Epitope Mapping

Why XL-MS for Epitope Mapping?

Traditional epitope mapping methods, such as alanine scanning or peptide arrays, can be labor-intensive, low-throughput, or limited to linear epitopes. XL-MS breaks through these constraints by enabling:

• Structural-level resolution: Capture both linear and conformational epitopes in native-like conditions
• Rapid turnaround: Generate actionable data in days, not weeks
• Minimal sample requirements: Compatible with purified proteins produced in smaller scale transient expressions
• Orthogonal validation: Complements cryo-EM, HDX-MS, or SPR with direct spatial constraints

How It Works

XL-MS leverages bifunctional cross-linkers to covalently tether interacting residues between antibody and antigen. After digestion and LC-MS/MS analysis, cross-linked peptides are identified and mapped onto structural models—pinpointing the epitope and paratope with sub-nanometer precision.

This approach is especially valuable for:

• Characterizing therapeutic antibody candidates
• Comparing epitope coverage across clones or formats
• De-risking IP and biosimilarity assessments
• Guiding rational affinity maturation and humanization

Applications

Whether you're developing monoclonals, bispecifics, or antibody-drug conjugates, XL-MS epitope mapping empowers teams to:

• Make informed platform selections
• Accelerate lead optimization
• Strengthen regulatory packages with structural evidence

Ready to Map What Matters?

Our XL-MS epitope mapping service combines cutting-edge instrumentation, proprietary cross-linking chemistries, and expert bioinformatics to deliver high-confidence results tailored to your program’s needs.

Let’s turn molecular insight into strategic advantage.