Quantitative ubiquitinomics service provides a specialized solution for the precise identification, quantification, and characterization of ubiquitinated proteins within complex biological samples. MtoZ Biolabs integrates mass spectrometry-based ubiquitinomics solutions with advanced technologies, utilizing Orbitrap Fusion Lumos, Q Exactive HF, and Orbitrap Exploris systems. These state-of-the-art platforms, combined with Nano-LC systems and optimized fragmentation techniques (HCD, ETD), enable high-resolution detection of ubiquitin-modified peptides, even at low abundances.
Ubiquitination, characterized by the attachment of ubiquitin to lysine residues on target proteins, is marked by a characteristic K-ε-GG motif and a mass shift of approximately 114.1 Da. This unique modification is detectable through high-resolution mass spectrometry, allowing for precise identification and quantification of ubiquitinated peptides. Our quantitative ubiquitinomics service delivers high-throughput analysis, providing detailed ubiquitination profiles, including site localization and dynamic quantification of ubiquitination events under physiological and pathological conditions. Through the integration of sophisticated bioinformatics, we offer researchers comprehensive and actionable data, enabling insights into ubiquitin-mediated protein regulation that are crucial for understanding disease mechanisms, protein homeostasis, and signaling networks.
Understanding Ubiquitination: The Ubiquitin Code and Its Biological Significance
Ubiquitination is a post-translational modification in which the ubiquitin protein, a 76-amino-acid polypeptide, is covalently attached to lysine residues on target proteins, forming an isopeptide bond. This modification plays a critical role in regulating protein stability, localization, and function. Ubiquitination can occur as mono- or poly-ubiquitin chains, with different types of linkages serving distinct functions. For instance, K48-linked chains typically signal proteasomal degradation, while K63-linked chains are involved in signal transduction.
The ubiquitin code is fundamental to a variety of essential cellular processes, such as DNA repair, endocytosis, immune response, and metabolic regulation. These processes are orchestrated through a network of ubiquitination events that control cellular responses to internal and external signals. The development of mass spectrometry-based ubiquitinomics solutions has greatly enhanced our ability to map and quantify these modifications, providing deeper insights into their role in cellular functions and disease pathogenesis
Applications of Quantitative Ubiquitinomics
- Oncology: Precision Mapping of Tumor Ubiquitin Landscapes
Quantitative ubiquitinomics plays a crucial role in understanding how ubiquitination regulates cancer progression. Studies have shown that E3 ubiquitin ligases and deubiquitinases regulate the stability of oncogenic proteins like Myc, p53, and β-catenin, which drive tumorigenesis. High-throughput ubiquitinomics has enabled the discovery of tumor-specific ubiquitin modifications and their dynamic changes in response to chemotherapeutic agents. For example, the ubiquitinome of triple-negative breast cancer cells has been mapped, identifying upregulated K63-linked ubiquitination on key signaling proteins, providing potential targets for therapeutic intervention. The integration of quantitative ubiquitinomics and phosphoproteomics can assist in stratifying patients for targeted treatments and predicting therapy resistance.
- Neurodegenerative Diseases: Profiling Pathological Ubiquitination
Neurodegenerative disorders, such as Alzheimer’s and Parkinson’s diseases, are characterized by the accumulation of misfolded and aggregated proteins. Quantitative ubiquitinomics enables the precise mapping of ubiquitin modifications associated with these aggregates. Recent studies on Alzheimer’s models have shown specific ubiquitination of tau and amyloid precursor protein (APP), shedding light on the mechanisms of aggregate formation. Moreover, integrating ubiquitinomics with single-cell proteomics allows for the discovery of cell-type-specific ubiquitination patterns, offering deeper insights into selective neuronal vulnerability.
