Differentiation of three pairs of Bocβ,γ and γ,βhybrid peptides by electrospray ionization tandem mass spectrometry

A new series of BocNβ3, γ4γ4, β3isomeric hybrid peptides containing repeats of β3Caa and γ4Caas, Caa Clinked carbo β3γ4amino acids derived from Dxylose have been differentiated by both positive and negative ion electrospray ionization ESI iontrap and high resolution quadrupole timeofflighttandem mass spectrometry QTOF MSMS. MSnof protonated isomeric peptides and M H − Boc Hproduce characteristic fragmentation involving the peptide backbone, the Bocgroup, and the side chain. The positional isomers are differentiated from one another by the presence of yn, bn, and other fragment ions of different mzvalues. It is observed that the peptides with βCaa at the Nterminus produce extensive fragmentation, whereas γCaa gave rise to much less fragmentation. Peptides with γCaa at the Nterminus lose NH3, whereas this process is absent for the carbopeptides with βCaa at the Nterminus. Two pairs of dipeptide diastereomers are clearly differentiated by the collisioninduced dissociation CID of their protonated molecules. The loss of 2methylprop1ene is more pronounced for BocNHRβCaaRγCaaOCH36 and BocNHRγCaaRβCaaOCH312, whereas it is insignificant or totally absent for its protonated diastereomeric pair BocNHSβCaaSγCaaOCH31 and BocNHSγCaaSβCaaOCH37. Further, ESI negative ion tandem mass spectrometry has also been found to be useful for differentiating these isomeric peptide acids. Copyright © 2008 John Wiley & Sons, Ltd.