AUTOMATING SAMPLE PREP AND DEMYSTIFYING LC-MS ASSAYS FOR FASTER DATA ANALYTICS IN BIOPRODUCTION

Importance of Automated Sample Preparation and LC-MS Assays

Automating sample preparation and integrating it with liquid chromatography mass spectrometry assays accelerates data generation and improves reliability in bioproduction monitoring. By reducing manual errors and variability while enabling round the clock sampling, such workflows support timely decision making and quality assurance in process development campaigns.

Study Objectives and Overview

The work aimed to develop a fully integrated platform combining automated sample preparation with automated LC-MS analysis to facilitate daily monitoring of product quality attributes and media nutrient profiles in bioreactors. The platform leverages robotics, specialized software workflows, and advanced analytics to streamline routine assays for glycoform profiling, aggregation analysis, and spent media metabolite quantification.

Methodology

Daily bioreactor samples were collected and processed on the Andrew+ Pipetting Robot, involving clarification, dilution, affinity cleanup or dilution steps as required. Samples were automatically sealed and transferred to the BioAccord LC-MS system. Workflow protocols were managed and executed via Onelab software, which monitored bioreactor aspiration files from Ambr 15 and 250 HT systems and triggered the appropriate assays without manual intervention.

Used Instrumentation

• Andrew+ Pipetting Robot (Waters Corporation)
• BioAccord LC-MS system (Waters Corporation)
• Onelab protocol library and control software
• Ambr 15 and 250 HT bioreactor systems (Sartorius Stedim Biotech)
• ACQUITY Automation Portal
• Intact Mass and Bioprocess Monitor software applications
• Waters_connect software platform
• JMP statistical software with Waters Bioprocess Monitor add-in

Main Results and Discussion

• Automated workflows enabled seamless generation of LC-MS sequence lists from bioreactor aspiration events and unified sample preparation and analysis in a single protocol.
• Assay 1 (Intact glycoform monitoring) compared direct dilute and shoot samples with Protein A purified samples and delivered rapid glycosylation profiles.
• Assay 2 (Aggregation monitoring) applied size exclusion chromatography with UV detection to quantify high and low molecular weight species, with automated integration by Intact Mass software.
• Assay 3 (Spent media analysis) quantified 17 amino acids and key metabolites using the BioAccord system and Bioprocess Monitor software, with results exported as CSV and visualized in JMP.
• Integrated data were readily available for multivariate analysis and visualization, supporting real time feedback during bioproduction campaigns.

Benefits and Practical Applications

• Significant reduction in manual handling and associated errors.
• Improved data consistency and faster access to critical process monitoring results.
• Scalable solution for routine PQA assays and nutrient profiling in process development and manufacturing.

Future Trends and Potential Applications

Future developments may include deeper integration with advanced data analytics and machine learning for predictive process control, expansion of automated protocols for additional quality attributes, and cloud-based data management to enable remote monitoring and collaborative decision making across global sites.

Conclusion

The presented fully automated sample preparation and LC-MS workflow demonstrates a robust and scalable approach to accelerating data analytics in bioproduction. The integration of robotics, software, and mass spectrometry instrumentation significantly enhances process monitoring capabilities, delivering timely and reliable results for quality assurance and process optimization.

References

1. LC-MS Analytics in Bioprocessing: Automation-Driven Analysis of Product Quality Attributes and Nutrient Monitoring Application Note 2024. Waters Corporation
2. New Software for Targeted Analysis of Titer and Media Components Using LC-MS in Bioproduction White Paper 2025. Waters Corporation
3. JMP Marketplace add-in – Bioprocess Monitor. JMP Statistical Discovery LLC