Ubiquitylomics Data Analysis Service

Protein ubiquitination is a highly conserved post-translational modification (PTM), involving the covalent attachment of the small protein ubiquitin to lysine residues on target proteins. This modification regulates key biological processes such as protein degradation, intracellular transport, signal transduction, and protein activation. Different types of ubiquitination—such as monoubiquitination, polyubiquitination, and chain-type–specific ubiquitination—play distinct biological roles in modulating protein fate and function.

 

With the advancement of high-resolution mass spectrometry, ubiquitylomics has emerged as a powerful strategy for systematically studying ubiquitination sites, expression patterns, and regulatory networks. It has been widely applied in areas such as cellular homeostasis regulation, tumor immune evasion, and inflammatory response.

 

Leveraging advanced mass spectrometry platforms and standardized data analysis workflows, MtoZ Biolabs offers accurate and reliable ubiquitylomics data analysis service. Our service covers the complete pipeline from modification site identification and quantitative analysis to functional annotation and pathway enrichment, enabling researchers to comprehensively understand the biological function and dynamic changes of ubiquitination.

 

Services at MtoZ Biolabs

MtoZ Biolabs’ ubiquitylomics data analysis service supports various data types, including samples enriched using K-ε-GG–specific antibodies (commonly used for capturing ubiquitinated peptides). We are compatible with TMT, iTRAQ, and Label-Free quantification strategies. Raw MS data are processed through a series of professional algorithms to perform modification site identification, peptide quantification, and functional enrichment analysis, ultimately delivering structured visual reports.

 



Figure 1. Functional Classification of the Ubiquitinated Proteins

 

If you are not satisfied with the quality or results of your existing data, we also offer an all-in-one Ubiquitinproteomics Analysis Service—from sample preparation and mass spectrometry analysis to comprehensive data interpretation—to ensure accurate identification of modification sites and high-quality data output.

 

For any inquiries or specific needs, please contact us. We are committed to enhancing your research outcomes.

 

Service Advantages

1. Advanced Mass Spectrometry Platform

We employ industry-leading high-resolution mass spectrometers including Thermo Orbitrap Fusion Lumos and Q Exactive HF, coupled with stable nano-LC systems. This ensures high-sensitivity detection and high-resolution separation of ubiquitinated peptides, even in complex biological backgrounds. The platform’s sub-ppm mass accuracy and wide dynamic range are ideal for identifying low-abundance and multi-site–modified proteins, helping researchers elucidate the dynamic regulation and biological significance of ubiquitination.

 

2. Standardized and Proven Workflow

We have developed a standardized analysis workflow based on K-ε-GG antibody enrichment, encompassing sample preprocessing, peptide enrichment, MS acquisition, and downstream data processing. Validated across hundreds of projects, this workflow offers excellent stability and reproducibility. Integrated with optimized search engines (e.g., MaxQuant, Proteome Discoverer), our workflow enables accurate site-specific localization and ubiquitinome profiling across diverse sample types such as cell lines, tissues, and animal models.

 

3. Compatibility with Diverse Data Types

Our analysis pipeline supports a variety of experimental designs and quantification strategies, including Label-Free, TMT, and iTRAQ. We accept a wide range of MS data formats including RAW (Thermo), mzML, and mzXML, allowing flexibility in project setup. Clients can submit existing datasets or choose our end-to-end service to cover both experimental and computational workflows, ensuring efficiency and consistency throughout the project.

 

4. Comprehensive Functional Annotation

Beyond basic protein identification and site mapping, we provide in-depth bioinformatics analysis, including GO/KEGG pathway enrichment, protein domain mapping, ubiquitination site visualization, and protein–protein interaction network construction. This enables researchers to transition from site-level observations to system-wide regulatory insights, supporting mechanistic studies, biomarker discovery, and target validation.

 

5. Full Technical Support

Our experienced technical team provides end-to-end support throughout the project lifecycle. Services include: pre-experimental consultation (e.g., sample selection, enrichment strategies, data QC guidelines), customized data analysis workflows (e.g., quantification strategy, database configuration, parameter settings), and comprehensive report interpretation (e.g., online consultations or data walkthroughs). We aim to ensure that every client receives not only high-quality data but also valuable insights suitable for publication and further research.

 

Applications

1. Systematic Identification of Modification Sites and Ubiquitin Chain Types

Precisely localize ubiquitinated residues and chain types to uncover how proteins are tagged and directed toward specific fates.

 

2. Analysis of Protein Stability and Degradation Mechanisms

Quantify changes in ubiquitination levels to identify key degradation signals and explore protein turnover regulation.

 

3. Construction of Ubiquitin-Regulated Signaling Networks

Reveal the dynamic roles of ubiquitination in pathways such as cell cycle, apoptosis, autophagy, and immune responses.

 

4. Identification of Disease-Associated Regulatory Nodes and Aberrant Modification

Compare ubiquitination profiles between normal and disease states to pinpoint potential pathogenic mechanisms and therapeutic targets.

 

5. Support for Targeted Drug Development and Mechanism-of-Action Validation
Assess whether candidate compounds induce ubiquitination and degradation of target proteins, enabling validation of PROTAC and related strategies.

 

Deliverables

1. Raw LC-MS/MS Data

Complete raw mass spectrometry files and metadata for traceability and reanalysis.

 

2. Ubiquitination Site and Protein Identification

High-confidence identification of ubiquitinated peptides with site-specific localization.

 

3. Quantitative Results

Normalized peptide intensities and differential analysis across experimental conditions.

 

4. Functional Annotation and Pathway Analysis

Enrichment of GO/KEGG terms and regulatory network insights based on ubiquitinated proteins.

 

5. Comprehensive Analysis Report

Publication-ready summary with visualizations, interpretation, and technical quality metrics.

 

Ubiquitination plays a pivotal role in regulating cell fate, signal transduction, and disease progression. Through advanced high-resolution mass spectrometry and standardized data analysis pipelines, MtoZ Biolabs provides stable, accurate, and reproducible ubiquitylomics data analysis service, empowering researchers to uncover the mechanisms and functions of ubiquitin modifications in biological systems.

 

If you have relevant analysis needs, please feel free to contact us for a customized service solution and expert support.