Information

Related Research Units

Intellectual and Developmental Disabilities Research Center Research
Neurology Research
Steen Laboratory Research
F.M. Kirby Neurobiology Center

Research Overview

  • he development of novel and improved mass spectrometric and proteomic methods for the analysis of complex protein mixtures and the detailed characterization of proteins within these mixtures, including the analysis of post-translational protein modifications and the quantitation of protein abundances.
  • Development of instrument platforms for the detection and identification of disease-markers with special emphasis on pediatric diseases.
  • The use of mass spectrometry to identify mechanisms of cell cycle control during neurogenesis.
  • Development and applications of strategies to solve systems biological questions and problems at the proteome level. To achieve our goals we use proteomic and mass spectrometric technology in addition to biochemistry and molecular biology approaches, cell culture systems and animal models, including the mouse, the rat, and the African clawfrog.

 

Research Background

Judith Steen studied chemistry and biochemistry at the University of Toronto. She then studied mass spectrometry and cell biology under the mentorship of Peter Roepstorff (University of Southern Denmark) and Marc Kirschner (Harvard University), respectively.

 

Publications

  1. Chemogenomic analysis reveals key role for lysine acetylation in regulating Arc stability. Nat Commun. 2017 11 21; 8(1):1659. View Abstract
  2. Human iPSC-Derived Neuronal Model of Tau-A152T Frontotemporal Dementia Reveals Tau-Mediated Mechanisms of Neuronal Vulnerability. Stem Cell Reports. 2016 09 13; 7(3):325-340. View Abstract
  3. FLEXITau: Quantifying Post-translational Modifications of Tau Protein in Vitro and in Human Disease. Anal Chem. 2016 Apr 05; 88(7):3704-14. View Abstract
  4. Doublecortin-Like Kinases Promote Neuronal Survival and Induce Growth Cone Reformation via Distinct Mechanisms. Neuron. 2015 Nov 18; 88(4):704-19. View Abstract
  5. Injury-induced decline of intrinsic regenerative ability revealed by quantitative proteomics. Neuron. 2015 May 20; 86(4):1000-1014. View Abstract
  6. Quantitative comparison of a human cancer cell surface proteome between interphase and mitosis. EMBO J. 2015 Jan 13; 34(2):251-65. View Abstract
  7. Quantitative profiling of peptides from RNAs classified as noncoding. Nat Commun. 2014 Nov 18; 5:5429. View Abstract
  8. Basal activity of a PARP1-NuA4 complex varies dramatically across cancer cell lines. Cell Rep. 2014 Sep 25; 8(6):1808-1818. View Abstract
  9. Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J. 2014 Feb 18; 33(4):385-99. View Abstract
  10. Nonparametric Bayesian evaluation of differential protein quantification. J Proteome Res. 2013 Oct 04; 12(10):4556-65. View Abstract
  11. Diaminothiazoles modify Tau phosphorylation and improve the tauopathy in mouse models. J Biol Chem. 2013 Jul 26; 288(30):22042-56. View Abstract
  12. Gas2l3, a novel constriction site-associated protein whose regulation is mediated by the APC/C Cdh1 complex. PLoS One. 2013; 8(2):e57532. View Abstract
  13. SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra. Mol Cell Proteomics. 2013 Jun; 12(6):1735-40. View Abstract
  14. A classifier based on accurate mass measurements to aid large scale, unbiased glycoproteomics. Mol Cell Proteomics. 2013 Apr; 12(4):1017-25. View Abstract
  15. A non-parametric cutout index for robust evaluation of identified proteins. Mol Cell Proteomics. 2013 Mar; 12(3):807-12. View Abstract
  16. FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanisms. Nat Methods. 2012 Apr 08; 9(5):504-8. View Abstract
  17. Pleiotropic effects of miR-183~96~182 converge to regulate cell survival, proliferation and migration in medulloblastoma. Acta Neuropathol. 2012 Apr; 123(4):539-52. View Abstract
  18. A practical guide to the FLEXIQuant method. Methods Mol Biol. 2012; 893:295-319. View Abstract
  19. mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics. 2012 Jan; 11(1):O111.011379. View Abstract
