Advanced Glycoproteomics Service: Site-Specific Analysis for Precision Translational Research
Traditional glycan analysis often misses the "site-specific" context, creating critical blind spots in molecular research. Creative Proteomics bridges this gap with an advanced Precision Glycoproteomics Platform. By integrating intact glycopeptide profiling with high-resolution LC-MS/MS and next-generation TMT/DIA quantitative pipelines, we transform complex samples into actionable insights for biomarker discovery and drug development.
Submit Your Request Now
×
- Why It Matters
- Our Services
- Workflow
- Advantages
- Application
- Platforms & Requirement
- FAQs
- Demo
- Case & publication
Why Glycoproteomics Matters
Linking Glycosylation to Disease and Therapeutics
Changes in glycosylation patterns are not random. In cancer, for example, tumour cells frequently display altered glycan structures that affect growth, immune evasion, and metastasis. Glycoproteomics provides a direct way to identify these molecular signatures, enabling researchers to uncover new biomarkers and pathways for early detection and therapeutic targeting.
In immunology, glycosylation controls antibody activity, immune checkpoint signalling, and host–pathogen interactions. By mapping glycan variation at the site-specific level, glycoproteomics helps clarify how immune responses are regulated and how therapeutic antibodies function in different disease settings.
For therapeutic proteins such as monoclonal antibodies, consistent glycosylation is critical for drug safety and efficacy. Glycoproteomics offers the precision needed to monitor glycoform ratios, characterise post-translational modifications, and support regulatory submissions with robust structural evidence.
Our Glycoproteomics Services
Creative Proteomics combines reductase digestion, N-glycosylated peptide enrichment, deglycosylation in H2O18, and highly sensitive LC-MS detection techniques to analyze and clarify N-glycosylation modification sites of samples. The deglycosylated N-glycan chains can also be interpreted by the MALDI-TOF, which can provide relevant experimental evidence, including XICs mass spectra, MS2 spectra, and MALDI-TOF glycan spectra to support data analysis.
Service Contents
- Analysis of N-Glycan modification sites (optional O18 labeling)
- MALDI-TOF Glycopeptide Mapping (including N-Glycan and O-Glycan)
- Glycoprotein Profiling of Intact Proteins
- Glycoform Ratio Analysis
- Analysis of glycosylation sites and
- Glycopeptide site mapping
- Quantitative Glycoproteomics (TMT & DIA)
TMT-based Labeling: Ideal for multiplexed analysis (up to 16-18 samples), providing high-precision relative quantification for clinical cohorts or time-series studies.
DIA (Data-Independent Acquisition): A label-free powerhouse for deep proteome coverage and superior reproducibility, enabling the detection of low-abundance glycopeptides in complex matrices.
Glycoproteomics Mass Spectrometry Workflow
Step 1: Sample Preparation
Proteins are denatured, reduced, and enzymatically digested to produce peptides. Careful desalting removes contaminants, ensuring clean inputs for downstream analysis.
Step 2: Glycopeptide Enrichment
We employ hydrophilic interaction liquid chromatography (HILIC) and lectin-based enrichment to selectively capture glycopeptides. These approaches preserve the complete glycan structure and improve detection of low-abundance glycoproteins.
Step 3: Mass Spectrometry Analysis
Our service integrates glycoproteomics mass spectrometry platforms, including Orbitrap, Q-Exactive, and MALDI-TOF. Using advanced fragmentation strategies (CID, HCD, ETD), we resolve intact glycopeptides, supporting both qualitative and quantitative analysis.
Step 4: Glycoproteomics Data Analysis
Spectral data are processed with high-accuracy pipelines, enabling intact glycopeptide identification and structural annotation. Both glycan and peptide fragments are analysed to provide site-specific assignments.
Step 5: Bioinformatics Integration
Results are interpreted using dedicated glycoproteomics software and curated glycoproteomics databases. This ensures high-confidence annotation of glycosylation sites, glycoforms, and relative abundances, with visualisation tools for easy interpretation.
