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FAIMS_PAPER_ChemRxiv_Final_RVG.pdf (722.86 kB)

Deeper Protein Identification by Using FAIMS in Top-down Proteomics

submitted on 28.01.2021, 03:07 and posted on 29.01.2021, 12:03 by Robert Gerbasi, Rafael D. Melani, Susan E. Abbatiello, Michael W. Belford, Romain Huguet, John P. McGee, Dawson Dayhoff, Paul M. Thomas, Neil. L Kelleher

Field Asymmetric Ion Mobility Spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity, and enables more proteins to be identified by providing additional gas phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications and an 8% increase in proteoform identifications as compared to samples analyzed without FAIMS. This increase was attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications.


Grant P41 GM108569 from the National Institute of General Medical Sciences


Email Address of Submitting Author


Pacific Northwest National Labs


United States

ORCID For Submitting Author


Declaration of Conflict of Interest

NLK consults for Thermo Fisher Scientific. MB and RH are employees of Thermo Fisher Scientific.