- Immunology: Decoding Ubiquitin-Dependent Immune Signaling
Ubiquitination is critical for regulating immune signaling pathways, including NF-κB, type I interferon responses, and T-cell receptor signaling. Quantitative ubiquitinomics has been used to chart dynamic ubiquitin landscapes in immune cells activated by pathogens or cytokines. Studies have identified novel E3 ligases and DUBs (deubiquitinases) as key regulators of immune checkpoints. Additionally, therapeutic modulation of ubiquitin pathways, such as targeting the E3 ligase cIAP1/2, shows promise in enhancing antitumor immunity and overcoming immune evasion by cancers.
- Plant and Microbial Systems: Ubiquitinomics in Non-Animal Contexts
In plant biology, ubiquitinomics has advanced our understanding of stress adaptation, hormone signaling, and developmental processes. For instance, in rice and Arabidopsis, the ubiquitin-modified protein mapping under drought and salt stress has highlighted key regulators such as transcription factors and metabolic enzymes. In microbial systems, recent research has uncovered prokaryotic ubiquitin-like proteins (PUPs), which target the proteasome in mycobacteria, offering new antimicrobial targets. The integration of ubiquitinomics with CRISPR-based gene editing offers promising applications in crop improvement and synthetic biology.
- Drug Discovery and Precision Medicine: Informing Therapeutic Strategies
Quantitative ubiquitinomics provides critical insights into drug-induced changes in ubiquitination profiles, helping identify compound specificity and potential off-target effects. For example, in PROTACs (proteolysis-targeting chimeras) development, ubiquitinomics is used to confirm target degradation and identify secondary ubiquitination events. Precision medicine efforts are leveraging patient-derived samples (e.g., xenografts, organoids) for personalized ubiquitin landscape mapping, aiding in targeted therapy selection and predicting therapeutic responses.
- Systems Biology and Future Perspectives
Integrating quantitative ubiquitinomics with multi-omics approaches (e.g., phosphoproteomics, transcriptomics, metabolomics) enables the construction of comprehensive cellular signaling models. These models reveal the interplay between ubiquitination and other regulatory mechanisms, providing a holistic understanding of complex biological processes. Future directions include applying real-time ubiquitinomics with novel technologies like trapped ion mobility spectrometry (TIMS) and data-independent acquisition (DIA) to capture dynamic ubiquitination events in live cells.
Additionally, machine learning algorithms are being developed to predict ubiquitin-mediated network behaviors.
MtoZ Biolabs offers a comprehensive, high-precision quantitative ubiquitinomics service that integrates cutting-edge mass spectrometry with targeted peptide enrichment to deliver reliable and reproducible data. Key advantages include:
- Advanced Analysis Platform
We utilize Orbitrap Fusion Lumos, Q Exactive HF, and Orbitrap Exploris systems, coupled with Nano-LC for high-resolution separation and accurate mass measurements, ensuring superior data quality across various sample types.
- Targeted Peptide Enrichment
Our service includes the use of anti-K-ε-GG antibodies to selectively enrich ubiquitinated peptides, enhancing detection sensitivity and enabling accurate quantification, even for low-abundance proteins.
- Versatility Across Sample Types
MtoZ Biolabs’ service is optimized for a wide range of sample types, including cells, tissues, biofluids, plants, and microbial cultures, ensuring scalability and consistency in high-throughput projects.
Rigorous sample preparation, digestion protocols (trypsin, Lys-C, Glu-C), and optimized peptide enrichment ensure high data fidelity, making our service reliable for diverse experimental needs.
To ensure optimal results from our quantitative ubiquitinomics service, please adhere to the following sample submission requirements:
≥100 μL, stored at -80°C, minimal freeze-thaw cycles.
≥2 mL, sterile handling, stored at -80°C.
≥200 mg (animal) or 10 g (plant), snap-frozen in liquid nitrogen.
≥1×10^8 cells, PBS-washed, frozen.
≥500 μL, labeled, contamination-free.
≥5 mg, quantified, buffer-compatible, free of interfering components.
Customized preprocessing is available for low-abundance or challenging samples.
