Monitoring specific process-related impurities

Ejvind Mortz, PhD in biochemistry

This page has been reviewed and verified by Ejvind Mortz, PhD in Protein Chemistry & Molecular Biology

During development and manufacturing, residual proteins derived from production, such as Host Cell Proteins (HCPs), growth factors, serums, and processing reagents, must be monitored through each downstream purification step to ensure efficient clearance and purity of the final drug substance. Residuals may cause unwanted biological activity, immunogenicity, or degradation of the therapeutic protein or polysorbate surfactants.

Alphalyse offers development of targeted liquid chromatography mass spectrometry methods (LC-MS). Multiple Reaction Monitoring (MRM) analysis is a highly specific and sensitive LC-MS technique that can target your residual protein(s) of interest in both the final drug product and individual process samples. MRM enables a low-to-sub ppm detection limit and is advantageous for identifying and quantifying key residuals, even in complex process samples.

USP on HCP strategies

Why use LC-MS for process-related impurity analysis?

Document and monitor process-derived residuals

Quantify target proteins throughout the purification process and in the final drug substance

Full validation of assay under GMP

Fully validate your assay according to ICH guidelines for use as a release assay under GMP

Assay targeting polysorbate-degrading HCPs in mAbs

Our standard assay targets the most common lipases and esterases found in monoclonal antibody products

Video case

Do you experience polysorbate degradation – but don’t know the cause?   

One of our mAb clients struggled with polysorbate degradation, affecting the efficacy and safety of their drug product. The client suspected the problem was a host cell protein – a lipase – which co-purified with the mAb through Protein A purification. But without knowing the identity or characteristics of the culprit, they were unable to remove it from the final drug product.

Case-24: Polysorbate degradation caused by LPL (lipoprotein lipase)

Typical project process

You typically work with
these experts:

Rie Bak Jäpelt

MSc Pharmacy, PhD Analytical Chemistry

Janne Skaarup Crawford

BSc in Cell Biology & Biochemistry

Solveig Bech Nielsen

PhD, Molecular Medicine

Christina Erika Hagensen

PhD, Molecular Medicine
  • Facilitate meetings

    Project scope

    We like to start with an online meeting to learn more about your project. Based on your needs, you will receive a draft proposal outlining the suggested analyses and expected timeframe. We will develop the MRM LC-MS analysis specifically for your protein and project.

  • Protein sample

    Samples

    After signing the final project proposal, we will contact you for details about your samples. We will inform you of an estimated report delivery date as soon as we receive your samples.

  • SWATH LC-MS analysis and protein quantification using amino acid analysis

    Execution

    A project leader will oversee the project and send you status updates by email at regular intervals.

    A typical analysis includes:

    • Identification of up to 3 unique signature peptides for each protein for quantitation.
    • Standard curves and linearity assessment for a dilution series of the quantification standards and, if possible, the residuals in your specific samples.
    • Absolute quantification of the proteins of concern by MRM LC-MS.
    • Reporting of the determined protein amounts and analysis details.
  • 5000 mass spectrometry reports

    Results

    You will receive the report by email, the analysis report includes:

    • Objectives, description of analytical procedure, results, and conclusions.
    • List of identified and quantified impurities in each sample.
    • Selected raw data, e.g., excel sheets. Additional raw data may be provided to you upon request.
  • Follow up on reports

    Follow up

    Upon completion of the project, your team is invited to go through the results at an online meeting.

Curious to know more?

Leading edge technologies

Whatever challenge or question you may have, we are here to help you solve it. One of our protein analysis experts will discuss the best analysis approach or method for your project by email or online meeting – without obligation.

Client stories

Lot-to-lot consistency and Host Cell Protein impurity profiling of an adenovirus-encoded vaccine using LC-MS

LC-MS results demonstrated that the final drug substance was exceptionally pure, with high lot-to-lot consistency.
Webinar USP 1132.1 with Victor Chrone Alphalyse

Webinar: Comparison of 3 USP 1132.1 MS quantitation methods

WEBINAR: Experimental demonstration of USP methods
Alphalyse provides cro services to Europe and North America

Blog: Problematic HCPs in drug development

How specific host cell proteins derail safety, stability, and regulatory approval
Polysorbate-degrading host cell proteins

Webinar: Polysorbate-degrading HCPs

Latest research on PS-degrading HCPs and regulatory revisions impacting mAb products
13 residual biocatalyst

Video: Residual biocatalysis in small molecule API

If your process uses added enzymes, residuals is a significant concern
Analyzing individual A549 HCPs by mass spectrometry

Analysis of individual human residual proteins

US-based C&ampGT developer: "We can follow the reduction of specific A549 HCP in our adenovirus-based product"
Getting Gag/Gag-Pol ratio to control viral capsid formation

Quantifying lentivirus and residual proteins in one assay

UK C&ampGT division: "We can now monitor the consistency of our viral capsid formations in lentivirus-based products"
Comparing viral protein quantities in AAV-based products

Comparing viral protein quantities in AAV batches and DS

Gene therapy CMO: "We could compare and document batch consistency and locate any differences in AAV products"
HCP MS analysis for gene therapy products

Analyzing heterogeneous HCP mix from multiple species

Gene therapy developer: "We went from inconsistent, low-coverage ELISAs to reproducible and detailed HCP analysis"

The advantages of LC-MS MRM analysis of residual proteins

  • Fast development of a protein-specific assay

  • Highly sensitive – sub-ppm level

  • Extensive dynamic range – up to 4-5 orders of magnitude

  • Accurate and reproducible quantification in very complex samples

  • Can be fully validated accordingly to ICH guidelines and used as a release assay under GMP

  • Multiplexing for monitoring up to 20 proteins in one assay

What clients say

Aicuris logo
"Alphalyse provided a very well-designed and executed HCP analysis, fruitful technical discussions, and flexibility in terms of writing the report."

