PNNL

Abstract

Many proteins and proteolytic peptides incorporate the same post-translational modification (PTM) at different sites, creating multiple localization variants with different functions or activities that may coexist in cells. Current analytical methods based on liquid chromatography (LC) followed by tandem mass spectrometry (MS/MS) are challenged by such isomers that often co-elute in LC and/or produce non-unique fragments. Application of ion mobility spectrometry (IMS) has previously been explored, but success was limited by insufficient resolution. We show that the recently developed high-resolution differential ion mobility spectrometry (FAIMS) using helium-rich gases can readily separate phosphopeptides with variant modified sites. Specifically, use of He/N2 mixtures containing up to 74% He has allowed separating to >95% three monophosphorylated peptides of identical sequence. Similar separation was achieved at 50% He, using an elevated electric field. Bisphosphorylated isomers that differ in only one modification site were separated to the same extent. We anticipate the FAIMS capabilities for such separations to extend to other PTMs.