Complete characterization of post-translationally modified isomeric peptides by linear and non-linear ion mobility, and tandem mass spectrometry

Abstract

Proteins often include covalently bound chemical groups (post-translational modifications, PTMs) that alter their biological functions. Attachment of the same PTM on alternative sites creates isomers with distinct functions, making their separation and identification critical to full understanding of biochemical processes. While a plethora of techniques were implemented to solve this problem, it remains a daunting task. A fast and efficient technology, ion mobility spectrometry (IMS) has emerged to help. This thesis describes the use of field asymmetric waveform IMS (FAIMS) to separate an array of modified peptides comprising of four to fifty-two amino acids. The FAIMS device is simply two parallel plates with a gap of 1.9 mm width, one carrying an asymmetric bisinusoidal waveform of ~4 kV peak amplitude. The typical carrier gas is a helium/nitrogen mixture, with helium serving to improve the resolution of separations by increasing ion mobilities and establishing a non-Blanc effect in gas mixtures. Ions selected by FAIMS were passed to a linear quadrupole ion trap or Orbitrap mass spectrometers (Thermo), where fragmentation via collision-induced and/or electron transfer dissociation was applied as needed. These separations were compared with linear IMS (based on absolute ion mobility) using the Waters Synapt G2 traveling wave ion mobility spectrometer and Bruker trapped ion mobility spectrometer. This FAIMS/MS technique was developed for the identification of the position of a given post translational modification, as well as the utilization of previously discovered techniques using a new approach. Nearly all investigated peptides were successfully resolved regardless of the peptide size and the nature and site of modification.