Thermo Scientific FAIMS Pro interface

Importance of the Topic

Proteomics workflows face challenges from complex samples, wide dynamic ranges, and the need for high throughput. The FAIMS Pro interface introduces gas-phase ion mobility separation to enhance selectivity and sensitivity, reducing offline fractionation and accelerating discovery of biomarkers and therapeutic targets.

Objectives and Overview of the Article

This article presents the Thermo Scientific FAIMS Pro interface and its seamless integration with next-generation LC-MS systems. It reviews how differential ion mobility filtering improves protein and peptide identification, enhances quantitative accuracy, and streamlines workflows from global profiling to targeted verification.

Methodology and Instrumentation

The FAIMS Pro interface uses optimized cylindrical electrodes and adjustable compensation voltage (CV) settings to transmit selected ion populations. Key methodological aspects include tool-free assembly under vacuum, compatibility with nanoflow LC and direct infusion, and automated CV scanning for total ion current or targeted monitoring. Instrument control software provides one-click method templates and automated tuning tools.

Použitá instrumentace

• Thermo Scientific EASY-nLC 1200 system
• Thermo Scientific Orbitrap Exploris 480 mass spectrometer
• Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer
• Thermo Scientific TSQ Altis triple quadrupole mass spectrometer
• Thermo Scientific EASY-Spray and Nanospray Flex ion sources

Main Results and Discussion

Integration of the FAIMS Pro interface delivered:

• 29% increase in unique peptides and 24% more protein identifications in data-dependent acquisition at 100 ng HeLa digest
• Up to 18% higher proteome coverage efficiency with shorter gradients and five-fold less sample
• Enhanced TMT multiplexing accuracy by reducing co-isolation interference and improving the interference free index
• Improved top-down proteoform characterization, enabling selective transmission of antibody light and heavy chains at different CVs
• Extended dynamic range and lower limits of quantification in SRM assays by clearing background noise

Benefits and Practical Applications of the Method

The FAIMS Pro interface provides:

• Deeper proteome coverage without additional offline fractionation
• Reduced sample consumption and shorter LC-MS runtimes
• Higher confidence in label-free and isobaric quantification workflows
• Intuitive setup via automated method templates and CV optimization
• Robust compatibility across multiple Thermo Scientific mass spectrometry platforms

Future Trends and Opportunities

Emerging opportunities include:

• Coupling FAIMS with advanced fragmentation techniques (HCD, ETD, UVPD) for comprehensive top-down analysis
• Expanding clinical biomarker verification and high-throughput targeted assays
• Integration with AI-driven method optimization and data analysis pipelines
• Development of novel FAIMS modes for enhanced detection of low abundance species

Conclusion

The Thermo Scientific FAIMS Pro interface significantly enhances selectivity, sensitivity, and throughput in proteomic analyses. Its seamless integration and user-friendly operation support a broad range of applications from deep discovery to precise targeted quantification, establishing a new standard for online gas-phase fractionation.

Reference

• A S Hebert et al Analytical Chemistry 2018 90(15) 9529–9537
• S Pfammatter et al Molecular & Cellular Proteomics 2018 17(10) 2015–2067