Capture the 5,000,000 Missing Pieces in Proteomics Enrichment by FAIMS

The diverse post translational modifications (PTMs) add up the already enormous in number, meanwhile low abundance for certain species of proteomes with even more complexity. As efforts to enrich peptides and proteins of interest out of complex mass spectral background, various fractionation, separation, enrichment, and feature detection strategies are extensively implemented. Hydrophilic interaction chromatography (HILIC), and its varieties are often seen as the unbiased universal separation & enrichment strategies, but them alone cannot effectively resolve the background complexity issue. Orthogonal separations such as size exclusion chromatography (SEC) and multidimensional protein identification technology (MudPIT) may have limited orthogonality and cumbersome. The unresolved complexity could diminish the recent advancements on mass analyzer end, e.g., data independent acquisition (DIA) and synchronous precursor selection (SPS). (High) field asymmetric waveform ion mobility spectrometry (FAIMS), alternatively known as differential (ion) mobility spectrometry (DMS and DIMS), can provide a distinctive front-end, differential ion mobility selectivity. However, the first generation cylindrical FAIMS was not accepted or adopted by broader community due to low ion transmission efficiency¹. Planar FAIMS and ultra FAIMS were thought to be more promising configurations, but they all bear fundamental limitations. In the most recent decade, several improvements have been made on cylindrical FAIMS, making it regain the balance of ion transmission and ion focusing feature. Complementary subsets of global phosphoproteome² and global glycoproteome³ which were previously inaccessible were identified using the new cylindrical FAIMS device.

1.     Winter, D. L.;  Wilkins, M. R.; Donald, W. A., Differential Ion Mobility–Mass Spectrometry for Detailed Analysis of the Proteome. Trends in Biotechnology 2019, 37 (2), 198-213.

2.     Muehlbauer, L. K.;  Hebert, A. S.;  Westphall, M. S.;  Shishkova, E.; Coon, J. J., Global Phosphoproteome Analysis Using High-Field Asymmetric Waveform Ion Mobility Spectrometry on a Hybrid Orbitrap Mass Spectrometer. Analytical Chemistry 2020, 92 (24), 15959-15967.

3.     Ahmad Izaham, A. R.;  Ang, C.-S.;  Nie, S.;  Bird, L. E.;  Williamson, N. A.; Scott, N. E., What Are We Missing by Using Hydrophilic Enrichment? Improving Bacterial Glycoproteome Coverage Using Total Proteome and FAIMS Analyses. Journal of Proteome Research 2021, 20 (1), 599-612.