To What Extent is FAIMS Beneficial in the Analysis of Proteins?

Abstract

High field asymmetric waveform ion mobility spectrometry (FAIMS), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. In this article, the benefits and limitations of FAIMS for protein analysis are discussed. The principles and mechanisms of FAIMS separation of ions are described, and the differences between FAIMS and conventional ion mobility spectrometry are detailed. Protein analysis is considered from both the top-down (intact proteins) and the bottom-up (proteolytic peptides) perspective. The roles of FAIMS in the analysis of complex mixtures of multiple intact proteins and in the analysis of multiple conformers of a single protein are assessed. Similarly, the application of FAIMS in proteomics and targeted analysis of peptides are considered.

Keywords: DMS; FAIMS; Peptides; Proteins; Proteomics.

Graphical Abstract

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Fig. 1

(a) Asymmetric waveform applied to the FAIMS electrodes; (b) ion trajectory through the FAIMS device

Fig. 2

Dependence of ion mobility on electric field. Three types of behavior are observed: A-, B-, and C-type

Fig. 3

Normalized FAIMS spectra for ubiquitin ions with charge states +5 to +13 (as denoted top right of each panel) obtained at dispersion field 28 kV/cm and carrier gas He:N₂ with % He indicated. Spectrum shown in black was obtained using a cylindrical FAIMS device at dispersion field 20 kV/cm and N₂ carrier gas. Selected conformers are labeled. Reprinted with permission from [49]. Copyright 2012 American Chemical Society

Fig. 4

FAIMS spectra for ubiquitin ions with charge states +5 to +14 (as denoted top right of each panel) obtained with carrier gas H₂:N₂ with % H₂ indicated. Smaller features are magnified for 85% H₂ only. Reprinted with permission from [50]. Copyright 2013 American Chemical Society

Fig. 5

LESA 2D-FAIMS mass spectrometry of mouse liver. (a) Single scan mass spectrum at DF = 130 Td, CF = 0.93 Td; (b) single scan mass spectrum at DF = 270 Td, CF = 2.68 Td; (c) single scan mass spectrum recorded in the absence of FAIMS field; (d) mass spectrum recorded in the absence of FAIMS field comprising 37 co-added scans (∼1 min data). Reprinted from [66]

Fig. 6

Total ion transmission maps obtained following LESA 2D FAIMS analyses of mouse liver. Reprinted from [66]

Fig. 7

Nano-liquid chromatography mass spectrometry analysis of a five protein digest (20 fmol each) (a) without and (b) with FAIMS. Extracted ion chromatograms of the doubly-charged ions at m/z 714.0, 584.9, and 536.3 (c) without and (d) with FAIMS. Extracted mass spectra for peak eluting at ~18 min from the nano-LC mass spectrometry analysis (e) without and (f) with FAIMS. Reprinted with permission from [72]. Copyright 2005 American Chemical Society