HDX-MS Epitope Mapping Service.

Through mass spectrometry based epitope mapping techniques, Rapid Novor can identify the binding site of an antibody to its corresponding antigen with the highest confidence and resolution.

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Benefits of Rapid HDX-MS Epitope Mapping

  • Identify linear, conformational and structural epitopes – understand complex binding
  • Resolution – higher than other methods
  • Speed – answers in weeks, not months
  • Cost effective – make it part of your routine

Why MS Epitope Mapping?

Epitope mapping is required for FDA and EMEA regulatory filings. It is also critical for IP protection and highly insightful for guided antibody engineering and development.

Mass spectrometry (MS) based antibody-epitope mapping service is the high throughput, high-resolution method of choice for rapid binding site characterization in therapeutic and diagnostic antibody development.

Reproducibility Impacts.

$0
USD $1.7 billion wasted each year on commercial antibodies that don’t work as expected. $25 billion wasted on non-reproducible pre-clinical research.
0%
As many as 50% of reagent antibodies are shown to not recognize their targets. 32% of Hybridomas produce unintended antibodies.
0%
Only 6 out of 53 landmark pre-clinical studies could be reproduced in one study. That’s a staggering 88% failure rate.

Applications of HDX-MS

While there are many possible applications of HDX-MS, Rapid Novor is highly focused on:

Antibody-Antigen epitope mapping studies

Augmenting epitope binning studies (e.g. via SPR)

Biosimilar characterization and comparability

Guided antibody discovery

Batch-to-batch reproducibility for antibody production

Antibody engineering and optimization

Who uses Epitope Mapping.

Researchers, Antibody Users

Researchers use tool antibodies every day, across many applications. Sequence confirmation is the first step in troubleshooting, or daily quality checks to prevent issues.

Antibody Venders, Producers

Easily verify each new lot. Offer premium Verified by MATCHmAb™ products, or an add-on service.

Antibody Engineering

Cell line instability could introduce mutations to humanized antibodies. Verify the CDRs have not changed or confirm the full expressed sequence matches the engineered one.

CRO, Custom Developers

Checkpoints to increase confidence. Avoid troubleshooting re-runs with clients.

How Epitope Mapping Works.

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 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.

Workflow:

  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
MATCHmAb™
Workflow LC-MS/MS, single or dual digest
Bioinformatics Real-time analysis, purpose built algorithms
Speed Fast: 1-4 days
Throughput High: > 100 per week
Coverage Higher, and amino acid level
 Traditional Peptide Mapping
Workflow LC-MS only, single enzyme only
Bioinformatics Post-processing, off the shelf tools
Speed Slow: weeks
Throughput Low
Coverage Lower, and only peptide level

Comparison With Other Methods.

Rapid Novor HDX Peptide Arrays and Peptide Scanning Crystal Structure
6 Weeks 3-10 weeks (peptide panel synthesis takes time) Months
Conformational, linear, structural Linear mostly Conformational, linear, structural
300μg of sample 50-100μg of sample
$35,000 $19500 $1000 to $15,000 $$$$

Getting Started is Easy.

Here’s what we need:

  1. 20 μM of each protein solution – e.g. for antibodies 300μg of the protein in solution. Any species any isotype
  2. Protein sequences (we can perform sequencing if required)
  3. Tell us what you hope to achieve
  4. We’ll provide a timely quote

Deliverables

  • Report of regions showing relative deuterium uptake on the sequence and on a 3D structure
  • Indication of the epitope region

Talk to Our Scientists.

We Have Sequenced 4000+ 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.

We Have Sequenced 5000+ 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 4000 antibodies and we are eager to help you.