Accelerate your Proteomic Workflow with the Thermo Scientific™ FAIMS Pro™ Interface

Significance of Topic

Proteomics delivers a comprehensive view of protein expression and modification, reflecting the dynamic state of cells in health and disease. The complexity of peptide mixtures generated by enzymatic digestion can overwhelm conventional mass spectrometry, creating a need for advanced separation methods that enhance selectivity and sensitivity.

Aims and Overview

This article introduces a high field asymmetric waveform ion mobility interface designed to accelerate proteomic workflows. It examines how gas phase ion separation, when coupled to high resolution mass spectrometers, can improve peptide and protein identification rates while reducing chemical noise and analysis time.

Methodology and Instrumentation

The interface applies alternating high and low electric fields to separate ions by mobility. Sequential transmission of targeted ion populations is achieved by scanning a compensation voltage, enabling online gas phase fractionation before mass analysis. This device integrates seamlessly with nano, capillary and microflow liquid chromatography systems and Orbitrap mass analyzers for both bottom up and top down proteomics.

Main Results and Discussion

In single shot analyses of tryptic peptides, the interface doubled the number of peptide precursors entering the mass spectrometer and increased protein identifications by up to 55 percent. A phosphoproteomics workflow uncovered 685 additional high confidence phosphorylation sites, including 20 percent novel sites. In antibody chain analysis, differential mobility separation eliminated the need for offline fractionation and improved chain resolution. When combined with high resolution Orbitrap detection, the interface reduced chemical interferences, raised signal to noise ratios and delivered more unique peptide identifications per unit time.

Benefits and Practical Applications

• Orthogonal gas phase separation reduces sample complexity and enhances dynamic range
• Improved quantitative accuracy in isobaric labeling workflows by limiting co isolation interference
• Reduced sample consumption and preparation time through elimination of offline fractionation
• Robust, tool free design with pre configured acquisition templates for rapid deployment

Future Trends and Applications

Emerging directions include integration with top down native mass spectrometry, in depth glycoproteomics and real time method optimization. Automation and increased throughput will facilitate adoption in clinical and industrial laboratories for large scale biomarker discovery and quality control.

Conclusion

The high field asymmetric waveform ion mobility interface provides a powerful additional separation dimension for proteomic mass spectrometry. By combining gas phase fractionation with high resolution mass analysis, it addresses key challenges of complex sample analysis and enhances overall sensitivity, selectivity and throughput.

Použitá instrumentace

• Thermo Scientific FAIMS Pro differential ion mobility interface
• Orbitrap Eclipse Tribrid and other Orbitrap mass spectrometers
• Thermo Scientific EASY nLC 1200 and allied nano capillary LC systems

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