ArticleNature communications2021
Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 2 of them syntheses that pooled it.
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The trial behind it
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Who cites it
68 citing papers in PubMed, 2 syntheses or guidelines pooled it, 124 citations in OpenAlex.
- Meta-analysis fails to show any correlation between protein abundance and ubiquitination changes.FEBS open bio · 2026Pooled it
- Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome.Journal of the American Society for Mass Spectrometry · 2024Pooled it
- RAF1 scaffold integrity shapes chemogenetic degradation outcomes in KRAS-driven lung cancer models.Life science alliance · 2026Article
- Ubiquitin signaling in tumor-associated macrophage reprogramming: mechanisms and therapeutic opportunities in cancers.Biomarker research · 2026Review
- UBA1 knockdown dysregulates UBA1-sensitive proteins and impairs muscle function in models of spinal muscular atrophy X-linked 2.Disease models & mechanisms · 2026Article
- Structural proteomics reveals that misfolded nascent proteins expose buried lysines for ubiquitination and rapid proteasomal degradation.Cell reports · 2026Article
- Mass spectrometry proteomics for studying mitostasis.Protein science : a publication of the Protein Society · 2026Review
- Global analysis of cancer cell responses to USP9X inhibition.The EMBO journal · 2026Article
- Identification of E3 ligase substrates and PROTAC-induced ubiquitylation sites using proximity-based identification of ubiquitin sites (PrIUS).Communications biology · 2026Article
- Computational Pipelines for Protein Ubiquitylation Analysis and Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integrative Omics Reveals Glutamine Catabolism-Driven Apoptotic Suppression in Monocytes upon Mechanical Unloading.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Decoding adult murine pancreatic islet cell diversity through cell type-resolved proteomics and phosphoproteomics.Communications biology · 2025Article
- The functional landscape of the human ubiquitinome.bioRxiv : the preprint server for biology · 2025Article
- Slice-PASEF: Maximising Ion Utilisation in LC-MS Proteomics.bioRxiv : the preprint server for biology · 2025Article
- The ribosome ubiquitination code: fine-tuning translation under stress.Trends in biochemical sciences · 2025Review
- Small Molecule-Induced Alterations of Protein Polyubiquitination Revealed by Mass-Spectrometric Ubiquitome Analysis.Angewandte Chemie (International ed. in English) · 2025Article
- The coming era of proteomics-driven precision medicine.National science review · 2025Review
- An accessible workflow for high-sensitivity proteomics using parallel accumulation-serial fragmentation (PASEF).Nature protocols · 2025Review
- The Molecular Toolbox for Linkage Type-Specific Analysis of Ubiquitin Signaling.Chembiochem : a European journal of chemical biology · 2025Review
- Analysis of p53-Independent Functions of the Mdm2-MdmX Complex Using Data-Independent Acquisition-Based Profiling.Proteomes · 2025Article
8 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.