
    Namrata D Udeshi
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Mol Cell Proteomics 12:825-31. 2013
    ..This refined and practical workflow enables routine identification and quantification of ∼20,000 distinct endogenous ubiquitination sites in a single SILAC experiment using moderate amounts of protein input...
  3. pmc iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics
    Philipp Mertins
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Mol Cell Proteomics 11:M111.014423. 2012
    ..Spike-in experiments using peptides of defined ratios in a background of nonregulated peptides show that iTRAQ quantification is less accurate but not as variable as mTRAQ quantification...
  4. pmc Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition
    Namrata D Udeshi
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Mol Cell Proteomics 11:148-59. 2012
    ..We attribute this finding to the low stoichiometry of the majority ubiquitination sites identified in this study...
  5. pmc Integrated proteomic analysis of post-translational modifications by serial enrichment
    Philipp Mertins
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Methods 10:634-7. 2013
    ....
  6. doi request reprint Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging
    Victoria Hung
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 55:332-41. 2014
    ..Our IMS proteome of 127 proteins has >94% specificity and includes nine newly discovered mitochondrial proteins. This approach will enable scientists to map proteomes of cellular regions that were previously inaccessible...
  7. pmc An unbiased approach to identify endogenous substrates of "histone" deacetylase 8
    David E Olson
    Stanley Center for Psychiatric Research, Proteomics Platform, Cancer Program, and Center for the Science of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
    ACS Chem Biol 9:2210-6. 2014
    ....
  8. pmc Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry
    Amanda L Creech
    The Broad Institute of MIT and Harvard University, 415 Main St, Cambridge, MA 02142, United States
    Methods 72:57-64. 2015
    ....
  9. pmc Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming
    Amit Choudhary
    Society of Fellows, Harvard University, Cambridge, Massachusetts, United States of America Center for the Science of Therapeutics, Broad Institute, Cambridge, Massachusetts, United States of America
    PLoS ONE 9:e95194. 2014
    ..Knock-down of these kinases in alpha cells resulted in expression of key beta-cell markers. These results provide evidence that perturbation of the kinome may be important for lineage reprogramming of alpha cells to beta cells. ..
  10. pmc Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging
    Hyun Woo Rhee
    Department of Chemistry, Massachusetts Institute of Technology MIT, Cambridge, MA 02139, USA
    Science 339:1328-31. 2013
    ..The specificity of peroxidase-mediated proteomic mapping in live cells, combined with its ease of use, offers biologists a powerful tool for understanding the molecular composition of living cells...
  11. pmc Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer
    Jean Philippe P Theurillat
    The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Harvard Medical School, Boston, MA 02115, USA Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Science 346:85-9. 2014
    ..DEK stabilization promoted prostate epithelial cell invasion, which implicated DEK as an oncogenic effector. More generally, these results provide a framework to decipher tumorigenic mechanisms linked to dysregulated ubiquitylation. ..
  12. pmc Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules
    Sally E Peach
    Broad Institute, Proteomics Platform, Cambridge, Massachusetts 02142, USA
    Mol Cell Proteomics 11:128-37. 2012
    ....