Ubiquitin Proteomics
Ubiquitin Proteomics
What Is Ubiquitination and Why Is Ubiquitin Proteomics Important?
MetwareBio’s Ubiquitination Proteomics Service leverages cutting-edge label-free LC-MS/MS technology to deliver high-resolution, quantitative profiling of ubiquitination modifications. Our platform enables precise identification and quantification of ubiquitination sites on target proteins, offering researchers deep insights into post-translational regulatory mechanisms and dynamic protein networks. This service is ideally suited for applications in mechanistic studies, drug target validation, and biomarker discovery, empowering translational research in oncology, neuroscience, immunology, and beyond.
The cycle of ubiquitin signaling and ubiquitin proteoforms. (A) The ubiquitin-proteasome system (UPS). (B) The various forms of ubiquitylation (Sun and Zhang, 2022)
Why Choose MetwareBio for Ubiquitinomics?
Ubiquitin Proteomics Workflow Using LC-MS/MS
Enrichment
Detection
Ubiquitin Proteomics Service Deliverables
Applications of Ubiquitination Analysis in Research
Ubiquitination is critically involved in the regulation of key disease pathways, including tumor progression, neurodegenerative disorders, and chronic inflammation. Abnormal ubiquitin signaling can lead to dysregulated protein degradation and impaired immune responses. Quantitative ubiquitinomics enables precise mapping of disease-associated ubiquitination events, facilitating the discovery of biomarkers, therapeutic targets, and novel mechanisms in cancer biology, neuroscience, and immunology.
In model organisms such as mice, zebrafish, and Drosophila, ubiquitination governs essential biological processes including development, immune regulation, and cellular homeostasis. Ubiquitinomics in animal studies supports functional exploration of signaling pathways, protein turnover, and gene regulation in both physiological and disease models. This approach provides valuable insights for in vivo validation, drug efficacy assessment, and genetic functional studies.
Microbes utilize ubiquitin-like pathways to regulate stress adaptation, protein degradation, and virulence factor expression. In host–pathogen interactions, many pathogens actively manipulate host ubiquitination to evade immune responses or enhance infection. Ubiquitination profiling in microbial or infection models reveals critical molecular interactions and supports research in pathogenesis, antimicrobial resistance, and vaccine development.
Ubiquitination is a key regulatory mechanism in plant development, hormone signaling, and stress response to environmental factors such as drought, salinity, and pathogen attack. In environmental biology, it also plays a role in organismal adaptation to complex habitats. Ubiquitinomics enables comprehensive analysis of protein regulation networks, supporting functional genomics, crop improvement, and ecological adaptation research.
Sample Requirements for Ubiquitination Analysis
We accept a variety of sample types. Recommended sample inputs:
| Category | Sample Type | Recommended Sample Size | Minimum Sample Size |
| Animal Tissue | Normal Tissues, Red Bone Marrow, Soft-bodied Insects | 100mg | 50mg |
| Chitinous Insects | 2 g | 1g | |
| Yellow Bone Marrow | 200mg | 100mg | |
| Plant Tissue | Young Leaves, Petals, Callus) | 1g | 500mg |
| Mature leaves, Stems, Algae, Macrofungi | 2g | 1g | |
| Bark, Roots, and Fruits | 5g | 3g | |
| Bioliquid | Amniotic Fluid, milk | 600μL | 300μL |
| Cell | Primary Cells | 2×10^7 | \ |
| Sperm, Platelets | 4×10^8 | 2×10^8 | |
| Passaged Cells | 2×10^7 | \ | |
| Microorganism | Bacteria | 500mg | 200mg |
| Fungi | 1g | 500mg | |
| Protein | Protein Solution | 5mg | 3mg |
- At least 3 biological replicates are recommended. For animal models, 3–6 subjects are suggested; for clinical samples, 6–10 cases are advised.
- Please refer to our Sample Preparation Handbook and Sample Submission Guidelines for detailed instructions, or contact us for customized support.
FAQ on Ubiquitin Proteomics and Ubiquitination Analysis
Ubiquitin is a small, 76-amino-acid protein that is highly conserved across eukaryotes. It serves as a regulatory tag that is covalently attached to lysine residues on substrate proteins. This modification controls protein degradation, signaling, trafficking, and cellular localization. Ubiquitin can be attached as a single molecule (monoubiquitination) or form polyubiquitin chains through linkage at different lysine residues (e.g., K48, K63), each conveying distinct cellular messages.
Ubiquitination is catalyzed through a sequential three-enzyme cascade involving: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, and E3 ubiquitin ligases, which confer substrate specificity. Additionally, deubiquitinating enzymes (DUBs) remove ubiquitin moieties, adding reversibility and regulation to the system.
Ubiquitination most commonly occurs on lysine (K) residues of substrate proteins, although non-lysine ubiquitination (e.g., on serine, threonine, or cysteine) has been observed in rare cases. After trypsin digestion, ubiquitinated lysines are marked by a diglycine (diGly) remnant, which serves as a unique signature used for site-specific enrichment and LC-MS/MS detection.
The type of ubiquitin chain linkage determines the downstream fate of the substrate protein: K48-linked chains usually signal for proteasomal degradation, K63-linked chains are involved in non-proteolytic processes like signal transduction, endocytosis, and DNA repair. Other linkages (e.g., K6, K11, K27, K29, K33, M1) also mediate distinct regulatory outcomes and are being actively studied in functional ubiquitinomics.
After tryptic digestion, peptides containing ubiquitinated lysines retain a diglycine (Gly–Gly) remnant on the ε-amino group. This signature is recognized by anti-K-ε-GG antibodies, allowing for specific enrichment of ubiquitinated peptides prior to mass spectrometry. This step significantly increases the sensitivity and specificity of ubiquitination site detection.
Absolutely. Site-specific data can reveal regulatory hotspots, mutation-sensitive residues, or PTM-dependent signaling events. This information is invaluable for target validation, CRISPR editing design, and pathway modeling in both basic and translational research.
Reference
Sun, M., & Zhang, X. (2022). Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture. Cell & bioscience, 12(1), 126. https://doi.org/10.1186/s13578-022-00870-y
