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Updated: Aug 22, 2025

Using a Cyclic Ion Mobility Spectrometer for Tandem Ion Mobility Experiments
Published on: January 20, 2022
High-Field Asymmetric Waveform Ion Mobility Spectrometry Interface Enhances Parallel Reaction Monitoring on an
Weixian Deng1,2, Jihui Sha1, Fanglei Xue3
1David Geffen School of Medicine, Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California 90095, United States.
Abstract:
High-field asymmetric waveform ion mobility spectrometry (FAIMS) enables gas-phase separations on a chromatographic time scale and has become a useful tool for proteomic applications. Despite its emerging utility, however, the molecular determinants underlying peptide separation by FAIMS have not been systematically investigated. Here, we characterize peptide transmission in a FAIMS device across a broad range of compensation voltages (CVs) and used machine learning to identify charge state and three-dimensional (3D) electrostatic peptide potential as major contributors to peptide intensity at a given CV. We also demonstrate that the machine learning model can be used to predict optimized CV values for peptides, which significantly improves parallel reaction monitoring workflows. Together, these data provide insight into peptide separation by FAIMS and highlight its utility in targeted proteomic applications.
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