Residual protein analysis of complex products

Regulatory authorities demand investigation, monitoring, and documentation of process-related protein residuals generated during biologics manufacturing. Such impurities can reduce drug efficacy and patient safety, and insufficient documentation may delay product approval.

Whereas traditional biologics have manufacturing processes that are well-defined and supported by a panel of established analytical test methods, the manufacturing processes for complex products, like mRNA vaccines, bacteriophages, and advanced therapies, are still in development. Therefore, improved analytical tools, such as mass spectrometry (LC-MS), are necessary to ensure process consistency and quality and to meet evolving requirements for product release and characterization.

Why use LC-MS for residual protein analysis of complex biologics?

Document process-related residual proteins

Identify and quantify cell substrate-derived, cell culture-derived, and downstream process-derived impurities

Evaluate clearance throughout purification steps

Show that your process efficiently clears process-derived impurities, resulting in a pure and safe product

Perform comparability studies

Assess protein impurity levels after process changes, upscaling, or tech transfer between CMOs to document a consistent, comparable product

Unlike traditional biologics, which are typically manufactured by expressing one recombinant protein in a single cell line, advanced therapies, viral vaccines, and oligonucleotide-based medicines contain highly heterogeneous protein mixtures from multiple sources and organisms.

Commercial HCP ELISA kits, typically used for monitoring Host Cell Proteins (HCPs) from CHO and E.coli expression systems, cannot simultaneously detect proteins from different species and often demonstrate low coverage of, e.g., HCPs from non-immunogenic human cell lines. As such, classical impurity assays often fail to detect a substantial proportion of the residual proteins in complex biotherapeutics.

Liquid chromatography-mass spectrometry (LC-MS) is a robust and reproducible orthogonal method to ELISA, which has high specificity, sensitivity, and dynamic range to detect highly heterogeneous HCPs. Using Data Independent Acquisition (DIA), LC-MS can quantify and characterize all protein impurities in a sample and provide thorough, precise, and robust HCP coverage.

Regulatory authorities often fast-track novel therapies and vaccines that have the potential to treat severe, life-threatening conditions. Furthermore, since they can be one-shot cures, being first to market can provide a competitive advantage. However, developing a process-specific ELISA for complex products requires 1 - 2 years for antibody development and assay validation. Even then, there is a risk of delayed regulatory approval due to inadequate impurity detection and clearance.  

LC-MS assays require only 6-8 weeks to be established and optimized for any biologic product. This can significantly accelerate the development, marketing approval, and commercial biomanufacturing of complex biologics. 

Manufacturing changes commonly happen for complex biologics, and comparability studies of residual proteins are frequently necessary for product development and regulatory filings. For instance, when improving the process consistency and product quality, upscaling, or transferring to GMP facilities for commercial release. However, demonstrating comparability in complex biologics is often challenging by still-evolving process knowledge, small numbers of batches, and material constraints for each batch.   

The LC-MS assays at Alphalyse have been developed for high robustness and tolerability toward different sample types, complexity, and proteins from multiple sources. It is a flexible method allowing for process changes and the use of various buffers and matrices. The use of the same intact internal protein standards enables comparable results between samples, across process changes, and for comparability between GMP batches.

Typical project process

You typically work with
these experts:

Solveig Beck Nielsen, expert on residual protein analysis

Solveig Beck Nielsen

PhD in Molecular Biology
Anette Holck Draborg, expert on HCP coverage analysis and ELISA characterization

Anette Holck Draborg

PhD in Immunology
Rikke Raaen Lund, Head of Impurity Analysis Dpt

Rikke Raaen Lund

Head of Impurity Analysis Dpt
  • Facilitate meetings

    Project scope

    We will 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.

  • Protein sample


    After signing the final project proposal, we will contact you for details about your samples. An estimated report delivery date will be sent as soon as we receive your samples.

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


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

    The analysis varies according to the project but typically includes:

    • Setting up a sequence database containing all the proteins used in your manufacturing process that could potentially end up in the drug substance.
    • An optimized sample preparation developed explicitly for complex products, e.g., viral vaccines and viral vector therapies.
    • Analysis using a robust microflow HPLC and SWATH® MS/MS system to ensure high reproducibility.
    • Spike-in of internal standard proteins (0-2000 ppm), enabling quantification linearity even to low ppm levels.
  • 5000 mass spectrometry reports


    You will receive the analysis report by email. Depending on the project, it includes:

    • Objectives, description of analytical procedure, results, and conclusions.
    • List of the total HCPs in the sample.
    • List of individual HCPs, process-related residuals, and their quantities.
    • Selected raw data, e.g., excel sheets. You may request additional raw data if needed.
  • Follow up on reports

    Follow up

    Upon completion of the project, your team is invited to go over 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

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Webinar: ELISA reagent characterization using LC-MS

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HCP-ELISA reagent characterization using LC-MS

