Using ion mobility spectrometry to resolve isotopomers, identify isomers by isotopologic shifts, and predict mobility changes for post-translationally modified peptides

Abstract

Differential or field asymmetric waveform ion mobility spectrometry (FAIMS) operating at high electric fields fully resolves isotopic isomers for a peptide with labeled residues. The naturally present isotopes, alone and together with targeted labels, also cause spectral shifts that approximately add for multiple heavy atoms. Separation qualitatively depends on the gas composition and field strength. These findings may enable novel strategies in proteomic and metabolomic analyses using stable isotope labeling. FAIMS delves more deeply into the naturally present isotopes and shows a method for characterization of isomers based upon their isotopologic shifts in a high electric field. It looks at the differentiating +1 Da shifts for identification with monohalogenated anilines. This produces an identifying fingerprint potentially for any ion based on isotopologic shifts. The rising profile of ion mobility spectrometry (IMS) in proteomics has driven the efforts to predict peptide cross-sections. In the simplest approach, these are derived by adding the contributions of all amino acid residues and post-translational modifications (PTMs) defined by their intrinsic size parameters (ISPs). It shows that the ISPs for PTMs can be calculated from properties of constituent atoms, and introduce the "impact scores" that govern the shift of crosssections from the central mass-dependent trend for unmodified peptides. The ISPs and scores tabulated for 100 more common PTMs enable predicting the domains for modified peptides in the IMS/MS space that would guide subproteome investigations.