Documentation of the manufacturing process

Downstream development is often a matter of trying different purification steps and evaluating the effect of each. Matrix experiments take time, and the success rate may depend on complex matrix experiments or pure luck. Analysis using a standard ELISA only provides a single number representing an estimate for the total HCP amount and does not provide details of the individual amounts.

On the contrary, mass spectrometry analysis provides each protein's identity, quantity, and attributes. Based on the data, you can evaluate the efficiency of current removal steps or design new steps targeting specific HCPs. The method produces highly reproducible data for quantifying proteins, which makes it possible to follow specific residuals down to 0.1 ppm throughout the process. You may use the resulting data for intelligent process development. 

MS data can also help increase the yield of the Drug Substance (in some cases 10-20%) by optimization of purification procedures (columns, pH, gradients, fraction-collection), thereby bringing down the cost of produced material (COGS) while monitoring HCPs to ensure that process changes do not increase the content of critical HCPs.

During process development, pre-clinical, and clinical phases, drug substance (DS) batches must be continuously compared (e.g., after scaling up manufacturing, transferring to a new site, or changing CMO), as inadvertent process changes may affect residual enzymes in the final drug substance. Failure to continuously monitor the residual protein profile risks may cause regulatory authority demands for more data in late-stage phases, sudden drops in product yield, unexplainable peaks in HPLC analyses, or particles in the drug product (DP) as a sign of decreased product stability.

You may already have a custom ELISA developed for your process but then decide to shift CMOs or re-design the purification process. Such changes may affect the ELISA's performance or coverage since the HCP profile may have changed. Often, this results in 1-2 years for developing a new set of anti-HCP antibodies and validating the assay.

Instead, you could consider using LC-MS as an orthogonal method to support your strategy. The current ELISA might still be fit-for-purpose if you can document the changes in the process and ELISA coverage. The method can be used for detailed characterization of the ELISA reagents and to evaluate the coverage of individual HCPs before and after process changes.

We can also set up an MS assay to quantify HCP levels within weeks. Thereby, you save valuable project time and costs. And in case your HCP ELISA fails, the MS assay may even be validated according to ICH guidelines and used for GMP release testing.

Process performance qualification (PPQ) is essential to process validation during or after clinical phase III manufacturing. With the PPQ runs, you must show that your process can consistently deliver a quality product and document that the HCP level in the end product is consistent. As authorities increasingly ask for detailed data by orthogonal methods to ELISA, i.e., MS, why not include detailed data on individual HCPs clearance across the three PPQ runs?

For each step in the purification process, from the early harvest sample through the different purification steps to the pure drug substance, mass spectrometry provides the quantity of each HCP and shows how they are cleared. Comparing the HCP clearance across PPQ runs gives the complete picture and control of process consistency. Furthermore, the data can form part of regulatory documentation in the Biologics License Application (BLA) for the regulatory agency.