Data for regulatory documentation

Regulatory requirements aim to ensure patient safety and efficacy of the pharmaceuticals. Maintaining compliance with increasingly complex regulatory requirements without unduly impacting production costs or time-to-market is one of the biggest challenges for biopharmaceutical companies.

Protein analysis by Mass spectrometry (LC-MS), produced to fulfill ICH guidelines, enables you to document the robustness of your downstream process, provides detailed information about critical quality attributes and host cell impurities, and shows batch-to-batch comparability. The analysis can even be validated according to ICH guidelines under GMP for use as product release testing.

Alphalyse HCP analyses comply with the upcoming U.S. Pharmacopeia general chapter 1132.1 on best practices for protein impurity identification and quantitation using LC-MS, including the USP's intact protein standards to support the identification and quantification of high-risk and high-abundance protein impurities.

Which data can Alphalyse provide for regulatory documentation?

Robust, reproducible data for process validation and risk assessment

Process and product characterization for documentation in accordance with regulatory guidelines

Chemistry, manufacturing, and control (CMC) information

Detailed data on drug substance identity, purity, and quality for CTD, IND, NDA, and BLA submissions

HCP analysis under GMP for release test and clinical trial documentation

Quality control of biological API using analysis under GMP conditions – for use as release assay for Phase III and market

Enzyme-linked immunosorbent assay (ELISA) is the standard method for monitoring Host Cell Protein (HCP) clearance. To ensure patient safety and product efficacy, the critical reagent of an HCP ELISA, the HCP antibody, must be demonstrated to cover a broad spectrum of the HCPs potentially present in the purified drug substance. However, traditional coverage methods for assessing HCP antibody coverage, such as 2D-Western blot or immunoaffinity-purification combined with 2D gel electrophoresis, are increasingly not sufficient to validate the coverage of an HCP ELISA with regulatory authorities.

Alphalyse's proprietary ELISA-MS™ analysis uniquely combines ELISA-based immunocapture with liquid chromatography mass spectrometry (LC-MS) under native conditions. Using ELISA-MS™, we provide accurate, reproducible data for evaluating and validating your ELISA as required by regulatory authorities.

We can assist you with:

  • Performing HCP-ELISA coverage analysis.
  • Demonstrating that your HCP-ELISA is fit-for-purpose.
  • Verifying ELISA results using orthogonal methods to identify and fully characterize individual HCPs of concern.
  • Performing detailed risk assessment and closely monitoring process performance parameters.
  • Thorough bridging between new ELISA kits and reagents or process changes.

Developing a process-specific ELISA usually requires 1 - 2 years for antibody development and assay validation. Furthermore, if the HCP coverage of your ELISA is insufficient, you risk delayed regulatory approval due to inadequate impurity detection and clearance.

LC-MS assays require only 6-8 weeks of development for any biologic product, which can significantly accelerate the development, marketing approval, and commercial manufacturing of biopharmaceuticals. Furthermore, a fully validated assay under GMP conditions can be in place within 4-6 months.

LC-MS provides the detailed analytical data needed for developing chemistry, manufacturing, and controls (CMC) and for satisfying regulatory requirements. Our clients have had Investigative New Drug (IND) submissions approved by US and EU regulatory authorities based only on LC-MS data; no time- and resource-consuming ELISA is required. LC-MS-based HCP analysis has also been approved as a release assay under Good Manufacturing Practice (GMP).

You need an IND (Investigational New Drug) application to seek an exemption to administer and dispense investigational drugs, whereas the BLA (Biologics License Application) is a request for permission to introduce a biologic into commerce. The data provided in these documents must fulfill the ICH Q6B guidelines to be accepted by the regulatory authorities.

There has been an increased focus from regulatory authorities on orthogonal data for HCPs using MS since traditional methods for HCP analysis do not allow for characterization of individual high-risk or high-abundance protein impurities. This is particularly concerning for mAb products, which are typically administered to patients with high frequency and concentration, but all drug product development benefits from good patient safety precautions. Regulatory authorities increasingly demand more detailed information about potential risks, and the lack of such data has delayed many projects.

All our analyses are made to fulfill ICH guidelines and can be submitted as part of regulatory documentation. Our clients routinely use the data for INDs, BLAs, and for moving through the clinical phases. You receive the data in easy-to-understand reports, and all raw data can be supplied in Excel sheets and mass spec formats if needed.

Typical project process

You typically work with
these experts:

Rie Bak Jäpelt, MSc Pharmacy, PhD Analytical Chemistry

Rie Bak Jäpelt

MSc Pharmacy, PhD Analytical Chemistry
Janne Skaarup Crawford, BSc in Cell Biology & Biochemistry

Janne Skaarup Crawford

BSc in Cell Biology & Biochemistry
Bente Mariann Jensen, QC Lab Manager at Alphalyse

Bente Marianne Jensen

QC Laboratory Manager
  • Facilitate meetings

    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.

  • Protein sample


    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.

  • 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.

