IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-020-20509-1.html
   My bibliography  Save this article

Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

Author

Listed:
  • Fynn M. Hansen

    (Max Planck Institute of Biochemistry)

  • Maria C. Tanzer

    (Max Planck Institute of Biochemistry)

  • Franziska Brüning

    (Max Planck Institute of Biochemistry
    Faculty of Medicine, LMU)

  • Isabell Bludau

    (Max Planck Institute of Biochemistry)

  • Che Stafford

    (Ludwig-Maximilians-Universität München)

  • Brenda A. Schulman

    (Max Planck Institute of Biochemistry)

  • Maria S. Robles

    (Faculty of Medicine, LMU)

  • Ozge Karayel

    (Max Planck Institute of Biochemistry)

  • Matthias Mann

    (Max Planck Institute of Biochemistry)

Abstract

Protein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent acquisition (DIA) with regards to sensitivity in single run analysis and data completeness have not yet been explored. Here, we develop a sensitive workflow combining diGly antibody-based enrichment and optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identifies 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells – double the number and quantitative accuracy of data dependent acquisition. Applied to TNF signaling, the workflow comprehensively captures known sites while adding many novel ones. An in-depth, systems-wide investigation of ubiquitination across the circadian cycle uncovers hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting new connections between metabolism and circadian regulation.

Suggested Citation

  • Fynn M. Hansen & Maria C. Tanzer & Franziska Brüning & Isabell Bludau & Che Stafford & Brenda A. Schulman & Maria S. Robles & Ozge Karayel & Matthias Mann, 2021. "Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20509-1
    DOI: 10.1038/s41467-020-20509-1
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-020-20509-1
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-020-20509-1?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Yi Yang & Qun Fang, 2024. "Prediction of glycopeptide fragment mass spectra by deep learning," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    2. Rongfeng Huang & Jianghui Chen & Meiyu Zhou & Haoran Xin & Sin Man Lam & Xiaoqing Jiang & Jie Li & Fang Deng & Guanghou Shui & Zhihui Zhang & Min-Dian Li, 2023. "Multi-omics profiling reveals rhythmic liver function shaped by meal timing," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    3. Liam C. Hunt & Vishwajeeth Pagala & Anna Stephan & Boer Xie & Kiran Kodali & Kanisha Kavdia & Yong-Dong Wang & Abbas Shirinifard & Michelle Curley & Flavia A. Graca & Yingxue Fu & Suresh Poudel & Yuxi, 2023. "An adaptive stress response that confers cellular resilience to decreased ubiquitination," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    4. Ulises H. Guzman & Henriette Aksnes & Rasmus Ree & Nicolai Krogh & Magnus E. Jakobsson & Lars J. Jensen & Thomas Arnesen & Jesper V. Olsen, 2023. "Loss of N-terminal acetyltransferase A activity induces thermally unstable ribosomal proteins and increases their turnover in Saccharomyces cerevisiae," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20509-1. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.