LC-MS/MS approaches of Proteomics and Glycoproteomics
TMT vs. DIA: Which Quantitative Strategy Fits Your Research?
Selecting the right quantification strategy is critical for the success of your glycoproteomics project. Both TMT (Tandem Mass Tag) and DIA (Data-Independent Acquisition) offer high-precision insights, but they excel in different research contexts.
1. TMT-based Glycoproteomics: The Gold Standard for Precision
TMT is a labeling-based approach that allows for the simultaneous analysis of multiple samples (multiplexing). It is highly effective when comparing discrete experimental groups with maximum quantitative accuracy.
Best for: Clinical cohorts with limited sample numbers, time-series studies, and drug treatment comparisons.
Key Advantage: Virtually zero "missing values" across samples within the same multiplexed set and superior sensitivity for low-abundance glycopeptides.
2. DIA-based Glycoproteomics: Unmatched Depth and Reproducibility
DIA is a label-free "scan-swath" technique that captures all detectable peptide ions within a given mass range. It creates a "digital record" of the glycoproteome.
Best for: Large-scale biomarker discovery, longitudinal studies involving hundreds of samples, and building permanent digital glycopeptide libraries.
Key Advantage: Exceptional data consistency across large batches and the ability to re-analyze data "in silico" as new glycan databases become available.
| Feature | TMT (Multiplexing) | DIA (Label-Free) |
|---|---|---|
| Quantification Principle | MS2/MS3 Reporter ions | MS1 & MS2 Fragment ions |
| Sample Throughput | Up to 18 samples per run | Theoretically unlimited (across batches) |
| Quantitative Precision | Excellent (highest for small sets) | High (consistent across large cohorts) |
| Missing Values | Minimal within a multiplex | Minimal across the entire project |
| Experimental Design | Fixed (limited by plex) | Flexible (add samples anytime) |
| Best Application | Target-driven / Clinical validation | Discovery-driven / Large biobanks |
Decision Guide: How to Choose?
Choose TMT if: You have a clearly defined set of samples (e.g., 6, 10, or 16) and require the highest possible quantitative precision to detect subtle fold-changes in site-specific glycosylation.
Choose DIA if: You are conducting a large-scale discovery project with hundreds of samples or wish to create a digital archive of your samples for future retrospective analysis.
Deep Dive: For a comprehensive analysis of sample throughput, cost-effectiveness, and data depth, read our [Label-free vs TMT Glycoproteomics 2026: Cohort Guide] to find the perfect fit for your specific study design.
Service Advantages
Our glycoproteomics service is built to address the limitations of conventional approaches and provide researchers with actionable, reproducible data. By integrating advanced instrumentation with specialised bioinformatics, Creative Proteomics delivers a solution that supports both discovery and applied research.
Key Advantages of Our Glycoproteomics Service
Intact glycopeptide profiling
Simultaneous mapping of glycosylation sites, glycan structures, and peptide backbones for both N- and O-linked glycans.
Low sample requirement
High-sensitivity LC-MS/MS platforms and efficient enrichment strategies enable robust analysis from limited or precious biological samples.
High detection sensitivity
Orbitrap and MALDI systems provide deep coverage, allowing detection of low-abundance glycopeptides that are often missed by conventional workflows.
Optimised glycoproteomics protocols
Proprietary enrichment and fragmentation methods minimise experimental error and enhance reproducibility.
Fast turnaround time
A streamlined workflow and in-house expertise enable efficient project completion, ensuring timely support for research needs.
Comprehensive deliverables
Clients receive raw mass spectrometry data, processed datasets, and visualised glycan maps for straightforward interpretation.
Key Applications of Glycoproteomics
Cancer research
Abnormal glycosylation patterns are hallmarks of many tumour types. Glycoproteomics enables the identification of glycan-based biomarkers, pathway alterations, and therapeutic targets.
Immunology and host defence
Glycosylation regulates antibody function, cytokine signalling, and immune checkpoint activity. Site-specific analysis provides insight into immune regulation and response to therapies.
