Explorations into isomeric peptides of opposite directionalities by high resolution electrospray collision induced dissociation tandem mass spectrometry

In this study, we have probed the influence of reversal of peptide bond directionality in S peptide vs Retro S (RS) peptide on the characteristics of collision induced dissociation (CID) tandem mass spectrometry (MS/MS) under electrospray ionization (ESI) conditions. S peptide: KETAAAKFERQHMDSS, which corresponds to residues (1-16) of bovine pancreatic ribonuclease A (RNase A) and RS peptide: SSDMHQREFKAAATEK were taken as models. CID was carried out within a linear trap quadrupole (LTQ) on the doubly protonated ([M+2H]2+) precursor ions (m/z 918.44) of the two peptides at different collision energies (CEs) and the product ion analysis was by high resolution mass analyzer, orbitrap. The degree of fragmentation - 'η' of each of the fifteen peptide bonds of the peptide molecular ions from each peptide was determined by estimating the relative abundance of product ions (b- and y-ions) with reference to precursor ions, at every CE. The greater fragility of RS peptide than S peptide was evident from determinations of CE50 and CE* (the minimum collision energy, at which, the precursor ion population is 50% and 0% of the initial populations, respectively). The values of CE50 were 23.6 and 22.6 and the values of CE* were 30 and 28 for S and RS peptides, respectively. In view of the previously determined conformational propensity of S peptide to be more structured than RS peptide (Pal-Bhowmick et al. [31]), our data suggest that the solution structures of these peptides may be preserved also in the gas phase. This augurs well for the application of high resolution CID MS/MS to probe conformational properties of peptides in gas phase.