Thermo Scientific™ Orbitrap Exploris™ 240 mass spectrometer - Industry-leading performance for protein identification depth and breadth of coverage

Importance of the Topic

Comprehensive proteome profiling is essential for understanding complex biological systems, enabling both identification of expressed proteins and accurate quantitation across varying sample amounts. High sensitivity and depth are critical for studies ranging from fundamental biology to large-scale clinical and industrial analyses.

Objectives and Study Overview

This study evaluates the performance of the Orbitrap Exploris 240 mass spectrometer equipped with the FAIMS Pro interface in shotgun proteomics experiments. Sample loads from 10 ng to 1,000 ng were assessed to determine achievable proteome depth, dynamic range, and throughput while maintaining stringent identification confidence.

Methodology and Instrumentation

Shotgun proteomics workflows employed data-dependent acquisition (DDA) with a Thermo Scientific EASY-nLC 1200 UHPLC system and an IonOpticks Aurora 250 mm × 75 µm column at 300 nL/min over a 90 min gradient. A FAIMS Pro interface applied compensation voltages of –50 V and –70 V to reduce chemical noise. Peptides from Pierce HeLa digest (10–1,000 ng) and PRTC calibration mixture were analyzed on the Orbitrap Exploris 240, with spectra processed in Proteome Discoverer 2.4 at 1% PSM FDR.

Main Results and Discussion

At the lowest input (10 ng), an average of 1,600 protein groups and 5,300 peptide groups were identified per run. At 1,000 ng, identifications increased to 6,700 proteins and 63,000 peptides, spanning five orders of dynamic range. Quantitative dynamic range exceeded six orders with reliable low-abundance detection. Gradient lengths from 30 to 90 min yielded 3,500–6,700 protein identifications, with a throughput of 6,500 protein groups per hour using Proteome Discoverer’s Feature Mapper to reduce missing values.

Benefits and Practical Applications

• Exceptional sensitivity for low-nanogram samples
• Broad dynamic range enabling detection of low-abundance proteins
• High throughput suitable for large cohort or clinical studies
• Accurate label-free quantitation with stringent FDR control

Future Trends and Applications

Advances may include integration of real-time FAIMS optimization, faster scan speeds, and applications in single-cell proteomics. The platform is well suited for biomarker discovery, translational research, and multi-omic workflows combining proteomics with metabolomics or lipidomics.

Conclusion

The Orbitrap Exploris 240 MS with FAIMS Pro provides best-in-class balance of sensitivity, depth, and throughput in shotgun proteomics, delivering high-confidence identifications across a wide range of sample amounts.

Reference

No external literature references were provided in the source.