Monitoring specific process-related impurities

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.

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.

Typical project process
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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.
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.
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.
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
Upon completion of the project, your team is invited to go through 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
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
Webinar: Comparison of 3 USP 1132.1 MS quantitation methods
Blog: Problematic HCPs in drug development
Webinar: Polysorbate-degrading HCPs
Video: Residual biocatalysis in small molecule API
Analysis of individual human residual proteins
Quantifying lentivirus and residual proteins in one assay
Comparing viral protein quantities in AAV batches and DS
Analyzing heterogeneous HCP mix from multiple species
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
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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.














