Data for regulatory documentation

Thomas Kofoed, PhD in chemestry

This page has been reviewed and verified by Thomas Kofoed, PhD in Organic Chemistry

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.

Experience with FDA and EMA views on MS-based HCP data

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

Typical project process

You typically work with
these experts:

Rie Bak Jäpelt

MSc Pharmacy, PhD Analytical Chemistry

Janne Skaarup Crawford

BSc in Cell Biology & Biochemistry

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

    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.

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

    Execution

    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

    Results

    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

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
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
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
Leaflet on what to expect from Alphalyse

PDF: The Alphalyse Approach

33 scientists, specialists, and researchers are ready to assist your team!
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
89bio collaboration on residual enzyme analysis

World’s first GMP-validated MS-based residual enzyme analysis

LC-MS-based assay with a low-to-sub ppm detection limit
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&ampGT division: "We can now monitor the consistency of our viral capsid formations in lentivirus-based products"

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

Bavarian Nordic logo
"Alphalyse developed and qualified an LC-MS method for monitoring host cell proteins in our MVA-BN® platform vaccine candidate"

Iben Schildt Sørensen, Director QC-K
Bavarian Nordic, Denmark
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.
Orchard logo
"C&GTs are quite complex, so it’s difficult to use a single ELISA assay – LC-MS is basically an integrated method that gives a quantifiable picture of each stage of production, like HCPs"

Albert Molina Gil, Process Development Scientist
Orchard Therapeutics plc, United Kingdom
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

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.