Thore Schmedt, Associate Director
AiCuris Anti-infective Cures AG, Germany
Sangamo logo
"Mass spec requires costly instruments and experts, so our strategy is to partner with field experts to get external help characterizing HCPs"

Yiling Bi, Senior Scientist
Sangamo Therapeutics Inc, USA
Bavarian Nordic logo
"Alphalyse developed and qualified an LC-MS method for monitoring host cell proteins in our MVA-BN® platform vaccine candidate"

Iben Schildt Sørensen, Director QC-K
Bavarian Nordic, Denmark
SSI logo
"Alphalyse's HCP analysis saved us the development of an ELISA assay that may not have worked anyway. The HCP team explained test results competently and was very open to discussing the method capabilities."

Max Kristiansen, MSc, Special Consultant Assay Development
Statens Serum Institut (SSI), Denmark
Targovax logo
"They handled the project professionally and rapidly, and the report was very well written, clearly explaining the findings."

Kristiina Hyvärinen, Director QC, viral products
Targovax ASA, Finland
Y-mAbs logo
"We enjoy collaborating with Alphalyse as part of our optimization of manufacturing processes. Not only do we gain access to their hands, but we also get to pick their brains for mass spectrometry knowledge."

Torben Lund-Hansen, PhD, SVP
Head of Technical Operations

Y-mAbs Therapeutics Inc., USA
Savara logo
"Using the Alphalyse LC-MS/MS coverage method in HCP ELISA selection, we estimate a savings of approximately $1M and, likely, one year of development time."

Lars Skriver Senior Science Officer
SAVARA Aps, Denmark
Actinobac Biomed Inc logo
"The FDA approved our IND! They accepted the MS data without also requesting the standard HCP-ELISA immunoassay."

Scott Kachlany, founder
Actinobac Biomed Inc.
Genmab logo
"We see a field that is moving towards mass spectrometry-based methods to enhance your knowledge of how ELISA reagents perform and the process performs"


Søren Skov Hansen, Senior CMC Specialist
Genmab, Denmark
Orchard logo
"C&GTs are quite complex, so it’s difficult to use a single ELISA assay – LC-MS is basically an integrated method that gives a quantifiable picture of each stage of production, like HCPs"

Albert Molina Gil, Process Development Scientist
Orchard Therapeutics plc, United Kingdom
Testimonial Alphalyse
"At first, I did not think an HCP-MS assay would be reproducible. I was wrong! And now we have used it to compare batch data during 5 years of process development."

CMC Project Lead
Scandinavian mAb developer
Testimonial Alphalyse
"The analysis showed that the new ELISA standard made the calibration slope shift, resulting in a misinterpretation of the total amount of HCPs in the drug sample"

Director QC
EU-based biotech
Testimonial Alphalyse
“I found the group at Alphalyse knowledgeable, easy to work with, and helpful in
planning the study”

VP CMC and Quality
US Biotech
Testimonial Alphalyse
“We found out why our PG13 ELISA kit had such low coverage of our gene therapy’s HCPs”

Chief Scientific Officer
Top10 Pharma Company
Testimonial Alphalyse
“Extremely professional service, high-level quality of the results, and excellent communication”

Program Manager
European Biotech
Testimonial Alphalyse
"Previously, we had no idea which clearance methods would be most efficient. With Alphalyse results, we could intelligently remove the HCPs"

Senior Manager, Process Development
Clinical-stage biotech company
Testimonial Alphalyse
"The mass spec results were extremely detailed and almost identical between replicates and can probably replace ELISA as the HCP analysis approach for our future C&GT projects"

Chief Scientific Officer
European biopharma company
Testimonial Alphalyse
"With the Gag to Gag-Pol ratio determined, we can monitor the consistency of viral capsid formations in our lentivirus-based product"

Head of CMC, C&GT division
UK pharma company
Testimonial Alphalyse
"We now use a mass spectrometry assay to follow the reduction of specific A549 HCPs in our downstream process"

Sr. Research Associate
US-based C&GTs developer
Testimonial Alphalyse
"Honestly, we were astonished to see the mass spec results: The detailed report enables us to optimize our CMC process and remove specific HCPs if we find it relevant."

Director, Regulatory CMC
Oncology-focused biopharmaceutical company

Knowledge center

Talk to us

Whatever protein-related challenge or question you may have, we would love to help. Our experts can help you decide on the best analytical approach for your project by email or online meeting - providing advice without obligation.