Data for risk assessment

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.

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.

Typical project process
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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.
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.
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.
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
Upon completion of the project, your team is invited to go over the results at an online meeting.
Curious to know more?

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: eleva case study
Webinar: Meet 2026 regulatory expectations for your HCP-ELISA
Lot-to-lot consistency and Host Cell Protein impurity profiling of an adenovirus-encoded vaccine using LC-MS
Webinar: Best practice Host Cell Protein analysis for vaccines by MS
Open Access article: Comparison of USP 1132.1 quantitation methods
PDF: 3 clinical trial failures caused by host cell proteins
Webinar: Comparison of 3 USP 1132.1 MS quantitation methods
Blog: Problematic HCPs in drug development
Article: Regulatory Consequences of New Protein-Impurity Guidelines
Webinar: Polysorbate-degrading HCPs
Article: Is mass spectrometry the future of impurity analysis?
Identifying a polysorbate-degrading lipase in mAbs
Blog: Why results obtained by new ELISA kit differ from the original
Troubleshooting HCP ELISA results using LC-MS and ELISA-MS™
Characterization of a mock sample before ELISA development
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
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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.






