Data for risk assessment

Ejvind Mortz, PhD in biochemistry

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

Regulatory authorities are increasingly aware that protein impurities, even at low levels, can affect patient safety and product stability. Some residual Host Cell Proteins (HCPs) have been observed to cause immunogenicity, adjuvant effects, or direct biological activity in patients and degradation of products or excipients during storage. Therefore, it is not enough that an ELISA reports a low number – you also need to investigate the individual HCPs.

For this reason, legal authorities call for an orthogonal method,  such as mass spectrometry (LC-MS analysis), to identify and quantify individual HCP impurities and for a thorough risk assessment of the resulting data. LC-MS can identify process-related impurities down to 0.1 ppm and allows for data-driven process optimization and evaluation of purification steps.

We use relevant ICH guidelines, protein standards, and follow the US Pharmacopeia General Chapter <1132.1>, resulting in very robust and comparable results, delivered in just 2-4 weeks.

The ELISA total HCP number is arbitrary
How common are HCPs of concern?

Why use LC-MS/MS for HCP analysis?

Patient safety and risk assessment

Rule out the presence of HCPs causing immunogenicity, adjuvant effects, or biological activity

Product stability and efficacy

Check for enzymes causing product degradation, modification, loss of activity, or excipient degradation

Manufacturing consistency and product purity

Evaluate purification process clearance, drug substance purity, or batch comparability

On demand webinar

Which HCPs to look for and how to measure them

In several clinical trials and during the development of many biologics, residual HCPs, such as flagellin, proteases, and the infamous PLBL2, have proved problematic. They may cause immunogenicity in patients, unwanted biological effects, or enzymatically degrade the drug, decreasing its efficacy and shelf life.

For mAbs, it is now well-described which HCPs from the CHO expression system to be concerned about. Regulatory guidelines assert that documentation should include risk assessments of the individual HCPs identified and removed.

Problematic HCPs can stop your biologics program!

Typical project process

You typically work with
these experts:

Melissa Fernard Pedersen

MSc in Medicine with Industrial Specialization

Peter Toft Jensen

PhD in Biochemistry and Molecular Biology

Dean Malte Zisco

MSc in Biochemistry and Molecular Biology

Freja Andersen

MSc in Biomedicine
  • 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

    Samples

    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

    Execution

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

    A typical analysis includes:

    • Spike-in of internal standard proteins, enabling quantification at low ppm levels.
    • Enzymatic digest and analysis of peptides using LC-MS.
    • ELISA-MS analyses with an in-well digest of immunocaptured HCPs.
    • Setup of a custom-specific database.
  • 5000 mass spectrometry reports

    Results

    You will receive the report by email. As standard, the LC-MS HCP analysis report includes:

    • Objectives, description of analytical procedure, results, and conclusions.
    • A list of the number and the total amount of HCPs in the sample.
    • A list of individual HCPs and their quantities, highlighting HCPs of potential concern, including the physiochemical properties of the HCPs.
    • The coverage percentage of HCPs in ELISA.
    • Match between the ELISA standard and the harvest or mock samples.
    • ELISA Coverage of HCPs found in DS, including coverage of potential problematic HCPs.
    • Selected raw data, e.g., excel sheets.
  • 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

Accelerating early-stage process development:

Accelerating early-stage process development: eleva case study

Detecting and quantifying HCPs in a moss-based system

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.
Victor et. al 2025

Open Access article: Comparison of USP 1132.1 quantitation methods

Experimental demonstration of LC-MS methods in USP 1132.1
3 clinical trial failures caused by host cell protein

PDF: 3 clinical trial failures caused by host cell proteins

Examples of why early, detailed analysis matters to clinical trial success
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
Regulatory consequences of USP 1132.1

Article: Regulatory Consequences of New Protein-Impurity Guidelines

The industry is on the brink of a paradigm shift with the release of the USP
Polysorbate-degrading host cell proteins

Webinar: Polysorbate-degrading HCPs

Latest research on PS-degrading HCPs and regulatory revisions impacting mAb products
Beyond ELISA - is mass spectrometry the future of impurity analysis?

Article: Is mass spectrometry the future of impurity analysis?

3 CMC specialists talks about current & future applications of LC-MS for impurity analysis
Identifying a polysorbate-degrading lipase in mAbs

Identifying a polysorbate-degrading lipase in mAbs

Lipases co-purifying with mAb products can degrade polysorbate even at trace levels
Alphalyse provides cro services to Europe and North America

Blog: Why results obtained by new ELISA kit differ from the original

Bridging from one HCP-ELISA kit to another, even just a new version, is not as straightforward as it sounds
Characterization of HCP ELISA standard

Troubleshooting HCP ELISA results using LC-MS and ELISA-MS™

Biotech: "We found out that the increase in HCP amount in our DS was due to a shift in the ELISA calibration
case study on ELISA standard

Characterization of a mock sample before ELISA development

CDMO: "The data saved us from using an unsuitable mock sample in development of a process-specific ELISA"

Benefits of LC-MS HCP analysis for risk assessment

  • Identify specific HCPs of concern found in you drug samples (e.g. lipases, heat-shock proteins)

  • Quantify each of the HCPs of concern

  • Use LC-MS data (pI and MW for each protein) for data -driven process optimization to remove specific unwanted HCPs

  • Evaluate if your ELISA is capable of detecting HCPs of concern found in your process

  • Set up an MRM-LC-MS assay to check for specific proteins of concern

  • Follow up with validation of the assay under GMP

What clients say

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
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
“Extremely professional service, high-level quality of the results, and excellent communication”

Program Manager
European Biotech
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
Testimonial Alphalyse
"We didn't want surprises in Phase 2 or 3, so we supplemented the HCP ELISA data with an orthogonal method. We got the results within a few weeks and could quickly implement them in our development process."

VP, Process Development and Manufacturing
Drug discovery company
Testimonial Alphalyse
"We hoped our biosimilar product was cleaner, more stable, and safer than the originator. However, the results were so favorable that not only can we use them as documentation for regulatory filing, but also as part of our marketing"

Head of Analytical Development
Developer of a mAb-biosimilar
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
Testimonial Alphalyse
"Based on the data provided by Alphalyse, we settled on a kit that rovided both excellent coverage of the HCPs overall and the individual HCPs of concern"

Senior CMC specialist

US-based Biotech

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.