Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics

Vincent R. Gerbasi, Rafael D. Melani, Susan E. Abbatiello, Michael W. Belford, Romain Huguet, John P. McGee, Dawson Dayhoff, Paul M. Thomas, Neil L. Kelleher*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


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, an 8% increase in proteoform identifications, and an improvement in proteoform identification compared to samples analyzed without FAIMS. In addition, utilization of FAIMS resulted in the identification of proteins encoded by lower-abundance mRNA transcripts. These improvements were 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.

Original languageEnglish (US)
Pages (from-to)6323-6328
Number of pages6
JournalAnalytical Chemistry
Issue number16
StatePublished - Apr 27 2021

ASJC Scopus subject areas

  • Analytical Chemistry


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