Host cell protein analysis

Our aim is to provide you with the best protein analysis service by providing access to our service-minded team of highly experienced and skilled scientists, hand-picked from leading universities and companies. Together, they cover most fields of protein chemistry, mass spectrometry and bioinformatics. They also apply top-of-the-line equipment and are experts in interpretation of its data for biopharmaceutical protein characterization.


Analysis of process-related impurities

To ensure process reproducibility and product comparability, include mass spectrometry in your HCP analysis strategy to identify, characterize, and quantify individual HCPs of concern.

Use mass spectrometry for enzyme-linked immunosorbent assay (ELISA) coverage and reagent characterization to ensure your ELISA is fit for purpose and as an orthogonal impurity analysis method to support your ELISA data.

If a generic ELISA is unavailable for your cell line or the time to develop a process-specific ELISA is limited, mass spectrometry (MS)-based HCP analysis is the fastest, most precise, and most convenient solution.

MS-based HCP analysis has high coverage and sensitivity and is customizable to your product within weeks.

Our MS assay is available for full validation following ICH guidelines and is applicable to release testing and commercial production.

Our Services

ELISA characterization and HCP coverage analysis

Data for risk assessment (HCPs of concern)

Monitoring specific process-related impurities (MRM)

Documentation of the manufacturing process

Residual protein analysis of complex products (GTP)

Data for regulatory documentation (GMP)

Identification and quantitation of Host Cell Protein in biologics

Alphalyse probably offers the most detailed Host Cell Protein analysis available. Where most other suppliers provide analysis based on ELISA kits or antibodies, we use advanced SWATH® mass spectrometry to analyze host cell proteins.

How does ELISA compare to a host cell protein assay by Mass Spectrometry (MS)?

MS analysis provides the total HCP content (ng HCP/mg DS) in each sample as with an ELISA. But MS analysis goes beyond this and also gets the ID and quantity of each Host Cell Protein. And it is fast – just 4-8 weeks – without needing a null-cell line.

Additionally, if you already use ELISA kits or antibodies, we can help you measure their HCP-antibody coverage.

Is there no commercial ELISA HCP assay available for your host cell line? Mass spectrometry analysis is the solution for detecting and measuring host cell proteins and other process-related impurities.

The HCP MS analysis applies to all types of samples and expression systems:

The approach can be applied to all process samples, from harvest to final drug product. It applies to all expression systems, including E. coli, CHO, yeast, HEK, adenovirus, etc. The only requirement is that the host cell proteome be sequenced and available in public databases or in your possession.

Please send us a request to start a dialogue. We would love to show you how the method can be applied to your project.

You are also recommended to watch one of our 30-minute webinars for more information. And in our videos, you will find examples of how other clients have used our host cell protein analysis.

Typical project

Two Alphalyse scientists analyzing complex data
  • Facilitate meetings

    Facilitate meetings to define the project scope and agree project proposal

  • appoint-assign-blue

    Assign an experienced project leader to your project to fulfill the project objectives, ensure timely delivery, and keep your team updated on progress

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

    Provide reproducible data using advanced instruments and robust workflows, with SOPs in place for all analyses to ensure the highest quality

  • Follow up on reports

    Follow up the report with an online meeting to review the results and answer your questions

Examples of biologics we analyze

Recombinant proteins

Recombinant proteins

  • Enzymes
  • Hormones
  • Fusion proteins
Antibody analysis


  • Monoclonal (mAbs)
  • Biosimilars
  • Bispecific (bsAbs)
Viral vaccines


  • Live attenuated
  • Recombinant VLP
  • Inactivated
Advanced therapy analysis


  • Adenovirus
  • AAV
  • Lentivirus
Bacteriophage product analysis

Bacteriophage products

  • Process samples
  • DS batches
  • Phage cocktails


MS-based HCP analysis gives information about specific HCPs and their quantity – to analyze the effect of various purification steps

Different HCP ELISAs detect different HCPs. That is because they depend on the specificity of the polyclonal HCP antibodies used.

You can use mass spectrometry methods based on trypsin digestion, HPLC separation of the peptides, and MS/MS peptide analysis

The ELISA-MS method provides both the coverage percent and also the identity of each Host Cell Protein. Use it to qualify your HCP ELISA.

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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