TY - JOUR

T1 - Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology

AU - Hansen, Fynn M

AU - Tanzer, Maria C

AU - Brüning, Franziska

AU - Bludau, Isabell

AU - Stafford, Che

AU - Schulman, Brenda A

AU - Robles, Maria S

AU - Karayel, Ozge

AU - Mann, Matthias

PY - 2021/1/11

Y1 - 2021/1/11

N2 - 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.

AB - 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.

KW - Circadian Rhythm/physiology

KW - HEK293 Cells

KW - Humans

KW - Peptide Library

KW - Proteome/metabolism

KW - Proteomics

KW - Reproducibility of Results

KW - Signal Transduction

KW - Tumor Necrosis Factor-alpha/metabolism

KW - Ubiquitin/metabolism

KW - Ubiquitination

U2 - 10.1038/s41467-020-20509-1

DO - 10.1038/s41467-020-20509-1

M3 - Journal article

C2 - 33431886

VL - 12

SP - 254

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

ER -