Question 1

What is de novo antibody protein sequencing?

Accepted Answer

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.

Question 2

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

Accepted Answer

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.

Question 3

Do you combine multiple fragmentation methods?

Accepted Answer

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

Question 4

How much antibody do you need?

Accepted Answer

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

Question 5

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

Accepted Answer

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.

Servicio de secuenciación de proteínas de anticuerpos de novo