Therapeutic protein development
For monoclonal antibodies and other biologics, glycosylation directly influences drug efficacy and stability. Glycoproteomics supports glycoform profiling, comparability studies, and regulatory submissions.
Cross-species studies
Our workflow is validated across human, mouse, plant, and microbial systems, making it suitable for diverse academic and industrial research.
By integrating glycan structure with protein sequence information, glycoproteomics bridges the gap between genomics, proteomics, and functional biology. This versatility makes it a cornerstone technology for both discovery-driven and application-focused projects.
By combining precision, flexibility, and efficiency, our service empowers researchers to accelerate biomarker discovery, explore disease mechanisms, and advance therapeutic protein development.
Platforms
- Mass Spectrometry Systems: MALDI-TOF, Q-Exactive Plus, Q-Exactive HF, Orbitrap Fusion, Orbitrap Fusion Lumos
- Chromatography Systems: Nanoflow UPLC (Easy-nLC 1000, Thermo Fisher Scientific)
Sample Requirements
| Sample Type | Requirement | Notes |
|---|---|---|
| Tissue (animal, microbial) | Wet weight > 30 mg | Ensure fresh or properly preserved tissue |
| Tissue (plant) | Fresh tissue > 300 mg | Avoid degradation prior to processing |
| Cells | Cell volume > 1 × 10⁷ | Suitable for cultured or isolated cells |
| Body fluids (e.g., serum) | Serum volume > 1500 μL | Collect using standard clinical protocols |
| Protein extracts | Total protein > 200 μg, concentration > 1 μg/μL | High-quality extract recommended |
| SDS-PAGE gel samples | Total target protein > 50 μg | Excised bands should be clearly identified |
Delivery
- Experimental report
- Raw data
- Experimental results
FAQs
What is Glycoproteomics
Glycoproteomics is the systematic, large-scale study of protein glycosylation—a pivotal post-translational modification (PTM) that dictates protein folding, immune evasion, and cellular signaling. While traditional glycomics focuses on total glycan structures, it fails to identify the specific attachment sites, leaving a critical gap in understanding disease mechanisms such as cancer metastasis and autoimmune responses.
Modern glycoproteomics bridges this gap by utilizing high-resolution mass spectrometry to capture intact glycopeptides. This site-specific insight is essential for biomarker discovery and the characterization of biopharmaceuticals. At Creative Proteomics, we elevate this analysis through next-generation quantitative workflows (including TMT and DIA), providing the precision and depth required for translational research and complex clinical cohorts.
What does "glycoproteomics" mean?
Glycoproteomics is the large-scale study of proteins with sugar attachments. It identifies which proteins are glycosylated, pinpoints the precise sites, and determines the glycan structure on each protein.
What does a standard glycoproteomics protocol include?
Typical workflows involve: denaturing protein samples; enzymatic digestion; glycopeptide enrichment via HILIC or lectin methods; mass spectrometry analysis; and data processing to assign glycosylation sites and glycoforms.
What kinds of samples are suitable for glycoproteomics?
We handle a variety of sample types, including tissues, cells, body fluids, protein extracts, and even SDS-PAGE gel bands. Our flexible requirements accommodate small sample volumes and diverse biological origins.
Which platforms are used for glycoproteomics mass spectrometry?
We deploy high-resolution instruments like Orbitrap, Q Exactive, and MALDI-TOF. Offering advanced fragmentation modes such as CID, HCD, and ETD, these tools support both qualitative and quantitative assessments in glycoproteomics workflows.
How is glycoproteomics data analysis performed?
Spectra are subjected to intact glycopeptide analysis, where both peptide and glycan fragments are matched. Our pipeline relies on advanced glycoproteomics software and curated databases to deliver accurate, site-specific glycosylation profiles.
Can glycoproteomics be used in cancer research?
Absolutely. Glycoproteomics enables detection of site-specific glycan alterations in tumour cells, aiding biomarker discovery and providing insights into oncogenic mechanisms.
