Thermo Scientific™ Orbitrap Exploris™ 240 mass spectrometer - Diverse applications for your core lab research and clients

Importance of the Topic

Protein identification and quantitation by LC–MS is essential in proteomics research and core laboratories, requiring systems that deliver robustness, flexibility and high throughput across diverse applications such as shotgun proteomics, gel-band analysis, label-free and multiplexed quantitation.

Study Objectives and Overview

This study evaluates the performance of the Orbitrap Exploris 240 mass spectrometer equipped with the FAIMS Pro interface to demonstrate:

• Deep proteome coverage across gradient lengths of 30, 60, 90 and 120 minutes.
• Rapid gel-band protein identification using short gradients (15 and 30 minutes).

Methodology and Instrumentation

Sample preparation and analytical setup:

• Complex proteome: 200 ng Thermo Scientific Pierce HeLa Protein Digest Standard per run.
• Gel-band analysis: 250 fmol Pierce 6 Protein Digest Standard extracted from SDS-PAGE bands.
• Liquid chromatography: Thermo Scientific EASY-nLC 1200 with a 25 cm IonOpticks Aurora UHPLC emitter column (250 mm × 75 µm, 1.6 µm particles) at 300 nL/min.
• Ionization and gas-phase separation: Thermo Scientific Nanospray Flex source and FAIMS Pro interface (compensation voltages –50 V and –70 V).
• Mass spectrometry: Data-dependent acquisition on an Orbitrap Exploris 240 high-resolution accurate-mass instrument.
• Data analysis: Thermo Scientific Proteome Discoverer 2.4 with 1% peptide-spectrum match false discovery rate.

Main Results and Discussion

The performance benchmarks reveal:

• Complex proteome runs identified up to 6,355 unique protein groups and 52,000 peptide groups at 1% FDR, with the number of identifications increasing with gradient length.
• Gel-band workflow detected all six target proteins (Serum Albumin, Cytochrome C, Lysozyme, β-galactosidase, Apo-Transferrin and Alcohol Dehydrogenase) with sequence coverage up to 75% in a 15-minute gradient, supporting analysis of up to 96 samples per day.

These findings demonstrate the system’s ability to tune between deep proteome coverage and high throughput according to experimental demands.

Benefits and Practical Applications

The combined features of the Orbitrap Exploris 240 MS and FAIMS Pro interface offer:

• Gradient flexibility for customized trade-offs between depth and speed.
• Enhanced selectivity and reduced background noise from FAIMS, improving identification confidence.
• Streamlined gel-band workflows, increasing daily sample throughput in core labs.

Future Trends and Opportunities

Ongoing developments in mass spectrometry hardware, ion mobility separations and real-time data analytics will drive further gains in sensitivity, dynamic range and automation. Integration with robotic sample handling and cloud-based processing promises to expand high-throughput proteomics in both research and clinical laboratories.

Conclusion

The Orbitrap Exploris 240 MS with FAIMS Pro interface delivers a versatile, high-performance platform for a broad spectrum of proteomic applications. Its robust design and adaptable workflows make it an ideal workhorse instrument for core facilities aiming to balance deep proteome analysis with rapid targeted workflows.