Antibody Sequencing Service

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Workflow of de novo Antibody Protein Sequencing

It is required to obtain the protein sequence of a monoclonal antibody (mAb) for development of novel biotherapeutics. The need to extensively characterize mAbs at the molecular level presents a unique challenge to drug developers and manufacturers.

PEAKS AB Antibody Protein Sequencing Service provides the answer to this.

Key Features:

  • Mass spectrometry (LC-MS/MS) analysis of 0.2mg mAb protein sample
  • de novo antibody protein sequencing
  • Works for all antibody isotypes and species
  • Quantify PTMs and sequence variants
  • Guarantee two-week turn-around and service quality

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BSI has developed the proprietary de novo antibody protein sequencing technology, based on our PEAKS AB Software, to sequence antibodies 1,2. The Antibody Sequencing Service consists of full length heavy and light-chain antibody sequencing for all species, isotypes and allotypes. Numerous successful cases from our antibody protein sequencing service have confirmed 100% accuracy and 100% coverage. Satisfaction is guaranteed to meet our customers’ needs.

PEAKS AB- de novo antibody protein sequencing service full coverage

100% Sequence Coverage


Our Antibody Sequencing Service guarantees each amino acid is typically mapped with more than 20 distinct peptides. The peptide mapping in the left is obtained using our PEAKS AB Software at 0.1% of FDR at peptide-spectrum level. Each bar under the sequence denotes a peptide identified from the MS/MS data and the color represents a specified enzyme used for sample digestion.

100% Sequence Accuracy


The Antibody Protein Sequencing Service carries out quality control at the amino acid level based on the de novo sequencing result. Direct fragment ion evidences from MS/MS data are required for each amino acid in the assembled protein sequences.

PEAKS AB - de novo Antibody Sequencing View

Antibody Sequencing Service - Modification Analysis

Comprehensive Modification Analysis


The Antibody Protein Sequencing Service provides qualitative and quantitative analysis for post-translational modifications (PTMs) and sequence variants. The screenshot illustrates a PTM analysis result using our PEAKS AB Software.

Confident Leucine & Isoleucine Differentiation

Leucine (Leu) and Isoleucine (Ile) residues are generally considered to be indistinguishable by MS. Due to this ambiguity, it is difficult to differentiate between the two residues and this can impose serious consequences on the overall performance of the antibody’s specificity and affinity. In our Antibody Sequencing Service, we use an integrated strategy that combines 1) w-ion detection in EThcD, 2) enzyme cleavage preference, and 3) homology statistics for unambiguous discrimination of Leu/Ile residues.

1. EThcD-based approach using diagnostic w-ions has proven to solve this problem 3,4,5.

 (Image cited from Ref. 4)

(Image cited from Ref. 4)

2. Enzyme digestion preference, e.g., chymotrypsin and pepsin selectively prefers digestion at C-terminal of Leu over Ile residues.

3. Homology database search for conservative sites in the constant region and framework region.