What is de novo antibody protein sequencing?

Unlike a classical hybridoma sequencing service, de novo antibody sequencing determines the amino-acid sequence of an antibody without requiring mRNA, DNA, or a hybridoma cell line. By analyzing mass differences between fragment ions, it becomes possible to reconstruct peptide sequences — most amino acids have unique masses, making the process feasible even without genetic information. Modern MS/MS interpretation relies on expert analysis or advanced algorithms (PEAKS, NOVOR). While challenges remain (post-translational modifications, noise, missing ions), state-of-the-art technologies now make the process fast, reliable, and highly accurate. Thanks to the latest advances in mass spectrometry, ProteoGenix guarantees near 100% sequence accuracy, including in CDR regions.

What are the advantages of protein-based sequencing compared with classical DNA sequencing?

You do not need a cell line. When the hybridoma is lost, the antibody can still be recovered. Post-translational modifications are detected, which is not possible with DNA sequencing. Works for any isotype and any species. Fits high-throughput sequencing projects. This makes it a valuable option when you need a fast, practical alternative to a traditional hybridoma sequencing service.

Do you combine multiple fragmentation methods?

Yes. We use EThcD, combining the strengths of ETD and HCD. This dual approach delivers: A double layer of sequence confirmation Better preservation of post-translational modifications Superior accuracy in complex regions such as CDR-H3

How much antibody do you need?

We typically require 50–100 μg of antibody at >80% purity.

Once you have the sequence, can you produce or optimize the antibody?

Of course. ProteoGenix is a leading provider of custom antibody production and downstream antibody engineering services, supporting every step from expression to functional optimization. All sequences obtained through our antibody protein sequencing service can be produced using our recombinant antibody production services, either by transient antibody expression or through custom cell line development for long-term manufacturing. To further refine your molecule, we also offer: Affinity maturation services Antibody humanization services Developability assessment services Whether you need rapid expression, large-scale recombinant production, or advanced engineering, our platform provides a complete and coherent workflow from sequencing to optimized antibodies.

Antibody protein sequencing service

Lost your hybridoma? Your antibody isn’t lost.

Save your antibody now

0 week

From purified antibody to sequence

Success rate

0 µg

Purified antibody needed

Losing your hybridoma doesn’t mean losing years of work. With just 50 μg of purified antibody, our de novo antibody sequencing service can recover your sequence.

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A guaranteed way to secure your antibody

Our success rate is close to 100%. That’s why we apply a clear rule: we determine your antibody sequence, or you pay nothing.

I want to sequence my antibody

Compatible with all antibody formats and species

Our de novo antibody sequencing service works with any isotype or format: IgG, IgA, IgM, IgY, Fab, scFv, VHH, bispecifics, polyclonals, from mouse, rat, rabbit, camelid, and many others.

Optional recombinant production at competitive rates

You can combine sequencing with our recombinant antibody production platform. This allows you to secure the sequence and obtain a recombinant version at a competitive price, all handled by a single experienced provider.
And again: if we cannot produce your recombinant antibody, you pay nothing for either step.

I want to sequence and produce my antibody

Our antibody protein sequencing service in detail : from purified antibody to sequence in 1 week

From purified antibody to your sequence in 1 week

Enzymatic digestion of the antibody

Cleaves the antibody into defined peptide fragments
Generates optimal peptide sizes for MS/MS acquisition
Ensures full coverage of variable and constant regions

LC-MS/MS

Separates peptides before ionization
Produces high-resolution spectra for each fragment
Captures both b/y and c/z ion series for robust analysis

De novo peptide sequencing

Reconstructs peptide sequences directly from MS/MS spectra
Validates coverage through overlap consistency
Highlights any ambiguous regions for expert review

Assembly of overlapping peptides

Reconstructs peptide sequences directly from MS/MS spectra
Validates coverage through overlap consistency
Highlights any ambiguous regions for expert review

Data analysis and report writing

Delivers a full annotated report including sequence and PTMs
Determines leucine/isoleucine with dedicated fragmentation signatures

FAQ about our de novo antibody protein sequencing service

Unlike a classical hybridoma sequencing service, de novo antibody sequencing determines the amino-acid sequence of an antibody without requiring mRNA, DNA, or a hybridoma cell line.
By analyzing mass differences between fragment ions, it becomes possible to reconstruct peptide sequences — most amino acids have unique masses, making the process feasible even without genetic information.
Modern MS/MS interpretation relies on expert analysis or advanced algorithms (PEAKS, NOVOR). While challenges remain (post-translational modifications, noise, missing ions), state-of-the-art technologies now make the process fast, reliable, and highly accurate.
Thanks to the latest advances in mass spectrometry, ProteoGenix guarantees near 100% sequence accuracy, including in CDR regions.
- You do not need a cell line. When the hybridoma is lost, the antibody can still be recovered.
- Post-translational modifications are detected, which is not possible with DNA sequencing.
- Works for any isotype and any species.
- Fits high-throughput sequencing projects.
This makes it a valuable option when you need a fast, practical alternative to a traditional hybridoma sequencing service.
Yes. We use EThcD, combining the strengths of ETD and HCD.
This dual approach delivers:
- A double layer of sequence confirmation
- Better preservation of post-translational modifications
- Superior accuracy in complex regions such as CDR-H3
Of course. ProteoGenix is a leading provider of custom antibody production and downstream antibody engineering services, supporting every step from expression to functional optimization.
All sequences obtained through our antibody protein sequencing service can be produced using our recombinant antibody production services, either by transient antibody expression or through custom cell line development for long-term manufacturing.
To further refine your molecule, we also offer:
Whether you need rapid expression, large-scale recombinant production, or advanced engineering, our platform provides a complete and coherent workflow from sequencing to optimized antibodies.