What is the typical turnaround time?
Our streamlined glycoproteomics protocols and calibrated workflow enable efficient delivery of results, with timelines adapted to sample complexity and study design.
Can you offer quantitative glycoproteomics?
Yes. Beyond label-free quantification, we support advanced quantitative methods like TMT/iTRAQ, SILAC, DDA, and DIA. These enable flexible and accurate comparative analysis across multiple conditions.
Can you accommodate unusual or custom requests?
Definitely. We offer flexible service options—from targeted site mapping to top-down intact protein analysis. Our team collaborates with clients to develop tailored workflows for unique samples.
Is this service research-use only?
Yes. All results are provided for research applications only and are not intended for diagnostic use.
Why choose DIA over TMT for large-scale glycoproteomics?
DIA provides higher data consistency across large sample sets without the limitations of labeling efficiency, making it the gold standard for clinical proteogenomics where sample numbers exceed the TMT multiplexing capacity.
Learn about other Q&A about proteomics technology.
Demo
Figure 1. LC-MS/MS identification of subclass-specific IgG N-glycomes
By combining efficient glycopeptide enrichment, nano-LC, and high-sensitivity mass spectrometry with the unique GlycanFinder software, glycosylation sites can be rapidly and comprehensively identified, glycopeptides can be separated, and the glycan types attached to each site can be determined.
Figure 2. MALDI-MS analysis of human peripheral blood N-glycan profiles
The established high-throughput orthogonal mass spectrometry approach enables comprehensive analysis of glycomes from samples of different origins and varying complexity.
Client Case Study
Conformational Differences Between Native HIV-1 Env Trimers and Stabilized Soluble Counterparts
Nguyen et al., Journal of Virology, DOI: 10.1128/jvi.01709 18
- Background
- Methods
- Creative Proteomics' Role
- Conclusion
The HIV 1 envelope (Env) glycoprotein trimer is critical for viral entry and a key vaccine target. Stabilized soluble forms (sgp140 SOSIP.664) facilitate structural studies and immunogen design—but it remains unclear how faithfully they mimic native, membrane anchored Env.
The study used cross linking mass spectrometry (XL MS) to compare the distance constraints in functional, membrane embedded Env versus the stabilized soluble sgp140 SOSIP.664 trimers. This approach helped map structural conformations at the molecular level.
Figure 1. Workflow comparison of cross linking mass spectrometry analysis between functional (membrane anchored) Env and stabilized soluble sgp140 SOSIP.664 trimers, showing peptide cross link identification and resulting distance constraints applied.
We provided our cross linking mass spectrometry platform to reproduce and validate XL MS distance constraints between Env subunits, ensuring data quality and supporting structural comparison with high confidence.
The study revealed significant conformational disparities: the functional Env retains a closed gp41 HR1 coiled coil until CD4 binding, whereas sgp140 SOSIP.664 exposes the HR1 region prematurely. These findings inform improvements in immunogen design to more closely mimic viral Env conformation
Our Glycoproteomics & Glycomics Review
- Modulation of the Endomembrane System by the Anticancer Natural Product Superstolide/ZJ-101. International Journal of Molecular Sciences.
- Identification of the O-Glycan Epitope Targeted by the Anti-Human Carcinoma Monoclonal Antibody (mAb) NEO-201. Cancer.
- Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. Science Advances.
- Conformational differences between functional human immunodeficiency virus envelope glycoprotein trimers and stabilized soluble trimers. Journal of Virology.
References
- Xu S, Xu X, Wu R. Deciphering the Properties and Functions of Glycoproteins Using Quantitative Proteomics. Journal of Proteome Research. 2023 Jun 2;22(6):1571-1588.
- Dalpathado DS, Desaire H. Glycopeptide analysis by mass spectrometry. Analyst. 2008 Jun;133(6):731-8.
- Fang P, Ji Y, Silbern I, et al. A streamlined pipeline for multiplexed quantitative site-specific N-glycoproteomics. Nature Communications. 2020 Oct 19;11(1):5268.