Webinar: ELISA reagent characterization using LC-MS

See results from ELISA reagent characterization using advanced LC-MS techniques on various biologics.
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Webinar: LC-MS HCP assay validation and GMP release testing

An MS-based assay is ideal when the complexity of a therapeutic makes it challenging to find an adequate ELISA
ICH Q8B characterization of complex products

Video: ICH Q8B characterization of complex products

The complexity of VLP-based vaccines makes characterizing them challenging
Vaccine HCP analysis

Webinar: Analyzing vaccine purity – without an HCP ELISA

Learn how to quickly measure & compare residual protein in any type of vaccine

Video: Analysis of bacteriophage product

HCP analysis on 6 bacteriophage drug substances expressed in 3 species
13 residual biocatalyst

Video: Residual biocatalysis in small molecule API

If your process uses added enzymes, residuals is a significant concern
12 residues viral products

Video: Analysis of residual protein in viral products

Looking for problematic HCPs from SF9 cells and baculovirus vector
Towards consistent C&GTs

Infographic: Analytical techniques for ensuring consistent C&GTs

An overview of analytical techniques for cell and gene therapies
Analyzing individual A549 HCPs by mass spectrometry

Analysis of individual human residual proteins

US-based C&GT 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&GT 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"
2021 gtp webinar

Webinar: Monitoring impurities and ensure consistent therapies

Quickly identify and quantify all proteins in complex products using only one assay
Comparison of HCP removal strategies

Video: Expression systems without a commercial ELISA kit

What to do when no commercial ELISA kit fits your expression system

Benefits of LC-MS-based impurity analysis of complex biologics

  • Analyze protein-based residuals from multiple organisms in one assay

  • Highly robust method not affected by process changes.

  • Includes quantification of product-specific proteins, viral proteins, etc.

  • Fast development of assay - within weeks.

  • Low amount of material required for assay development and analysis

What clients say

Testimonial Alphalyse
"We received a very professional report. It included an excellent overview of the peaks and their identity in the different batches and degradation samples. With the documentation from the study, we finally had everything we needed to send in the Biologic drugs license application (BLA) for FDA approval."

CMC Project Leader, R&D
UK biopharma company
Testimonial Alphalyse
"With the results from the extensive characterization, we identified a scale-up problem and could optimize the process to increase mAb stability. Therefore, we now use the analysis on an ongoing basis to test the quality of all our batches"

Director, Protein and Analytical Chemistry
Research-based pharmaceutical company
DTA consulting
"The collaboration with Alphalyse was superb! They quickly presented an optimized method that provided excellent data and separated product-related impurities. The contribution made it possible to keep our milestones"

Dorrit Andersen, Regulatory Affairs Consultant
DTA Consulting, Denmark
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
“Extremely professional service, high-level quality of the results, and excellent communication”

Program Manager
European Biotech
Testimonial Alphalyse
"Thanks to the ELISA-MS data, we knew which kit to use for the setup and validation of our HCP ELISA assay! Furthermore, we knew exactly which individual HCPs were covered by
the ELISA antibodies"

Director CMC
US Biotech
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
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
GTP Bioways logo
"We are very pleased with the work of Alphalyse because they provide us with a high-quality antibody characterization service. Most importantly, we can ship them hundreds of samples at once and always receive the analytic results shortly after. "

Head of CMC, C&GT Division
GTP Bioways, France

Knowledge center

Can residual protein testing be performed on lentiviral vectors?

Yes, and we have also performed impurity testing on other viral vectors. Viral vectors are typically highly complex and can contain proteins from multiple sources, such as the growth medium, added cellular growth factors, vector proteins, and Host Cell Proteins (HCPs) produced as part of the natural cellular metabolism.

Since viral vectors are highly complex, impurity analysis using ELISA would require several custom-made assays targeting different protein groups. Using LC-MS, it is possible to analyze both the viral vector itself and any additive material quickly, robustly, and accurately - regardless of their source.

Is it possible to analyze harvest and clarification steps?

We routinely run all types of in-process samples, from harvest to drug product and in-process samples, since our mass spectrometry-based assay works for all kinds of samples and expression systems. The sample preparation is optimized for various matrices, and only minor adjustments are needed to customize the setup for individual projects.

What are the criteria for successfully identifying a protein? Are there protein residuals that you cannot identify?

We require that at least two peptides are identified for each protein before we report the protein as identified.

The MS and MS/MS data are searched against protein sequence databases to identify peptides. We require a match for the peptide mass and peptide fragment masses for known sequences. MS-based assays achieve a very low-ppm sensitivity, making identifying even low abundant impurities possible. The method is not biased against specific proteins but requires observation of at least peptides from a protein. On request, we can set up absolute quantification MRM LC-MS for specific protein impurities of interest and perform spike-in experiments to confirm their identity.

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.

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