Partnering with MtoZ Biolabs for your quantitative ubiquitinomics service ensures access to a uniquely balanced combination of technological sophistication, scientific rigor, and client-oriented service. Here’s why we stand out:
- Comprehensive Technological Support
Our mass spectrometry solutions leverage top-tier instrumentation, including Orbitrap Fusion Lumos and Q Exactive HF, with automated workflows that ensure high sensitivity and reproducibility.
Our bioinformatics platform integrates curated databases (e.g., PhosphoSitePlus, Unimod) with custom algorithms to generate detailed ubiquitination profiles, including site localization and quantification, with expert interpretation tailored to your needs.
We offer tailored workflows to accommodate different sample types and research objectives, from clinical samples to rare specimens, ensuring precision and scalability in every project.
- Transparent and Client-Friendly Pricing
We offer a one-time, transparent pricing model that includes all aspects of the service, from sample preparation and enrichment to mass spectrometry analysis and bioinformatics reporting. Clients can confidently plan projects without concerns about hidden fees or incremental costs.
Upon project completion, clients receive a detailed, customized report containing:
- Comprehensive Experimental Details
A thorough description of all experimental procedures, including sample collection and handling, buffer compositions, digestion protocols, and specific enrichment techniques tailored to ubiquitinated peptide capture.
- Materials, Instruments, and Methods
A complete list of materials used, including reagents, consumables, antibodies, as well as detailed instrument configurations such as mass spectrometer settings (e.g., resolution, AGC target, maximum injection time) and Nano-LC gradient conditions.
- Total Ion Chromatogram & Quality Control Assessment (Project-Dependent)
Visual representations of chromatographic profiles and internal standards for quality control, including signal stability and retention time reproducibility for both enriched and unenriched fractions.
- Data Analysis, Preprocessing, and Estimation (Project-Dependent)
A breakdown of data preprocessing workflows including noise filtering, baseline correction, charge state determination, and false discovery rate (FDR) thresholds. Estimation of peptide abundances and dynamic range across experimental replicates.
- Comprehensive Bioinformatics Analysis
- Ubiquitination Site Mapping: High-confidence localization of ubiquitination sites with site probability scores, cross-referenced against known databases (e.g., PhosphoSitePlus).
- Functional Annotation: Gene ontology (GO) and KEGG pathway analysis highlighting biological processes and molecular functions affected by ubiquitination.
- Protein Interaction Networks: Visualization of protein-protein interactions and signaling pathways influenced by ubiquitin modifications, including subnetworks of disease
- Custom Visualizations: Graphical representations such as volcano plots, heatmaps, and site occupancy maps, providing intuitive insights into the data.
Raw Data Files
Complete raw data generated by mass spectrometry runs, provided in vendor-compatible formats (e.g., Thermo RAW) for downstream reanalysis. Processed data files (e.g., mzML, mzIdentML) with metadata annotations are also included.
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider, provides advanced proteomics, metabolomics, and biopharmaceutical analysis services to researchers in biochemistry, biotechnology, and biopharmaceutical fields. Our ultimate aim is to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample consumption.
As research into protein post-translational modifications continues to advance, quantitative ubiquitinomics has emerged as a core technique for unraveling the mechanisms of protein homeostasis regulation. By combining advanced mass spectrometry platforms, highly specific enrichment strategies, and systematic data analysis methods, MtoZ Biolabs offers high-quality, reliable mass spectrometry-based ubiquitinomics solutions to researchers worldwide. Our vision is to bring new vitality to life science research through continuous innovation in this field, helping to reveal molecular mechanisms, identify disease targets, and accelerate new drug development.
If you would like to learn more about how our quantitative ubiquitinomics service can advance your research outcomes, please contact us for a free one-on-one technical consultation.
Media Contact
Organization: MtoZ Biolabs
Contact Person: Terry
Website: https://www.mtoz-biolabs.com
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Contact Number: +18573629535
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City: Boston
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