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Mapping intact protein isoforms in discovery mode using top-down proteomics

Author

Listed:
  • John C. Tran

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Leonid Zamdborg

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign)

  • Dorothy R. Ahlf

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Ji Eun Lee

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Doping Control Center and Center for Theragnosis, Korea Institute of Science and Technology)

  • Adam D. Catherman

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Kenneth R. Durbin

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Jeremiah D. Tipton

    (Northwestern University)

  • Adaikkalam Vellaichamy

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Present addresses: Department of Nanomedicine, The Methodist Hospital Research Institute, Houston, Texas 77030, USA (A.V.) ; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA (N.S.).)

  • John F. Kellie

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Mingxi Li

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Cong Wu

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign)

  • Steve M. M. Sweet

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Bryan P. Early

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Nertila Siuti

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Present addresses: Department of Nanomedicine, The Methodist Hospital Research Institute, Houston, Texas 77030, USA (A.V.) ; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA (N.S.).)

  • Richard D. LeDuc

    (University of Wisconsin-Madison)

  • Philip D. Compton

    (Northwestern University)

  • Paul M. Thomas

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

  • Neil L. Kelleher

    (and the Institute for Genomic Biology, University of Illinois at Urbana-Champaign
    Northwestern University)

Abstract

Intact proteins yield to proteomics Conventional 'bottom-up' proteomics, in which mass spectrometry is used to analyse peptide mixtures made by tryptic digestion of target proteins, is a powerful way of characterizing complex proteomes. However, the technique has limitations when considering different protein isoforms and combinations of post-translational modifications. The 'top-down' approach is generally thought to be impractical because of the limitations of mass spectrometry and difficulties with automation. A new top-down system presented here avoids these problems by using a four-dimensional separation system that achieves greater proteome coverage than conventional methods. A proof-of-principle experiment shows that the method is capable of identifying previously undetected isoforms and isoform-specific post-translational modifications caused by cellular senescence.

Suggested Citation

  • John C. Tran & Leonid Zamdborg & Dorothy R. Ahlf & Ji Eun Lee & Adam D. Catherman & Kenneth R. Durbin & Jeremiah D. Tipton & Adaikkalam Vellaichamy & John F. Kellie & Mingxi Li & Cong Wu & Steve M. M., 2011. "Mapping intact protein isoforms in discovery mode using top-down proteomics," Nature, Nature, vol. 480(7376), pages 254-258, December.
    • Handle: RePEc:nat:nature:v:480:y:2011:i:7376:d:10.1038_nature10575
    DOI: 10.1038/nature10575
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    Cited by:

    1. Emily A. Chapman & David S. Roberts & Timothy N. Tiambeng & Jãán Andrews & Man-Di Wang & Emily A. Reasoner & Jake A. Melby & Brad H. Li & Donguk Kim & Andrew J. Alpert & Song Jin & Ying Ge, 2023. "Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    2. Xijun Wang & Aihua Zhang & Guangli Yan & Wenjun Sun & Ying Han & Hui Sun, 2013. "Metabolomics and Proteomics Annotate Therapeutic Properties of Geniposide: Targeting and Regulating Multiple Perturbed Pathways," PLOS ONE, Public Library of Science, vol. 8(8), pages 1-9, August.

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