Protein Sequencing

Protein Sequencing & Primary Structure Analysis

Protein sequencing is the first and most fundamental step in the structural characterization of biologics and biosimilars. While the amino acid sequence is encoded at the DNA level, the full characterization of a therapeutic protein goes far beyond the theoretical sequence. It starts with a robust confirmation of the expected primary structure and continues with the detection of sequence variants, terminal modifications and molecular weight differences that can affect function, stability and safety.

For any protein-based drug, verification of the theoretically expected primary structure should form the first pillar of detailed structural analysis. At Biofidus, our comprehensive analytical portfolio includes a range of state-of-the-art protein sequencing services to determine the exact amino acid sequence, identify N- and C-terminal modifications, confirm intact molecular weight and detect potential sequence variants or mutations.

Our extensive experience allows us to guide you through the available methods and define the optimal analytical strategy for your project.

In accordance with your needs, we adapt and, where required, qualify (according to ICH guidelines) our platform methods, tailored to your drug substance, its formulation matrix and your specific analytical questions, from early research to comparability, biosimilarity and commercial lifecycle management.

Get in contact with us to find the optimal strategy for your project and to speak directly from scientist to scientist.

Our Capabilities

  • Intact molecular weight & mass confirmation
  • Full amino acid sequence confirmation (primary structure)
  • N-terminal and C-terminal characterization
  • Detection of sequence variants & mutations (SVs)
  • Verification of disulfide bond pattern and cysteine connectivity
  • Assessment of clipping and truncation (N- or C-terminal truncations, internal deletions)
  • Characterization of engineered sequence features (tags, linkers, fusion junctions)
  • Support for comparability & biosimilarity
  • Integration with PTM & glycosylation analysis
  • Method development & qualification for primary-structure CQAs

Just what you need? Contact us!

FAQ

Find answers to frequently asked questions about our analytical services, methods, technologies, and studies, from molecular characterization and bioactivity to comparability, stability, and fit-for-purpose method development. 

Yes. We support N-/C-terminal characterization and verification of disulfide bond patterns/cysteine connectivity using tailored MS workflows (including non-reduced mapping) and complementary approaches when appropriate.

Yes. We can characterize engineered sequence features (tags, linkers, fusion junctions) as part of sequence confirmation and integrity assessment.

Yes. Our MS-based primary-structure workflows can detect truncations, clipping and other sequence integrity issues and help interpret their potential impact on product quality.

Yes. Primary-structure confirmation is commonly combined with PTM and glycosylation characterization to support comparability and biosimilarity packages and to ensure sequence-related CQAs are controlled.

We confirm primary structure using high-coverage LC‑MS/MS peptide mapping (coverage mapping) and complement it with intact mass/native MS where appropriate, enabling detection of sequence variants, truncations and molecular weight differences.

CQA relevant techniques

Advancing research through tailored bioanalytical solutions.

  • Intact mass confirmation → (Intact LC-ESI-MS / native MS)
  • Full sequence confirmation → (LC-MS/MS peptide mapping, coverage mapping)
  • N- and C-terminal characterization → (Terminal-specific LC-MS/MS, Edman where appropriate)
  • Sequence variants / mutations → (High-coverage mapping + variant search)
  • Disulfide pattern → (Non-reduced peptide mapping, disulfide mapping)

TECHNOLOGIES USED

  1. LC-FLD
  2. LC-ESI-TOF
  3. MALDI-TOF
  4. Edman
  5. RP-UV
  6. CEX-UV

Tell us about Your Project

We‘ll advise you to define your assay needs.

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Our Expert

Across end-to-end delivery, our experts remain on hand with deep scientific expertise whenever needed, providing oversight to streamline and de-risk milestone delivery.
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