Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics

Area of Science:

• Proteomics
• Analytical Chemistry
• Biochemistry

Background:

• Field Asymmetric Ion Mobility Spectrometry (FAIMS) is crucial for analyzing limited biological samples.
• Optimizing FAIMS parameters is key to maximizing its performance in complex analyses.

Purpose of the Study:

• To investigate the impact of FAIMS resolution tuning on sensitivity and ion transmission.
• To demonstrate the benefits of electrode temperature modulation for low-input proteomics.

Main Methods:

• Modulation of FAIMS electrode temperature to adjust ion mobility resolution.
• Analysis of ion transmission, ion counts, quantitative precision, and peptide identifications.
• Application of the method to single-cell and low-input proteomic samples.

Main Results:

• Lowering FAIMS resolution by temperature modulation broadens the compensation voltage window.
• Increased ion transmission led to significant improvements in ion counts (25-34%).
• Enhanced quantitative precision and a 25-34% increase in peptide identifications were observed.

Conclusions:

• Electrode temperature modulation is an effective strategy to tune FAIMS resolution and improve sensitivity.
• This approach offers substantial benefits for single-cell and low-input proteomics.
• Optimized FAIMS resolution enhances data quality and analytical throughput.