Ubiquitinproteomics Analysis Service

Ubiquitinproteomics is a cutting-edge technology dedicated to analyzing protein ubiquitination. As a key post-translational modification (PTM), ubiquitination regulates protein stability, activity, and interactions, playing a crucial role in cellular signaling, disease progression, and drug response. By systematically identifying ubiquitination sites and deciphering their biological functions, ubiquitinproteomics provides essential insights for disease mechanism research, drug target discovery, and therapeutic strategy optimization.  

 



Zhong, Q. et al. MedComm (2020). 2023. 

Figure 1. The Protein Ubiquitination Pathway

 

Traditional ubiquitination analysis methods, such as immunoprecipitation and Western blot, have limitations in sensitivity and specificity. In contrast, high-resolution mass spectrometry (LC-MS/MS) enables comprehensive and precise identification of ubiquitination events, offering researchers a reliable tool for molecular mechanism studies. MtoZ Biolabs integrates state-of-the-art technology and expert knowledge to deliver high-quality ubiquitinproteomics analysis service, supporting both fundamental research and clinical applications by providing accurate data and in-depth biological interpretation.  

 

MtoZ Biolabs provides end-to-end ubiquitinproteomics analysis service, covering all stages from sample preparation to advanced data analysis. With cutting-edge instrumentation and an experienced scientific team, we support ubiquitination analysis across various sample types, including:  

• Cell Samples (cultured cells, organoids)  
• Tissue Samples (fresh/frozen tissues, FFPE samples)  
• Biofluids (serum, plasma, cerebrospinal fluid)  
• Immunoprecipitated Ubiquitinated Proteins  

 

Our service offerings include:  

1. Ubiquitination Site Identification  

2. Quantitative Ubiquitin Proteomics (Label-Free or TMT-Based Quantification)  

3. Ubiquitinated Protein Analysis Service  

4. Histone Ubiquitination Analysis  

5. Other Post-Translational Modification Analysis Services  

 

Analysis Workflow  

Our standardized yet flexible workflow ensures high data quality and reliability:  

1. Sample Processing & Enrichment  

• Protein extraction and quality control with stringent protocols  
• Ubiquitinated proteins are enriched using high-specificity ubiquitin antibodies or UBAN domain probes  

 

2. Enzymatic Digestion & Peptide Processing  

• Optimized digestion strategy for high peptide recovery  
• TMT labeling (optional, for multiplexed quantitative analysis)  

 

3. High-Resolution LC-MS/MS Analysis  

• Orbitrap-based mass spectrometry for precise detection of ubiquitinated peptides  
• Advanced database search algorithms for accurate site identification  

 

4. Bioinformatics Analysis & Functional Interpretation  

• Functional annotation and pathway enrichment (GO, KEGG)  
• Construction of ubiquitination-modulated regulatory networks  

 

5. Comprehensive Report Delivery  

Includes raw data, visualization, and expert interpretation  

 

Why Choose MtoZ Biolabs?  

1. High Sensitivity & Specificity  

• Advanced Enrichment Technology: Optimized antibody combinations and chemical probes significantly improve the detection of low-abundance ubiquitinated proteins, especially in complex samples like serum.  
• Strict Quality Control: Multi-step noise reduction algorithms minimize false positives, ensuring data reliability.  

 

2. Advanced Mass Spectrometry Platform  

• High-resolution Orbitrap LC-MS/MS technology for ultra-precise detection of ubiquitination events.  
• Supports DIA-based proteomics for deep and comprehensive ubiquitome analysis.  

 

3. Expert Technical Support  

• One-on-One Consultation: Our experienced scientists provide full project guidance, from experimental design to data interpretation.  
• Customizable Solutions: Tailored analysis strategies for specific research needs, such as ubiquitination-phosphorylation crosstalk.  

 

4. Fast Turnaround & Cost-Effective Solutions  

• Standard turnaround time: 3-6 weeks, ensuring timely project completion.  
• Transparent pricing with no hidden costs, offering 30% lower costs compared to similar high-precision services.  

 

Applications 

1. Disease Mechanism Studies: Investigating the role of ubiquitination in cancer, neurodegenerative diseases, and immune-metabolic disorders.  

   

2. Drug Target Discovery: Supporting the development of small-molecule inhibitors targeting E3 ligases or deubiquitinases, and validating the mechanism of action for protein degradation therapies.  

 

3. Biomarker Discovery: Identifying ubiquitination patterns associated with disease onset, progression, and treatment response, aiding in precision medicine and prognostic assessment.  