    A typical project includes:

    • Analysis of at least three batches and relevant process samples by LC-MS to identify the HCPs across batches.
    • Selection of signature peptides for assay set-up.
    • Optimized sample preparation explicitly for your samples.
    • Spike-in of internal standard proteins (0-2000 ppm), enabling quantification linearity typically to low ppm levels.
    • Design of validation protocol according to ICH Q2 guidelines.
    • Execution of the validation experiments.
  • 5000 mass spectrometry reports


    You will receive the report by email, the analysis report includes:

    • Objectives, description of analytical procedure, results, and conclusions.
    • Selected raw data, e.g., excel sheets. You may request additional raw data if needed.
  • Follow up on reports

    Follow up

    We invite your team to review the results at an online meeting upon project completion.

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

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"
Evaluating five commercial HCP-ELISAs kits

Selecting the best HCP-ELISA kit out of five

Antibody therapeutics developer: "We found the kit with best coverage of HCPs overall and individual HCPs of concern"
Standard HCP assay qualification protocol

PDF: Standard HCP assay validation protocol

Accuracy, precision, robustness, specificity, and dynamic range are parameters we investigate
Process webinar

Webinar: #Rethink your HCP strategy

Monitor HCP clearance for expression systems without access to an ELISA kit
FDA approves IND without ELISA Host Cell Protein data

FDA approves IND using LC-MS-based Host Cell Protein assay

Actinobac Biomed received FDA approval for IND using only MS data to monitor HCPs
HCP coverage analysis on uncommon expression system

HCP-ELISA coverage analysis without a null cell line

Developer of immuno-oncology biologics: "Thanks to the data, we knew which HCP-ELISA kit to use!"
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"
HCP purification optimization - from harvest to final DS

Video: HCP purification optimization from harvest to final DS

Optimization of the purification process using PI and MW data of each HCP
GMP validated HCP analysis using LC-MS

Webinar: Moving LC-MS analysis into a GMP environment

Controlling variability in HCP analysis by LC-MS and qualifying the data
6 hcp qualification ind application

Video: Qualification report used for IND application

First example of regulatory authorities accepting IND without ELISA data
hcp clearance ppq runs

Video: Convincing documentation of HCP Clearance in PPQ runs

Comparing the consistency of PPQ runs and following specific Host Cell Proteins
Principles of SWATH LC-MS analysis

Webinar: The principles of mass spectrometry for HCP analysis

Host cell protein analysis assay using mass spectrometry
HCP MS analysis for gene therapy products

Analyzing heterogeneous HCP mix from multiple species

Gene therapy developer: "We went from inconsistent, low-coverage ELISAs to reproducible and detailed HCP analysis"

Benefits of LC-MS data for regulatory documentation

  • Suitable for providing data packages to the FDA, MHRA, and EMA.

  • A process- and product-specific assay can be developed within weeks. 'Furthermore, it is possible to validate the assay for release testing.

  • It can easily be adjusted to changes in your process or production.

  • Avoid project delays due to regulatory authorities' request for orthogonal HCP characterization (MS-data).

What clients say

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
"The mass spec results were extremely detailed and almost identical between replicates and can probably replace ELISA as the HCP analysis approach for our future C&GT projects"

Chief Scientific Officer
European biopharma 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
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
SSI logo
"Alphalyse's HCP analysis saved us the development of an ELISA assay that may not have worked anyway. The HCP team explained test results competently and was very open to discussing the method capabilities."

Max Kristiansen, MSc, Special Consultant Assay Development
Statens Serum Institut (SSI), Denmark
Savara logo
"Using the Alphalyse LC-MS/MS coverage method in HCP ELISA selection, we estimate a savings of approximately $1M and, likely, one year of development time."

Lars Skriver
Senior Science Officer

SAVARA Aps, Denmark
Actinobac Biomed Inc logo
"The FDA approved our IND! They accepted the MS data without also requesting the standard HCP-ELISA immunoassay."

Scott Kachlany, founder
Actinobac Biomed Inc.

Knowledge center

What is the future role of LC-MS for release testing?

We expect that the use of LC-MS protein analysis will increase rapidly over the next couple of years and that it will soon be the industry release testing assay of choice for:

  1. Fast-tracked projects for which a suitable commercial ELISA kit is unavailable and developing custom-made assays is too time-consuming, e.g., during pandemics
  2. Complex products with proteins from multiple sources
  3. Monitoring clearance of specific proteins of concern, e.g., enzymes added during manufacturing and HCPs affecting product stability or patient safety.

Has anyone filed a Phase 1 product with HCP analysis based solely on MS results?

Yes, several of our clients have received IND submission approvals using HCP analysis based solely on MS data provided by Alphalyse. Several have also been approved for Phase 3 clinical trials using an MS-only strategy, and we expect one of our clients to file for their BLA with an MS-based HCP release test very soon.

Why has no one else been able to set this up under GMP?

Setting up robust and quantitative mass spectrometry-based impurity analysis is complicated. It requires complex and costly top-of-the-line instruments, a diverse team of highly-skilled experts with LC and protein analysis experience, and reproducible (preferably automated) sample preparation. It has taken us 10+ years of dedicated research to achieve this as the first and so far only laboratory in the world.

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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