Oral Presentation HUPO 2019 - 18th Human Proteome Organization World Congress

High-Resolution Differential Ion Mobility Separations with Orbitrap Mass Spectrometry for Middle-Down Analyses of Histone Proteoforms (#156)

Matthew A Baird 1 , Pavel V Shliaha 2 , Gordon A Anderson 3 , Eugene Moskovets 4 , Victor Laiko 4 , Alexander A Makarov 5 , Ole N Jensen 2 , Alexandre A Shvartsburg 1
  1. Wichita State University, Wichita, KS, United States
  2. University of Southern Denmark, Odense, Denmark
  3. GAA Custom Engineering, Kennewick, WA, USA
  4. MassTech, Columbia, MD, USA
  5. Thermo Scientific, Bremen, Germany

The histone code central to epigenetics comprises a multitude of co-existing proteoforms with distinct PTM marks, including isoforms differing only in the PTM localization but having different biological functions. Characterizing that exceptionally complex mixture of highly similar species over wide abundance range is an astounding proteomic challenge, requiring the utmost from separation and identification methods. As nearly all histone PTMs reside on "tails" of ~50 residues protruding from the nucleosome, their characterization approaches that of complete histone. High-definition differential ion mobility spectrometry (FAIMS) has recently achieved broad resolution of common tail isoforms featuring methylation, acetylation, or phosphorylation. Separated forms were identified using standards or electron transfer dissociation (ETD). Those analyses previously employed ion trap MS platforms rather than Fourier-Transform MS (providing the ultimate mass resolution and accuracy mandatory for confident stoichiometric assignments) because requisite FAIMS resolution depended on gas buffers rich in helium or hydrogen that were incompatible with ultra-high vacuum needed for Orbitrap MS. We report enabling the high-resolution FAIMS/Orbitrap MS/ETD capability employing novel FAIMS devices with unprecedented voltages that reach sufficient resolution utilizing only nitrogen, tandem ion funnel FAIMS/MS interfaces removing light gases before the MS stage, and reconfiguration of Orbitrap vacuum pumping that permits operation with He inflow. The performance of resulting instruments is demonstrated for exemplary modified tail isoforms and D-amino acid containing peptides. An analogous platform with custom curved (rather than planar) FAIMS devices provides better sensitivity at lower specificity. That version is employed in initial analyses of endogenous histone tails from human HeLa cells with online liquid chromatography in "external convolution" for pre-fractionation into isomer groups. Preliminary data indicate significant separation of multiple isoforms within all targeted groups and identification of numerous proteoforms not found in the benchmark LC-MS data without FAIMS or pre-existing public databases.