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Comprehensive Protein Expression and Biomarker Analysis for Advanced Therapy Medicinal Products (ATMPs)

PROVEN INTELLIGENCE ACCELERATING NEXT-GENERATION THERAPIES

Comprehensive Protein Expression and Biomarker Analysis for Advanced Therapy Medicinal Products (ATMPs)

Comprehensive Protein Expression and Biomarker Analysis for ATMPs

CELL & GENE | RNA | BIOLOGICS

Precision Mass Spectrometry for Complex Biologics.

    What is the typical sensitivity and dynamic range of your mass spectrometry assays for transgene protein quantification?

    A: Our hybrid LC-MS/MS platforms are developed to achieve high sensitivity, tailored to the specific requirements of each therapeutic program. The assays are validated to cover a wide dynamic range, effectively accommodating the non-linear expression patterns often observed with AAV-mediated therapies in complex matrices like tissue and plasma.

    How do you manage species-specificity when developing assays for human proteins expressed in non-human models?

    A: We develop assays using species-specific surrogate peptides that are unique to the human transgenic protein and absent in the endogenous ortholog. This strategy ensures precise quantification of the therapeutic protein without cross-reactivity.

    What GxP-compliant data packages are provided for IND-enabling studies?

    A: We provide a full, audit-ready data package compliant with GxP standards. This includes the validation summary report, all raw data, detailed analytical methods, instrument calibration records, and a certificate of analysis suitable for direct inclusion in regulatory filings.

    Can your platforms differentiate between precursor, mature, and post-translationally modified forms of a therapeutic protein?

    A: Yes. Our high-resolution mass spectrometry methods can be configured to target specific peptide sequences corresponding to different protein isoforms or PTMs. This allows for precise characterization of the active therapeutic agent and its metabolic profile in vivo.

Quantifying therapeutic protein expression from Advanced Therapy Medicinal Products (ATMPs) requires highly specific, sensitive, and robust bioanalytical methods. Franklin Biolabs develops and validates custom mass spectrometry assays to measure protein expression and pharmacodynamic biomarker changes in complex biological matrices. These GxP-compliant services provide the decision-making data required to characterize dose-response, confirm target engagement, and support regulatory submissions for cell and gene therapies.

Quantifying Therapeutic Expression in Target Tissues

The efficacy of an ATMP is directly linked to the level and duration of therapeutic protein expression within the target tissue. Accurately measuring this expression presents a significant analytical challenge, particularly for gene therapies where expression can be low, localized, and non-linear relative to the administered vector dose. Standard ligand-binding assays may lack the required specificity or dynamic range to navigate these complexities.

Our approach utilizes hybrid liquid chromatography-tandem mass spectrometry (LC-MS/MS) to build custom assays from the ground up. Operating within our >100,000 sq ft facility, we design methods to precisely quantify your specific therapeutic protein in tissues and biofluids. This capability is central to de-risking development programs and accelerating the typical 18-24 month IND timeline.

A scientist in a lab coat and gloves looks through a microscope in a laboratory setting, with a blue color overlay.

A scientist pipetting a red liquid into a multi-well plate in a laboratory setting.

Strategic Insights from Complex Bioanalysis

A successful bioanalytical strategy requires both precise technical execution and deep strategic insight. As demonstrated in recent studies on AAV-mediated gene replacement, the ability to develop species-specific mass spectrometry methods is a key enabler for preclinical programs (PMID: 37891254). The strategic insight from this work highlights the necessity of quantifying robust, non-linear protein expression directly in target tissues to establish a clear pharmacokinetic and pharmacodynamic relationship. This level of analytical precision provides definitive evidence of biological activity.

Core Bioanalytical Capabilities

Our protein and biomarker quantification services are designed to support every stage of preclinical development. Since the Franklin Biolabs brand launch in 2024, programs utilizing our bioanalytical data have maintained a 100% IND success rate, a record established by our core scientific team since 2019.

  • Custom LC-MS/MS Assay Development: Targeted quantification of therapeutic proteins, peptides, and biomarkers.

  • Multiplexed Biomarker Panels: Simultaneous measurement of multiple pharmacodynamic markers to assess biological response.

  • Tissue and Biofluid Analysis: Expertise in sample processing and analysis from a wide range of matrices, including plasma, CSF, and complex tissue homogenates.

  • Full GxP Validation: Method validation executed in accordance with current regulatory guidance for IND-enabling studies.

A female scientist in a lab coat analyzes complex biological data, including cellular imagery and DNA models, on a computer screen.

Commitment to Animal Welfare

All in vivo studies are conducted in strict accordance with our Animal Welfare and 3Rs (Replacement, Reduction, and Refinement) principles. Our programs are executed in facilities that are AAALAC-accredited and USDA-registered, ensuring the highest ethical standards are maintained throughout every preclinical program.

Scientific Process Diagram

This content is for informational purposes. For guidance specific to your therapeutic program, please contact our team for a consultation.

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