Orbitrap Exploris 240 mass spectrometer - Faster time to results–intelligent data acquisition and processing with applications software

Importance of the Topic

High-resolution accurate-mass Orbitrap mass spectrometry has transformed proteomics by delivering detailed, reproducible protein quantification within increasingly complex biological samples.
This capability supports advances in cell biology, biomarker discovery and pharmaceutical research.

Study Objectives and Overview

This evaluation aims to demonstrate the performance of the Thermo Scientific Orbitrap Exploris 240 mass spectrometer when combined with TMTpro 16plex isobaric labeling for high-throughput proteomic analysis.
The study compares data acquisition speed, quantitative accuracy and sample throughput against traditional multiplexing approaches.

Methodology and Instrumentation

Four treatment conditions of HeLa cell lines were prepared, each in triplicate, plus one pooled reference channel to normalize reporter intensities across runs.
Samples were labeled with TMTpro 16plex reagents and subjected to a two-hour LC-MS separation on an IonOpticks Aurora 25 cm column.

• LC system: Thermo Scientific EASY-nLC 1200
• Ion source: Thermo Scientific EASY-Spray NanoSpray Flex
• Interface: Thermo Scientific FAIMS Pro (–60 V and –80 V compensation voltages)
• Mass spectrometer: Orbitrap Exploris 240 with pre-built data acquisition templates
• Data analysis: Thermo Scientific Proteome Discoverer 2.4 with 1% FDR and a preset TMT workflow

Key Results and Discussion

The optimized workflow quantified approximately 4,000 proteins in a single 120-minute run across all 16 channels without missing values.
Principal component analysis clearly separated biological conditions based on proteome profiles, while hierarchical clustering confirmed consistent grouping of replicates.
TMTpro 16plex reagents leveraged the Orbitrap’s resolving power to baseline resolve reporter ions, ensuring accurate quantitation.

Benefits and Practical Applications

• High sample throughput: simultaneous quantitation of 16 samples in one LC-MS run
• Rapid turnaround: integrated instrument templates and software reduce setup time
• Quantitative depth: HRAM data provide precise and reproducible measurements
• Ease of use: customizable acquisition templates simplify method development

Future Trends and Applications

• Expansion to higher plex reagents for even greater multiplexing
• Integration of artificial intelligence for real-time data analysis
• Application to clinical proteomics and biomarker validation
• Automation of sample preparation and data processing workflows

Conclusion

The Orbitrap Exploris 240 mass spectrometer paired with TMTpro 16plex labeling and dedicated software delivers fast, accurate and high-throughput proteomic quantitation.
Its combination of resolving power, sensitivity and user-friendly workflows makes it a valuable tool for advanced applications in research and core facilities.

References

• Thermo Scientific Proof of Performance Note XX-65862
• Thermo Scientific Proof of Performance Note XX-65879