Enabling resolution of isomeric peptides using tri-state ion gating and Fourier-transform ion mobility spectrometry

Using Fourier-Transform ion gate modulation technique, we compare the ability of the tri-state ion shutter (3S-IS) to the two-state ion shutter (2S-IS) in separating three pairs of isomeric peptide including 1.Gly-Arg-Gly-Asp-Ser (GRGDS) / Ser-Asp-Gly-Arg-Gly (SDGRG); 2.Sar-Arg-Gly-Asp-Ser-Pro (SRGDSP) / Gly-Arg-Gly-Asp-Thr-Pro (GRGTP); 3.Kemptide / (Val 6 , Ala 7 )-Kemptide using electrospray ionization and ion mobility spectrometry. Mobility separation was evaluated for peptide individually and as simple mixtures. Baseline resolution of both singly and doubly charged ions of the isomeric pentapeptide mixture of GRGDS / SDGRG was attainable with the described IMS system using the 3S-IS configuration, illustrating the capacity of the present instrument to resolve isomeric compounds with differences in ion neutral collision cross section (CCS) of less than 1% for the singly charged ions. However, with the 2S-IS, both singly and doubly charged ions of the same peptide mixture were unresolved in the mobility domain. To our knowledge, this is the first-time baseline separation has been reported for the singly charged ions of the isomeric reversed sequence pentapeptide mixture using Fourier transformed drift tube IMS with nitrogen as the drift gas. For all the peptide mixtures, the ion counts for the ion mixture recorded with the 3S-IS were substantially higher (> 50%) in comparison to the 2S-IS. The resolving power of the instrument ranged between 82 to 128 for the target analyte ions analyzed in a mixture using the 3S-IS. Whereas, the resolving power of the 2S-IS ranged between 60 and 100 for the target analytes. Overall, a 20% increase in resolving power was obtained with the 3S-IS in comparison to the 2S-IS. Separation of the different isomeric peptide ion mixture depicted in this present study clearly shows the unique size-to-charge separation ability of IMS that complements the mass-to-charge ratio measurement capacity of mass spectrometry.