  20. NMDA mediated contextual conditioning changes miRNA expression. PLoS One. 2011; 6(9):e24682. View Abstract
  21. A screen for regulators of survival of motor neuron protein levels. Nat Chem Biol. 2011 Jun 19; 7(8):544-52. View Abstract
  22. Interaction of survival of motor neuron (SMN) and HuD proteins with mRNA cpg15 rescues motor neuron axonal deficits. Proc Natl Acad Sci U S A. 2011 Jun 21; 108(25):10337-42. View Abstract
  23. libfbi: a C++ implementation for fast box intersection and application to sparse mass spectrometry data. Bioinformatics. 2011 Apr 15; 27(8):1166-7. View Abstract
  24. Estimating the confidence of peptide identifications without decoy databases. Anal Chem. 2010 Jun 01; 82(11):4314-8. View Abstract
  25. MGFp: an open Mascot Generic Format parser library implementation. J Proteome Res. 2010 May 07; 9(5):2762-3. View Abstract
  26. Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. Bioinformatics. 2010 Jun 15; 26(12):1535-41. View Abstract
  27. Phosphoproteomics. Wiley Interdiscip Rev Syst Biol Med. 2010 May-Jun; 2(3):255-276. View Abstract
  28. When less can yield more - Computational preprocessing of MS/MS spectra for peptide identification. Proteomics. 2009 Nov; 9(21):4978-84. View Abstract
  29. Computational protein profile similarity screening for quantitative mass spectrometry experiments. Bioinformatics. 2010 Jan 01; 26(1):77-83. View Abstract
  30. The mechanism and pattern of yolk consumption provide insight into embryonic nutrition in Xenopus. Development. 2009 May; 136(9):1539-48. View Abstract
  31. NITPICK: peak identification for mass spectrometry data. BMC Bioinformatics. 2008 Aug 28; 9:355. View Abstract
  32. Different phosphorylation states of the anaphase promoting complex in response to antimitotic drugs: a quantitative proteomic analysis. Proc Natl Acad Sci U S A. 2008 Apr 22; 105(16):6069-74. View Abstract
  33. Temporal variations of the postnatal rat urinary proteome as a reflection of systemic maturation. Proteomics. 2008 Mar; 8(5):1097-112. View Abstract
  34. Brain-specific phosphorylation of MeCP2 regulates activity-dependent Bdnf transcription, dendritic growth, and spine maturation. Neuron. 2006 Oct 19; 52(2):255-69. View Abstract
  35. Global methods for protein glycosylation analysis by mass spectrometry. Biochim Biophys Acta. 2006 Dec; 1764(12):1870-80. View Abstract
  36. A new hybrid electrospray Fourier transform mass spectrometer: design and performance characteristics. Rapid Commun Mass Spectrom. 2006; 20(2):259-66. View Abstract
  37. Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins. J Am Soc Mass Spectrom. 2005 Dec; 16(12):1985-99. View Abstract
  38. Phosphorylation analysis by mass spectrometry: myths, facts, and the consequences for qualitative and quantitative measurements. Mol Cell Proteomics. 2006 Jan; 5(1):172-81. View Abstract
  39. Stable isotope-free relative and absolute quantitation of protein phosphorylation stoichiometry by MS. Proc Natl Acad Sci U S A. 2005 Mar 15; 102(11):3948-53. View Abstract
  40. Using optimized collision energies and high resolution, high accuracy fragment ion selection to improve glycopeptide detection by precursor ion scanning. J Am Soc Mass Spectrom. 2003 Jul; 14(7):777-84. View Abstract
  41. Tome-1, a trigger of mitotic entry, is degraded during G1 via the APC. Cell. 2003 Apr 04; 113(1):101-13. View Abstract
  42. Toll and interleukin-1 receptor (TIR) domain-containing proteins in plants: a genomic perspective. Trends Plant Sci. 2002 Sep; 7(9):388-91. View Abstract
  43. A rapid screening method to monitor expression of recombinant proteins from various prokaryotic and eukaryotic expression systems using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Anal Biochem. 2002 Jun 15; 305(2):242-50. View Abstract
  44. Association of carbonic anhydrase with a Calvin cycle enzyme complex in Nicotiana tabacum. Planta. 1998 Feb; 204(2):177-82. View Abstract

Contact Judith A.J. Steen

Phone: 617-919-2450
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