 

Case Study

1. Quantitative Proteomics Reveals Extensive Lysine Ubiquitination and Transcription Factor Stability States in Arabidopsis

Ubiquitination is widely present in plants and plays a crucial role in regulating protein activity, abundance, and stability. This study employed antibody-based enrichment of ubiquitinated peptides combined with isobaric labeling quantification to achieve high-throughput analysis of 18 samples. A total of 17,940 ubiquitinated lysine sites on 6,453 proteins were identified in the roots, seedlings, and rosette leaves of Arabidopsis thaliana. Functional analysis revealed that these ubiquitinated proteins are involved in various biological processes, including hormone signaling, plant defense, protein homeostasis, and metabolism. Additionally, the study demonstrated that ubiquitination regulates the stability of the transcription factors CIB1, CIL2, and STOP1, and CRISPR/Cas9 base editing was used to prevent CIB1 K166 ubiquitination, leading to altered flowering time and FT gene expression. This research provides a comprehensive dataset of the plant ubiquitinome, laying the foundation for further studies on the functional roles of ubiquitination in biological processes. Our Ubiquitinproteomics Analysis Service utilizes antibody-based enrichment combined with quantitative mass spectrometry to efficiently analyze ubiquitination sites, revealing their impact on protein degradation, signal transduction, and transcriptional regulation, making it suitable for both plant and animal proteomics research.

 



Song, G. et al. Plant Cell. 2024.

Figure 3. Analysis of TF Ubiquitination

 

2. Data-Independent Acquisition Method for Ubiquitinome Analysis Reveals Regulation of Circadian Biology

Protein ubiquitination plays a crucial role in various cellular processes. Current ubiquitin proteomics studies primarily rely on diGly antibody enrichment combined with mass spectrometry (MS), but the potential of data-independent acquisition (DIA) in ubiquitinome analysis remains underexplored. This study develops a high-sensitivity workflow integrating Orbitrap-based DIA and diGly antibody enrichment, constructing a spectral library containing over 90,000 diGly peptides. The approach identifies 35,000 diGly peptides in a single run of proteasome inhibitor-treated cells, doubling the sensitivity and quantitative accuracy compared to data-dependent acquisition (DDA). When applied to TNF signaling, the workflow not only captures known ubiquitination sites but also identifies numerous novel ones. Additionally, a systematic analysis of ubiquitination across the circadian cycle reveals hundreds of cycling ubiquitination sites and ubiquitin clusters within membrane protein receptors and transporters, highlighting new connections between ubiquitination, metabolism, and circadian regulation. Ubiquitinproteomics Analysis Service offers high-resolution mass spectrometry combined with DIA-based ubiquitin proteomics to enable global identification and quantification of ubiquitination modifications, supporting research on ubiquitin-mediated cellular regulation.

 



Hansen, FM. et al. Nat Commun. 2021.

Figure 4. Quantification of the Rhythmic Ubiquitinome

Deliverables

• Raw Data Files

  • Full LC-MS/MS raw files (Thermo RAW format or converted mzML/mzXML upon request)

  • Metadata on instrument settings and sample run order

• Peptide and Protein Identification Results

  • Identified ubiquitinated peptides and corresponding modification sites (with localization probability)

  • Protein inference tables including gene names, sequence coverage, and peptide count

• Quantitative Data Output

  • Relative quantification results (Label-Free, TMT, or DIA-based)

  • Normalized peptide intensities and fold changes across conditions/groups

  • Volcano plots, clustering heatmaps, and statistical significance tables

• Functional Annotation and Pathway Analysis

  • Gene Ontology (GO) enrichment analysis (Biological Process, Molecular Function, Cellular Component)

  • KEGG pathway enrichment and mapping

  • Ubiquitination network construction and visualization (if applicable)

• Customized Report

  • Project summary and experimental overview

  • Quality control metrics (e.g., MS performance, labeling efficiency, peptide yield)

  • Annotated figures, tables, and detailed result interpretations

  • Biological insights and potential regulatory implications

 

Ubiquitination is a fundamental regulatory mechanism in cellular biology, and its precise analysis is reshaping both basic research and clinical applications. MtoZ Biolabs’ ubiquitinproteomics analysis service leverages cutting-edge technology and research-driven expertise to transform your samples into actionable biological insights. Whether you are investigating disease mechanisms, validating drug targets, or developing novel biomarkers, we are your trusted partner in ubiquitin proteomics research. Contact MtoZ Biolabs today and advance your research with confidence!