Ubiquitination serves as a key regulatory mechanism in nearly all cellular processes, though it was originally identified as a post-translational modification that targets proteins for degradation. Accordingly, these two molecular events have since been tightly linked, and changes in protein abundance are frequently interpreted as indirect indicators of ubiquitination dynamics. Nevertheless, the relationship between protein abundance and ubiquitination has not been systematically examined across distinct biological systems. Here, we conducted a comprehensive meta-analysis to assess the correlation between protein abundance and ubiquitination levels determined by mass spectrometry in mammals, plants, and yeast. Quantitative proteomics and diGly-ubiquitin peptides data from 19 independent studies encompassing over 50 experimental conditions were analyzed. The findings indicate that alterations in protein abundance cannot reliably be used to infer ubiquitination events - and vice versa - highlighting the need for caution when interpreting proteomic data as a proxy for ubiquitin-mediated regulation.
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| Evidence ID | Analyze ID | Gene/Complex | Systematic Name/Complex Accession | Qualifier | Gene Ontology Term ID | Gene Ontology Term | Aspect | Annotation Extension | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Phenotype | Experiment Type | Experiment Type Category | Mutant Information | Strain Background | Chemical | Details | Reference |
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| Evidence ID | Analyze ID | Gene | Gene Systematic Name | Disease Ontology Term | Disease Ontology Term ID | Qualifier | Evidence | Method | Source | Assigned On | Reference |
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| Evidence ID | Analyze ID | Regulator | Regulator Systematic Name | Target | Target Systematic Name | Direction | Regulation of | Happens During | Regulator Type | Direction | Regulation Of | Happens During | Method | Evidence | Strain Background | Reference |
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| Site | Modification | Modifier | Source | Reference |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Allele | Assay | Annotation | Action | Phenotype | SGA score | P-value | Source | Reference | Note |
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| Evidence ID | Analyze ID | Interactor | Interactor Systematic Name | Interactor | Interactor Systematic Name | Assay | Annotation | Action | Modification | Source | Reference | Note |
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| Complement ID | Locus ID | Gene | Species | Gene ID | Strain background | Direction | Details | Source | Reference |
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| Evidence ID | Analyze ID | Dataset | Description | Keywords | Number of Conditions | Reference |
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