Real-Time, Absolute Quantitation of Critical Bioprocessing Metabolites with the AI-Powered PyxisTM Metabolomics Platform

Evaluate and validate Matterworks’ Pyxis metabolomics platform to improve bioprocessing. Pyxis provides rapid, absolute quantitation of ~150 metabolites across intracellular pathways. Also explore use of Pyxis for early detection/monitoring of glycoforms.
Categories
Drug substance
Process control

Industry Need

The industry need addressed by this project is centered on improving efficiency and accuracy in bioprocessing metabolite analysis, which is critical for biopharmaceutical manufacturing. Specifically:

  • Rapid, High-Throughput Analysis: Traditional LC-MS methods for metabolite quantitation are labor-intensive, slow, and require specialized expertise. The industry needs faster, automated solutions to handle large sample sets from bioreactors without compromising accuracy.
  • Real-Time Process Monitoring: Biopharma manufacturers require real-time insights into metabolite levels to optimize bioprocess conditions, reduce variability, and prevent costly batch failures.
  • Cost Reduction and Scalability: Current methods increase operational costs and limit scalability. Automating metabolomic profiling can significantly reduce labor costs and accelerate decision-making, supporting large-scale production


Approach

The goal of this project is to evaluate and validate Matterworks’ Pyxis metabolomics platform to improve bioprocessing consistency and efficiency.  

  • A proprietary consumable kit that can fit into current LCMS workflows and automated data processing will enable the analysis of cell lysates and media. 
  • Pyxis provides rapid, absolute quantitation of ~150 metabolites across intracellular pathways that impact cell growth, protein production and processing, and glycosylation.  
  • Project input from partners will provide important feedback to optimize Pyxis product specifications and help guide future development for at-line monitoring.  

Impacts

Develop Pyxis as a proprietary consumable kit that fits seamlessly into current LCMS workflows and automated data processing enable the analysis of cell lysates and media

Explore using Pyxis for early detection and monitoring of glycosylation activity impacting glycoform profiles and process excursions

Value Statement/Outcomes

The implementation of Matterworks’ Pyxis™ platform enables real-time, absolute quantitation of critical bioprocessing metabolites with accuracy comparable to traditional LC-MS methods, while significantly reducing labor and expertise requirements. By automating analysis and cutting time by up to 70–80%, manufacturers can save approximately $150–$250 per sample in labor costs, accelerating metabolomic profiling across large bioreactor sample sets to optimize processes faster—translating into substantial financial benefits for large-scale biopharmaceutical manufacturing.

Outputs/Deliverables

Demonstration of Pyxis™ Accuracy: Verified that the AI-powered Pyxis platform can replicate the accuracy of traditional LC-MS metabolite quantitation methods.

High-Throughput Metabolomic Profiling: Showed that metabolomic data can be rapidly obtained from large bioreactor sample sets, enabling real-time monitoring of critical metabolites.

Advancement of BRL: Increased Bioprocessing Readiness Level from 3 to 5, positioning Pyxis as an early-stage commercial product launched at ASMS.

Posters

Geremia, J., Henriques da Costa, A., Kassis, T., Reger, L., & Niemann, J., Direct comparison of rapid absolute quantification of metabolites – ML based Pyxis and traditions LC-MS methods, NIIMBL National Meeting, Washington, DC, June 25, 2024.

Henriques da Costa, A., Campbell, J. M., Pollard, D., Niemann, J., Reger, L., Lauterbach, J., Kassis, T., Pruyne, J., Ferro, L., Howland, J., Geremia, J., Hooper, S., & Delmar, M. C., Direct comparison of a machine learning-based tool for rapid absolute quantification of metabolites in biological samples with traditional isotopologue analysis, American Society for Mass Spectrometry 72nd Conference, Anaheim, CA, June 6, 2024.

Additional Project Information (Members Only)

Login to the NIIMBL member portal to access additional project information, including presentations, progress updates, reports, and more.

Not yet a member? Learn more about which level of NIIMBL membership is right for you and your organization.

Project Lead

Matterworks, Inc.

Matterworks, Inc.

Participating Organizations

Eli Lilly and Company

Eli Lilly and Company

Sartorius Stedim

Sartorius Stedim