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

Fynn M. Hansen, Maria C. Tanzer, Franziska Brüning, Isabell Bludau, Che Stafford, Brenda A. Schulman, Maria S. Robles (), Ozge Karayel () and Matthias Mann ()
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Fynn M. Hansen: Max Planck Institute of Biochemistry
Maria C. Tanzer: Max Planck Institute of Biochemistry
Franziska Brüning: Max Planck Institute of Biochemistry
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

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-020-20509-1

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