Oral Presentation 24th Annual Lorne Proteomics Symposium 2019

Application of ion mobility and electron capture dissociation (ECD) mass spectrometry to top-down and bottom-up proteoform characterization (#51)

Blaine R Roberts 1 , Eugene Kapp 1 , Soumya Mukherjee 1 , Yury V Vasil'ev 2 , Valery G Voinov 2 , Joesph S Beckman 2
  1. Florey Institute of Neuroscience and Mental Health, Parkville, VIC, Australia
  2. eMSion, Corvallis, Oregon, USA

Bottom-up approaches using collision induced dissociation for characterizing target proteins yield incomplete information, particularly concerning the colocalization of post translational modifications. We have developed a device that yields efficient ECD of proteins that can be reversibly retrofitted into Q-ToFs without diminishing performance. The ECD device does not require trapping ions as needed for ETD and thus is compatible with ion mobility separations.  Nearly complete sequence coverage is obtained with “native”-folded proteins such as the 5+and 6+charge states of ubiquitin. Sequence coverage of 80-95% was obtained for small proteins like ubiquitin, amyloid beta and alpha-synuclein (14 kDa). Sequence coverage was 93% for carbonic anhydrase (29kDa); half of the human proteome is smaller than 30kDa. The protein spectra consisted primarily of cand zions, though the ECD cell also produced a substantial number of dand wsidechain fragments. These side-chain fragments allow leucine/isoleucine or lysine/glutamine pairs to be distinguished, facilitating de novosequencing. Labile post-translational modifications were also retained. The copper and zinc cofactors in superoxide dismutase (17 kDa) remained bound to their respective binding sites in ECD fragments. We then applied this technology to protein extracts from human brain to show that we can conduct top-down protein identification on LC time scales. The simpler fragmentation patterns made possible with the ECD device allows existing mass spectrometers to be able to characterize mid-sized proteins even using fast front-end separations such as ion mobility.