Bayer Pharma AG implements a fully automated interpretation workflow for finding target masses

Importance of the Topic

The ability to detect target masses rapidly and reliably is essential in pharmaceutical research to accelerate compound development, reduce manual effort, and ensure data quality in high-throughput environments.

Objectives and Study Overview

Bayer HealthCare Pharmaceuticals sought to replace a manual LC-UV/MS workflow with a fully automated LC-MS solution. The goal was to integrate chromatography and mass spectrometry control, automate target mass detection in positive and negative ionization modes within a single run, and reduce turnaround time.

Methodology and Instrumentation

The laboratory implemented two identical analytical platforms comprising:

• Thermo Scientific Dionex UltiMate 3000 RSLC for ultrahigh-performance liquid chromatography
• Thermo Scientific Exactive Plus Orbitrap Mass Spectrometer for accurate mass detection in both positive and negative modes
• Thermo Scientific Chromeleon Chromatography Data System software to manage sequence setup, data acquisition, processing, and reporting

Chromatographic runs were optimized to three minutes with injection overlap to maximize throughput. The mass spectrometer collected data at 4 Hz (two scans per ionization mode per second). A custom eWorkflow in Chromeleon automated sequence preparation, system startup at 6:30 am, QC checks, and end-of-day shutdown.

Key Results and Discussion

Over five months, more than 9 000 samples were analyzed, with each system processing about 140 injections per day. In 90 percent of cases, target masses present in reaction samples were identified automatically. Average turnaround from sample entry to report delivery was reduced to approximately 15 minutes. Chromeleon reports combined UV and MS data on three pages per injection, separating hits, non-hits, blanks, and QC samples into distinct folders.

Benefits and Practical Applications

• Significantly increased throughput, enabling analysis during lunch, evenings, and weekends without additional staff
• Elimination of manual data processing steps and software switching
• Consistent MS calibration stability over weeks and automated QC monitoring using System Suitability Tests and Intelligent Run Control
• Consolidated reporting that delivers all relevant metrics in a single PDF

Future Trends and Opportunities

The flexible architecture of Chromeleon CDS paves the way for further expansion into new application areas and integration with laboratory information management systems. Potential developments include advanced adduct screening, real-time data analytics, machine-learning-driven peak detection, and remote monitoring of workflows.

Conclusion

The integrated LC-MS solution controlled by Chromeleon CDS has demonstrated robust performance, high throughput, and fully automated target mass detection, substantially improving laboratory efficiency and data quality in pharmaceutical analysis.