Epitope Mapping Services via HDX-MS2024-05-14T15:13:13-04:00

Epitope Mapping Service via HDX-MS.

RapidHDX-MS™ is our mass spectrometry based epitope mapping service, that can identify the binding site of an antibody to its corresponding antigen with the highest confidence and resolution. Our HDX MS service can study complex binding, identify linear and conformational epitopes. Integrated MAbSilico AI enables us to scale up to 100’s of mAbs at a time.

How our HDX-MS Service works with AI for Epitope Mapping.

The HDX-MS Epitope Mapping Workflow

Hydrogen-Deuterium-eXchange Mass Spectrometry (HDX-MS) measures the exposure levels of amide hydrogen atoms on the surface of a protein or protein complex. The first step causes the exposed hydrogen atoms to be readily exchanged with deuterium. Hydrogen atoms that are buried within the protein structure – for instance at the binding site of an antibody-antigen complex – are not exchanged as readily. By examining the peptides using Bottom-up mass spectrometry, and comparing them with the amino acid sequence, it is then possible to determine which regions are the binding locations between the interacting partners.

  1. Labeling – incubate different fractions with D2O solution in a time series
  2. Quench – chill and control temperature to prevent further exchange or back-exchange
  3. Digest – prepare peptides for analysis
  4. LC-MS/MS
  5. Data processing – determine deuterium uptake of digested peptides acid and identify binding site(s)
  6. Comparison – compare similar samples – e.g. antibodies with similar sequences
hdx ms workflow

How AI-Based Epitope Mapping Works

Your antibody sequence is used to create a 3D structure. Docking analysis models interactions between your mAb and the target and reveals the most likely location of the interface. The result is a fast and medium resolution epitope prediction.

NEW – Integrating AI with our HDX-MS Epitope Mapping Service

In epitope screening analyses, 100’s of antibodies are first sorted into bins based on their predicted epitopes using MAbSilico AI. Subsequently, HDX-MS experiments confirm epitope predictions and increase resolution. These experimentally determined epitope maps are fed back to the AI to refine the epitope predictions for related antibodies. In single antibody-antigen analyses, MAbSilico AI generated epitope predictions can guide experimenters to more detailed study of certain regions, or simply increase confidence in the results.

hdx ms epitope mapping applications

Applications of our HDX-MS + AI and HDX-MS Services

While our RapidHDX-MS™ service is commonly used for epitope mapping in an antibody-antigen interaction, it can also be used to study other protein-protein interactions, protein conformation changes, multi-protein complexes, small molecule interactions with proteins, disulfide linked proteins, glycosylation sites, protein interactions with DNA or RNA, disordered proteins, etc. Note that the AI-powered workflows are only available for antibody-antigen interactions at this time.

Advantages of Our HDX-MS Services.

High Resolution Epitopes Even for Large Ab:Ag Complexes.

We are able to achieve higher coverage with more overlapping peptides, and resolve epitope regions to within a few amino acids using our multi-enzyme approach.

Quality and Expertise in Epitope Mapping.

With over 7 years of experience in HDX-MS services, we are capable of working with a variety of analytes and ligands, and novel projects. No two projects are ever the same and so experimental conditions are always individually optimized for overall project success.

Part of a Complete Epitope Characterization and Antibody Sequencing Platform.

Our HDX-MS service is one part of our antibody solution platform that also offers isolation, protein sequencing, recombinant expression, kinetic analysis and epitope mapping. Combining more than one service into a single workflow gives convenient access to richer, higher quality results.

HDX-MS Epitope Mapping Pricing.

HDX-MS Epitope Mapping

$19,500+
  • Detailed epitope mapping analysis for 1 antibody-antigen pair.
  • Requirements: Antigen 200 μg, Antibody 200 μg, Antigen sequence
  • Add ons: AI predictions, Paratope mapping, additional mAbs
  • Turn around time: 4 weeks

HDX-MS + AI Epitope Screening

Inquire
  • Epitope mapping for 100’s of antibodies against one antigen.
  • Requirements: Antigen 500 μg, Antibodies 100 μg each, Antibody sequences, Antigen 3D structure
  • Add ons: additional antibodies
  • Turn around time: 4-6 weeks

Customized HDX-MS Projects

$19,500+
  • Custom analysis of protein complexes, conformation changes, ligands and other structural questions.
  • Please inquire about experiment design, and sample requirements.

Getting Started.

Requirements

  1. For antibodies: 200μg of antigen and the monoclonal antibody for each epitope.
  2. For other proteins: 20 μM of each
  3. Protein sequence (e.g. of the antigen)
  4. Protein structure (only required for epitope screening service)
  5. Antibody sequences (only required for epitope screening service)

Deliverables

  • Report of regions showing relative deuterium uptake on the sequence and on a 3D protein structure
  • Indication of the epitope region(s)
  • Uptake plots and heatmap
  • For epitope screening service: antibody bins and additional epitope maps
Dominic Narang, PhD
Dominic Narang, PhDManager of HDX and Core Services, Sr. Research Scientist

Talk to Our Scientists.

We Have Sequenced 9000+ Antibodies and We Are Eager to Help You.

Through next generation protein sequencing, Rapid Novor enables reliable discovery and development of novel reagents, diagnostics, and therapeutics. Thanks to our Next Generation Protein Sequencing and antibody discovery services, researchers have furthered thousands of projects, patented antibody therapeutics, and developed the first recombinant polyclonal antibody diagnostics.

Talk to Our Scientists.

We Have Sequenced 9000+ Antibodies and We Are Eager to Help You.

Through next generation protein sequencing, Rapid Novor enables timely and reliable discovery and development of novel reagents, diagnostics, and therapeutics. Thanks to our Next Generation Protein Sequencing and antibody discovery services, researchers have furthered thousands of projects, patented antibody therapeutics, and ran the first recombinant polyclonal antibody diagnostics

Talk to our scientists. We have sequenced over 9000+ antibodies and we are eager to help you.

Antibody Sequencing, Discovery and Characterization Services.

Antibody Sequencing & Discovery Services.

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Monoclonal antibody sequencing from small antibodysamples, no need for hybridoma or DNA information. Full sequence in record time.
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REmAb® Protein Sequencing

Monoclonal antibody sequencing from small antibodysamples, no need for hybridoma or DNA information. Full sequence in record time.
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REpAb® pAb Sequencing

Polyclonal antibody sequencing and antibody discovery service. Sequence antibodies from blood or a polyclonal mixture.
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MATCHmAb

Antibody verification by rapid peptide mapping. Antibody sequence confirmation and full detailed mapping for development purposes.
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RapidSPR Analysis

Label-free evaluation of antibody-antigen binding using surface plasmon resonance on Biacore or Nicoya. Can be employed for detailed kinetic profiling, kinetics screening, or epitope binning.
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Antibody Characterization

LC-MS analysis for study of antibody glycosylation, disulfide bonds, post-translational modifications, sequence variants, intact mass and size.
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