ArticleAnalytical chemistry2017
Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry Enables Characterization of Branched Ubiquitin Chains in Cellulo.
Article in Analytical chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed.
- Emerging tools and methods to study cell signalling mediated by branched ubiquitin chains.Biochemical Society transactions · 2025Review
- UbiREAD deciphers proteasomal degradation code of homotypic and branched K48 and K63 ubiquitin chains.Molecular cell · 2025Article
- Programmed Cell Death Ligand as a Biomarker for Response to Immunotherapy: Contribution of Mass Spectrometry-Based Analysis.Cancers · 2025Review
- A new approach to RNA synthesis: immobilization of stably and functionally co-tethered promoter DNA and T7 RNA polymerase.Nucleic acids research · 2024Article
- Decoding Ubiquitin Modifications by Mass Spectrometry.Advances in experimental medicine and biology · 2024Review
- Biocompatible Lysine Protecting Groups for the Chemoenzymatic Synthesis of K48/K63 Heterotypic and Branched Ubiquitin Chains.ACS central science · 2023Article
- Proteomic approaches to study ubiquitinomics.Biochimica et biophysica acta. Gene regulatory mechanisms · 2023Review
- Quantitative Analysis of Diubiquitin Isomers Using Ion Mobility Mass Spectrometry.Journal of the American Society for Mass Spectrometry · 2023Article
- Neutron-encoded diubiquitins to profile linkage selectivity of deubiquitinating enzymes.Nature communications · 2023Article
- Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions.Methods in molecular biology (Clifton, N.J.) · 2023Review
- USP7 and SET9 Expression in The Oligospermic Human Semen: A Case-Control Study.International journal of fertility & sterility · 2022Article
- Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture.Cell & bioscience · 2022Review
- The E3 ubiquitin ligase HECTD1 contributes to cell proliferation through an effect on mitosis.Scientific reports · 2022Article
- The ubiquitin proteoform problem.Current opinion in chemical biology · 2021Review
- Proteasome in action: substrate degradation by the 26S proteasome.Biochemical Society transactions · 2021Review
- Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers.Cancers · 2021Review
- VPS34 K29/K48 branched ubiquitination governed by UBE3C and TRABID regulates autophagy, proteostasis and liver metabolism.Nature communications · 2021Article
- Emerging functions of branched ubiquitin chains.Cell discovery · 2021Review
- Proteasome-Bound UCH37/UCHL5 Debranches Ubiquitin Chains to Promote Degradation.Molecular cell · 2020Article
- Branched Ubiquitination: Detection Methods, Biological Functions and Chemical Synthesis.Molecules (Basel, Switzerland) · 2020Review
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
Ubiquitin (Ub) has a broad functional range that has been ascribed to the formation of an array of polymeric ubiquitin chains. Understanding the precise roles of ubiquitin chains, however, is difficult due to their complex chain topologies. Branched ubiquitin chains are particularly challenging, as multiple modifications on a single ubiquitin preclude the use of standard bottom-up proteomic approaches. Developing methods to overcome these challenges is crucial considering evidence suggesting branched chains regulate the stability of proteins. In this study, we employ Ubiquitin Chain Enrichment Middle-down Mass Spectrometry (UbiChEM-MS) to identify branched chains that cannot be detected using bottom-up proteomic methods. Specifically, we employ tandem ubiquitin binding entities (TUBEs) and the K29-selective Npl4 Zinc Finger 1 (NZF1) domain from the deubiquitinase TRABID to enrich for chains from human cells. Minimal trypsinolysis followed by high resolution mass spectrometric analysis reveals that Ub chain branching can indeed be detected using both Ub binding domains (UBDs) tested at endogenous levels. We find that ∼1% of chains isolated with TUBEs contain Ub branch points, with this value rising to ∼4% after proteasome inhibition. Electron-transfer dissociation (ETD) analysis indicates the presence of K48 in these branched chains. The use of the NZF1 domain reveals that ∼4% of the isolated chains contain branch points with no apparent dependence on proteasome inhibition. Our results demonstrate an effective strategy for detecting and characterizing the dynamics of branched conjugates under different cellular conditions.
Indexed as
Identifiers
What OpenQuestion holds
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.