Protein Structure Characterisation and Conformation

Protein structure and conformation characterisation in line with EMA, FDA and ICH guidelines includes sequencing, peptide mapping and post-translational modification studies

Protein structure characterisation is fundamental to biologic development and ongoing quality control, in terms of identification and product homology. Proteins have complex structures which must characterised from the primary sequence of amino acids, through to higher order structure. In accordance with the ICH Q6B Guidelines, it is important to perform an overall assessment of structural heterogeneity to demonstrate protein identity and consistency of manufactured batches. The tests selected can be qualitative in nature, but should be highly specific for the drug product and should be based on unique aspects of the molecular structure. 

Our protein scientists have a great deal of expertise in delivering analytical programs that are strategically designed to optimise the data required to determine or confirm identity, explore patterns of heterogeneity and demonstrate consistency in quality of the drug substance. 

We provide extensive protein characterization during the development phase and, where necessary, following significant process changes.  To support your submission, we can provide data to Good Laboratory Practice (GLP) or Good Manufacturing Practice (GMP), as appropriate, with comparison against the most suitable reference standard, if available. Our laboratories are equipped with a broad technology base and our strengths in mass spectrometry (Orbitrap and QToF) analysis, in particular, allow the ability to provide high-resolution, accurate-mass (HRAM) data.

Our Total Quality Assurance expertise makes Intertek the perfect partner to expedite your protein structural characterisation programs to meet your development, submission or ongoing processing needs.


We apply a number of approaches to initially quantitate the distribution of amino acids. This is then accompanied by sequencing studies using a broad range of enzymatic followed analysis with high resolution accurate-mass spectrometry (Orbitrap, QToF) coupled with U(H)PLC technology.

Intertek conduct selective fragmentation of protein into discrete peptides by enzyme or chemical digestion followed by high resolution mass spectrometry (Orbitrap, QToF) analysis. Once the methodology is established, we can take the methods through validation for application in batch release or stability studies.
Confirmation of the amino-terminal  (N-terminal) and carboxy-terminal (C-terminal) amino acids is performed by MALDI-MS and high resolution mass spectrometry (Orbitrap, QToF) for product identification and to establish homogeneity, where understanding the type and extent of modifications at either termini, is a fundamental aspect of product quality control.
Where cysteine residues are present in the molecule, our scientists perform a qualitative / semi-quantitative assessment of the position and extent of expected and mismatched disulphide bridges by high resolution mass spectrometry (Orbitrap, QToF) and colorimetric tests for free sulfhydryl groups.
Our post translational modification analysis experts apply a strategic approach to PTM analysis during early development phases to help you to establish product acceptance criteria and as part of structural characterization studies and comparability programs, stability studies or release testing.
The higher-order structure is examined using far and near-UV circular dichroism (CD), nuclear magnetic resonance (NMR), infrared (FTIR), intrinsic fluorescence studies or ultraviolet-visible (UV-vis) spectroscopy (second derivative) spectroscopy. Our biophysical characterisation suite of technologies also includes protein aggregation studies through dynamic light scattering, SEC with multi-angle laser light scattering (MALS) and sedimentation velocity analytical ultracentrifugation (SV-AUC).
Glycosylation studies are designed product specific, however, these typically include determination of the levels of neutral and amino monosaccharides as well as sialic acids, assessment of glycoform distribution and  glycan structure elucidation.  Multiple technologies are applied in these determination including selective enzymatic cleavage and MALDI-TOF Mass spectrometry HPLC, HILIC, IEX or CE-LIF, to provide the level of structural information required.
For antibody drug conjugates (ADCs) our scientists determine the  position of attachment of the toxin to the linker and subsequently protein, also known as the sites of conjugation. This is typically achieved using high resolution mass spectrometry (Orbitrap, QToF) following enzymatic digestion.  The same logic methods can also be applied to establishing the position of PEGylation and other conjugated forms.
Need help or have a question? +1 800 967 5352

Need help or have a question?

+1 800 967 5352
+44 161 721 5247
+41 61 686 4800