Glycosaminoglycan (GAG) Profiling and LC–MS/MS Analysis Service

What Is GAG Analysis and LC–MS/MS Profiling?

Glycosaminoglycans (GAGs) – including heparan sulfate (HS)/heparin (HP), chondroitin sulfate (CS), dermatan sulfate (DS), keratan sulfate (KS), and hyaluronan (HA) – are key components of the extracellular matrix and cell surface glycocalyx. Their chain length, sulfation pattern, and degradation dynamics are tightly linked to:

• Cell signaling and growth factor binding
• Tumor and immune microenvironment remodeling
• Vascular/endothelial glycocalyx integrity
• Cartilage and intervertebral disc degeneration
• Metabolic and rare disease mechanisms

Our GAG profiling and LC–MS/MS analysis service characterizes GAGs at multiple levels: overall content, class-specific composition, disaccharide patterns, and structural remodeling under different experimental conditions. The service is designed for basic and translational research, and can be seamlessly integrated with broader metabolomics studies.

GAG Analysis Services We Provide

Quantitative GAG profiling

• Total and class-specific levels of HS/HP, CS, DS, KS and HA
• Relative or absolute quantification where suitable standards are available

Disaccharide and sulfation-pattern profiling

• Enzymatic depolymerization of GAG chains to defined disaccharides
• LC–MS/MS measurement of non-sulfated and sulfated disaccharides to reveal composition and remodeling

Focused HS / CS structural profiling

• Higher-resolution disaccharide panels for HS and CS/DS
• Detection of changes in key N- and O-sulfation motifs relevant to signaling and microenvironment studies

Integration with metabolomics and other omics

• Optional combination with global or targeted metabolomics
• Pathway-level interpretation of GAG metabolism, ECM–receptor interaction and related metabolic networks

Analytical Coverage: GAG Types and Disaccharide Panels

GAG Classes and LC–MS/MS Coverage

Disaccharide Panel Options

Why Choose Our GAG Analysis Services?

• Specialized in GAGs and ECM biology
  Our methods and reporting are built around real projects in oncology, vascular biology, cartilage/disc research and functional polysaccharides – not generic, one-size-fits-all metabolomics.
• High information per run
  Multi-class panels (HS/HP, CS/DS, KS, HA) and broad disaccharide coverage in a single LC–MS/MS workflow help reduce batch effects and keep per-sample costs under control.
• Efficient with precious samples
  The workflow works with small volumes and diverse matrices, including plasma/serum, tissues, cell pellets, organoids, ECM extracts and biomaterials.
• Robust QC and easy-to-use results
  Internal standards, pooled QCs and controlled batch design support reproducible quantitation, while standardized tables and clear visual summaries make downstream analysis and reporting straightforward.

Platform and Analytical Methods for GAG Analysis

Our GAG assays are built on mainstream LC–MS platforms widely used in metabolomics and glycomics, with settings optimized for disaccharide sensitivity and reproducibility.

UHPLC separation

• Systems: high-performance UHPLC (e.g., Agilent 1290)
• Columns: 2.1 × 100–150 mm, 1.7–2.6 μm amide or C18 columns for GAG disaccharides
• Typical run time: ~20–30 min per sample, optimized for baseline separation of key GAG species

Targeted LC–MS/MS quantification

• Mass spectrometers: triple quadrupole instruments (e.g., Agilent 6495C)
• Ionization & mode: ESI negative, MRM transitions for each disaccharide
• Performance: linear dynamic range ≥ 3–4 orders of magnitude; typical intra-batch CVs < 15% for qualified peaks

High-resolution LC–MS for structural confirmation (on demand)

• Platforms: Orbitrap-type MS (e.g., Q Exactive class) for selected samples
• Use: full-scan and MS/MS to confirm disaccharide identities and complex sulfation motifs when required

Built-in QC and stability control

• Stable or structural analog internal standards where available
• Pooled QC injections throughout the batch to monitor retention time, signal stability and system performance

Agilent 1260 Infinity II HPLC (Figure from Agilent)

Agilent 6495C Triple quadrupole (Figure from Agilent)

Thermo Fisher Q Exactive (Figure from Thermo Fisher)

How Our GAG Analysis Works

Research Applications of GAG Profiling

Tumor and Immune Microenvironment

• Compare GAG composition and sulfation patterns between tumor and matched control tissues or 3D models.
• Track HS/CS remodeling under targeted therapy, chemotherapy or immunotherapy.
• Correlate GAG changes with growth factor/chemokine binding, immune cell infiltration and ECM markers.

Endothelial Glycocalyx and Vascular Biology

• Characterize GAGs shed from the endothelial glycocalyx into plasma or serum in vascular injury or inflammation models.
• Evaluate how different interventions influence glycocalyx integrity and vascular function.
• Integrate GAG data with lipidomics or metabolomics to obtain a systems view of vascular stress.

Cartilage, Intervertebral Disc and ECM Remodeling

• Quantify CS/DS, KS and HA in cartilage, disc tissue and engineered constructs.
• Monitor GAG loss and structural remodeling during degeneration, mechanical loading or treatment.
• Relate GAG profiles to biomechanical properties, chondrogenic differentiation and ECM quality.

Metabolic and Genetic Perturbation of GAG Pathways

• Investigate GAG metabolism in knockout, knock-in or gene-edited models and corresponding cell systems.
• Assess how changes in glycosyltransferases, sulfotransferases and hydrolases reshape GAG composition.
• Combine GAG profiling with other omics to map pathway-level effects and potential early biomarkers.

Marine-Derived and Functional Polysaccharides

• Characterize GAG-rich extracts from marine organisms or animal-derived materials.
• Compare structural features (chain integrity, sulfation motifs) across species, batches or processing conditions.
• Link GAG profiles to in vitro or in vivo bioactivity in functional ingredient and biomaterial research.

How to Prepare and Submit Samples for GAG Analysis

General Recommendations

• Labeling：Use clear, waterproof labels with sample ID, matrix and group information.
• Aliquots：If possible, send single-use aliquots to avoid repeated freeze–thaw cycles.
• Documentation：Include a sample list (Excel or CSV) with sample IDs, groups, species, matrix and any key treatments or time points.

Deliverables: What You Receive from GAG Analysis

Sample and ID summary – A clear sample list with IDs, groups, matrix and any key metadata (Excel/CSV).

Processed quantitative tables – GAG class-level and disaccharide-level values for each sample, with units and basic annotations (Excel/CSV).

Basic group comparison – Mean, SD/SEM, fold-change and simple significance flags (e.g. p-values) for defined groups.

Key overview figures – 1–3 core plots (such as heatmaps, bar charts and/or PCA/cluster overviews) in common image formats.

Method and QC summary – A concise description of sample preparation, LC–MS/MS settings, quantification and QC strategy suitable for methods sections.

Raw data on request – LC–MS(/MS) raw files can be provided if you need to perform additional in-house analyses.

LC–MS/MS analytical performance. (a) Overlaid MRM chromatograms of GAG disaccharides. (b) Linear calibration curve (R² > 0.99). (c) Sample signal intensity versus LLOQ.

Differential GAG profiling. (a) Hierarchical clustering heatmap of disaccharide abundances. (b) Quantification of key disaccharides across groups (mean ± SEM).

Quality control and stability. (a) PCA score plot showing tight QC clustering. (b) Distribution of feature RSDs. (c) Longitudinal QC signal stability.

Integrated disease model study. (a) Study design schematic. (b) Altered HS/CS disaccharide levels across groups. (c) Correlation between GAG motifs and phenotypic markers.