Fragmentation reactions of an (n = 4–8) ions containing only alanine residues

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A detailed study of the fragmentation reactions of an (n=4–8) ions containing only Ala residues has been carried out using collisional activation on an electrospray/QqToF instrument. Two distinct fragmentation pathways are observed. One, which we have called the “imine” pathway, involves initial elimination of an imine (an→bn−1) followed by elimination of Ala residues (bn−1→bn−2, etc.). This pathway most likely involves the protonated substituted imine R2C(O)NH+CHR1. The second pathway, which we have called the “amide” pathway, involves initial elimination of NH3 to form an an* ion followed by elimination of Ala residues to form a series of a* ions (an*→an−1*→an−2*, etc.). This latter reaction sequence begins from a protonated C-terminal amide which has been identified by IRMPD studies as the major species present for the A-A-A-A a4 ion (Bythell et al., 2010). The present results strongly indicate that the larger an ions fragment in a manner similar to that elucidated for the all-Ala a4 ion and that the “amide” pathway is the dominant fragmentation channel for all the an ions studied in the present work.