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Proteins & Peptides Primary Structure Characterization

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Structural characterization is fundamental to the development and quality control of protein and peptide biopharmaceuticals. According to the ICH Q6B guideline, a comprehensive structural analysis of proteins and peptides is required to prove the identity of the protein or peptide biopharmaceutical and the consistency of production batches. Protein and peptide molecules are composed of many amino acids connected by peptide bonds and have complex structures that must be characterized from the primary sequence of amino acids to the higher-order structure. CD Formulation has extensive experience in protein structural characterization and provides a wide range of protein primary structure characterization services at every stage of your product development and manufacturing.

Why Characterize the Primary Structure of a Protein & Peptide?

The structure of a therapeutic protein or peptide is the three-dimensional arrangement of atoms in an amino acid chain molecule. In order to perform its biological function, the protein folds into one or more specific spatial conformations, which makes the molecular structure complex and has great structural heterogeneity. Among them, the primary structure of a therapeutic protein or peptide is the linear sequence of amino acids in the polypeptide chain, including the location of disulfide bonds, which is also the basis of the biological function of the protein or peptide. Regulations require that the primary structure of proteins or peptides must be characterized to identify batch-to-batch differences and ensure product safety. Characterizing the primary structure of a protein or peptide, not only can its source, purity, and stability be determined, but also its biological activity and the relationship between structure and function can be deeply understood, thus providing important references for drug design, disease diagnosis, and treatment.

Fig. 1 Protein primary structure. Fig.1 Protein primary structure, amino acid residues. (CD Formulation)

Explore our Protein & Peptide Primary Structure Characterization Services

Our experienced scientists have extensive expertise and successful project experience in performing primary structural characterization of proteins or peptides, and will strategically design experimental protocols based on your needs to obtain the data required for identity, explore heterogeneity patterns, and demonstrate consistent quality of the drug substance.

In addition, we support you at every stage of the development and manufacturing of your therapeutic protein or peptide, whether it is drug discovery, design, or process development. Our laboratories are equipped with a broad technology base, especially our strengths in mass spectrometry (Orbitrap and QToF) analysis, which can provide high-resolution, accurate mass (HRAM) data.

Our Solutions for Protein & Peptide Primary Structure Characterization

At CD Formulation, our team of protein experts can perform in-depth and highly sensitive analysis of the primary structure of any type of therapeutic protein or peptide, obtaining information such as their amino acid sequence, the location of leucine and cysteine, glycosylation sites, possible modifications, potential oxidation and degradation products, etc. Our protein scientists are able to perform the following:

Molecular weight determination.
Amino acid sequence analysis.
Amino acid composition analysis.
Protein disulfide bond identification and quantification.
Edman N-segment sequencing.
C-terminal sequencing.
Mass spectrometry-based sequencing.
Peptide mapping.
De novo sequencing.
Post-translational modification analysis.

Our Technology Platforms

With our advantages in protein and peptide structural analysis and successful project experience, we have successfully established multiple advanced protein structural analysis platforms. Our protein scientists can analyze any type of protein or peptide structure for you, including natural proteins, recombinant proteins, antibodies, enzymes, and peptide drugs, etc.

Technology & Platform	Description
Edman Degradation	It refers to the process of sequencing the N-terminus (i.e., end) of a protein, which is based on chemically removing one N-terminal amino acid at a time for sequence analysis. N-terminal sequencing ensures consistency in biopharmaceutical production by confirming the integrity of the N-terminus of a protein between batches.
C-terminal Sequencing	It refers to the process of sequencing the C-terminus (i.e., end) of a protein, which is achieved by partially hydrolyzing the protein and then sequencing the resulting protein fragments. Protein C-terminal sequencing reveals the amino acid sequence of the protein, which is a regulatory requirement for quality control and ensures that the correct protein sequence is present in the final product.
Peptide Mapping	Our peptide mapping analysis is the selective fragmentation of the protein or peptide to be tested into peptide fragments by enzymatic or chemical digestion, followed by high-resolution mass spectrometry (Orbitrap, QToF) analysis. Peptide mapping is routinely used for batch release or stability studies.
De Novo Sequencing	Our de novo sequencing is the determination of the primary structure of the protein by acidic hydrolysis or enzymatic digestion of the protein or peptide to be tested to obtain the amino acid sequence, which is analyzed by mass spectrometry.
Amino Acid Analysis	Amino acid analysis is the gold standard for accurate quantification of samples such as peptides and proteins. The amino acid composition and sequence of a protein are determined by hydrolyzing the protein into amino acids and separating and detecting the content and sequence of each amino acid.
Bioinformatics	Bioinformatics uses a known protein sequence database to compare the amino acid sequence of the target protein and find similar protein sequences to infer the possible structure of the target protein. In addition, bioinformatics can also use computer simulation technology to predict the secondary structure of proteins, such as α-helix and β-fold, to further help identify the primary structure of proteins.

Why Choose Us for Protein & Peptide Primary Structure Characterization?

We have extensive experience in the primary structure characterization of proteins and peptides.
Our laboratories are equipped with state-of-the-art instruments.
Comprehensive primary structure characterization testing capabilities, including but not limited to molecular weight determination, C-terminal sequencing, Edman n-segment sequencing, post-translational modification analysis, peptide mapping, etc.
Decades of experience supporting biopharmaceutical product development using protein and peptide primary structure characterization.
Flexible experimental design and testing options can meet any customer's specific needs.

Publication

Published Data

Technology: Development of an LC-MS/MS peptide mapping protocol for the NISTmAb

Journal: Proceedings of the National Academy of Sciences of the United States of America

IF: 4.3

Published: 2018

Results:

Peptide mapping is a component of the analytical toolbox used within the biopharmaceutical industry to aid in the identity confirmation of a protein therapeutic and to monitor degradative events such as oxidation or deamidation. The authors describe the optimization of a tryptic digestion protocol used for peptide mapping of the IgG1κ monoclonal antibody NISTmAb RM 8671 (NISTmAb) ,i.e. PS 8670. The result show that tryptic digestion was performed using an optimized protocol and followed by LC-UV-MS analysis. Finally, a peptide map of the NISTmAb generated which allowed us to confirm its identity at the level of primary structure.

Fig. 2 The PS 8670 tryptic digest was analyzed by LC-UV-MS. Fig. 2 The PS 8670 tryptic digest was analyzed by LC-UV-MS in quadruplicate. (Mouchahoir T, et al., 2018)

CD Formulation aims to provide a powerful analytical tool for your protein or peptide biopharmaceutical development and manufacturing. Our protein and peptide primary structure analysis services can accurately determine the amino acid sequence of the protein and peptide being tested, helping you confirm the purity and integrity of your drug product. Please feel free to contact us if you are interested in our services. We will provide you with the most professional advice and support to ensure the smooth launch and implementation of your project.

References

Deutzmann R. Structural characterization of proteins and peptides. Methods Mol Med. 2004, 94:269-97.
Zhang G, Annan RS, Carr SA, et al. Overview of peptide and protein analysis by mass spectrometry. Curr Protoc Protein Sci. 2010, Chapter 16:Unit16.1.
Syka, John EP, Melanie J. et al. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. 2004, 101(26):9528-33.
Mouchahoir T, Schiel JE. Development of an LC-MS/MS peptide mapping protocol for the NISTmAb. Anal Bioanal Chem. 2018, 410(8):2111-2126.

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