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Quantitative ubiquitinomics service employs high-resolution mass spectrometry to comprehensively profile ubiquitinated proteins at both qualitative and quantitative levels, elucidating their critical roles in cellular processes such as signal transduction, protein degradation, and stress response. In 1975, Gideon Goldstein et al. first characterized ubiquitin as a small regulatory protein, and its role in targeting substrates for proteasomal degradation was later elucidated by Aaron Ciechanover et al. in the 1980s. In the early 2010s, the integration of high-resolution mass spectrometry with stable isotope labeling techniques (e.g., SILAC) enabled high-throughput and dynamic quantification of ubiquitin-modified proteins. These breakthroughs have made quantitative ubiquitinomics a powerful tool in cancer biology, immunology, neurodegenerative disease research, and plant sciences.

MtoZ Biolabs offers comprehensive quantitative ubiquitinomics service utilizing advanced high-resolution mass spectrometry platform integrated with nano-liquid chromatography (Nano-LC) system. For the analysis of low-abundance ubiquitinated proteins, our mass spectrometry–based ubiquitinomics solutions employ highly specific CST K-ε-GG antibodies for targeted peptide enrichment and utilize multiple proteases to ensure comprehensive digestion and maximum site coverage, ensuring reliable data quality and high-confidence identification of ubiquitination sites.

Workflow of MtoZ Biolabs’ Quantitative Ubiquitinomics Service

Accurate identification and comprehensive quantification of ubiquitination sites are critical for understanding the dynamic changes and biological functions of protein ubiquitination. The standardized workflow at MtoZ Biolabs is as follows:

1. Sample Preparation and Protein Extraction

MtoZ Biolabs follows a standardized protocol for protein extraction from cells, tissues, and other biological samples, ensuring protein integrity and consistent concentration. The use of specific lysis buffers and protease inhibitors minimizes sample degradation and prevents nonspecific modifications. Accurate protein quantification guarantees that sample quality aligns with analytical standards, establishing a robust foundation for subsequent peptide enrichment and mass spectrometry analysis.

2. Ubiquitinated Peptide Enrichment

Ubiquitinated proteins are typically present at low abundance in cells, posing challenges for direct mass spectrometry-based detection. MtoZ Biolabs’ quantitative ubiquitinomics service employs highly specific ubiquitin antibody (CST Ubiquitin antibody) for peptide enrichment, effectively reducing background noise and increasing the sensitivity for detecting low-abundance ubiquitinated peptides.

3. Protein Digestion

MtoZ Biolabs utilizes a multi-enzyme digestion strategy, including enzymes such as Trypsin and Lys-C, to achieve maximal coverage of ubiquitination sites through their distinct cleavage specificities. The digestion process is carefully optimized with strict control over time, temperature, and pH to reduce non-specific cleavage events, ensuring high efficiency and precision. This optimized approach generates a comprehensive peptide map, providing robust data for quantitative ubiquitinomics service.

4. LC-MS/MS Analysis

Leveraging the Orbitrap Fusion Lumos and nanoLC platform, MtoZ Biolabs’s mass spectrometry–based ubiquitinomics solutions enable the detection of ubiquitinated peptides at levels as low as 1 fmol. By combining DDA/DIA dual acquisition modes—where DDA facilitates novel site discovery and DIA ensures high-reproducibility quantification—the platform guarantees comprehensive coverage of low-abundance modifications without omission.

For quantitative analysis, flexible methodologies are available:

• TMTpro 16-plex labeling supports integrated multi-omics studies (e.g., ubiquitination + phosphorylation + transcriptomics), allowing simultaneous exploration of cross-regulatory mechanisms.

• Label-Free quantification coupled with AI-driven algorithms effectively eliminates batch effects, making it ideal for large-scale cohort studies requiring robust data harmonization.

5. Data Analysis and Bioinformatics Analysis

MtoZ Biolabs performs mass spectrometry data analysis to identify ubiquitination sites and quantify their levels. Through the integration of bioinformatics tools, we conduct functional enrichment analysis, pathway analysis, and protein-protein interaction network analysis. These approaches aim to elucidate the functional roles of ubiquitination in cellular signaling, protein degradation, and related biological processes.

Why Choose MtoZ Biolabs?

1. High-Throughput Ubiquitinomics Analysis

With advanced high-resolution mass spectrometry platforms, we can analyze thousands of ubiquitinated proteins in a single experiment, delivering comprehensive datasets for quantitative ubiquitinomics service.

2. Precise Detection of Low-Abundance Ubiquitinated Proteins

Through targeted enrichment strategies for ubiquitinated peptides, MtoZ Biolabs significantly enhances the sensitivity of detecting low-abundance ubiquitinated proteins, ensuring precise identification and quantification of rare modification sites.

3. Multi-Enzymatic Digestion Strategy

MtoZ Biolabs employs multiple proteolytic enzymes for protein digestion, minimizing the risk of missing ubiquitination sites and ensuring comprehensive site coverage, thereby improving data reliability and completeness in quantitative ubiquitinomics service.

4. High-Resolution LC-MS/MS Platforms

The integration of Nano-LC with the Thermo Fisher Orbitrap Fusion mass spectrometer enables high-resolution separation and precise detection of ubiquitinated peptides, delivering data with superior sensitivity, resolution, and consistency.

5. One-Time-Charge

Our pricing is transparent, no hidden fees or additional costs.

6. High-Data-Quality

Deep data coverage with strict data quality control. AI-powered bioinformatics platform integrates all quantitative ubiquitinomics analysis data, providing clients with a comprehensive data report.

Applications

1. Disease Mechanism Analysis

Quantitative ubiquitinomics service systematically analyzes the dynamic ubiquitination modifications of key proteins in disease models, uncovering the core regulatory mechanisms underlying tumor progression, neurodegenerative diseases, and immune dysregulation. This provides a theoretical foundation for precision medicine by elucidating protein homeostasis imbalances in pathological processes.

2. Drug Target Discovery and Validation

By deeply mapping substrate interaction networks of E3 ligases and deubiquitinating enzymes, quantitative ubiquitinomics service facilitates the development of targeted protein degradation therapies, such as PROTAC. Additionally, it enables real-time monitoring of drug-induced global ubiquitination changes, helping to decipher the molecular basis of drug resistance.

3. Biomarker Development

Quantitative analysis of ubiquitination-specific sites in biofluid and tissue samples enables the establishment of novel molecular marker systems for early disease diagnosis, classification, and therapeutic response prediction. This approach facilitates the development of personalized medicine strategies, enhancing precision in disease management and treatment planning.

What Could be Included in the Report?

1. Comprehensive Experimental Details

2. Materials, Instruments, and Methods

3. Total Ion Chromatogram & Quality Control Assessment (project-dependent)

4. Data Analysis, Preprocessing, and Estimation (project-dependent)

5. Bioinformatics Analysis

6. Raw Data

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.

Interested in learning more about how our quantitative ubiquitinomics service can enhance your research?

Contact Detail:

Company Name: MtoZ Biolabs
Contact Person: TerryE.Chenier
Email: Send Email
Phone No: 1-857-362-9535
Address: 155 Federal Street, Suite 700
City: Boston
State: Massachusetts
Country: United States
Website Url: https://www.mtoz-biolabs.com/index.html