It has been determined experimentally that a 3 ions are generally not observed in the tandem mass spectroscopic (MS/MS) spectra of b 3 ions. This is in contrast to other b n ions, which often have the corresponding a n ion as the base peak in their MS/MS spectra. Although this might suggest a different structure for b 3 ions compared to that of other b n ions, theoretical calculations indicate the conventional oxazolone structure to be the lowest energy structure for the b 3 ion of AAAAR, as it is for other b n ions of this peptide. However, it has been determined theoretically that the a 3 ion is lower in energy than other a n ions, relative to the corresponding b ions. Furthermore, the a 3 ¡ b 2 transition structure (TS) is lower in energy than other a n ¡ b nϪ1 TSs of AAAAR, compared with the corresponding b ions. Consequently, it is suggested that the b 3 ion does fragment to the a 3 ion, but that the a 3 ion then immediately fragments (to b 2 and a 3 *) because of the excess internal energy arising from its relatively low energy and the facile It has been shown that significant rearrangement can occur upon peptide dissociation, particularly in mass spectrometers with relatively long activation/dissociation times such as ion trapping instruments [23][24][25][26][27][28]. However, rearrangements are not limited to ion trapping mass spectrometers [29 -32]. In actuality even b and y ions are formed by rearrangements involving hydrogen atom transfers (y ions) or intramolecular cyclization (b ions). The ubiquitousness of the mechanism for formation of b and y ions has been shown through kinetic energy loss measurements [33].Initially it was thought that b ions had a simple acylium ion structure [5,34,35]. However, this theory was discredited because b 1 ions are not often observed in MS/MS spectra (i.e., these ions should also be acylium ions by the preceding rationale). The current consensus is that b ions most commonly have a protonated oxazolone structure [36 -39]. This has been demonstrated in gas-phase IR studies on the b 4 ions of YGGFL [38,40]. Additionally, recent experimental and theoretical data suggest that larger oxazolones can undergo head-to-tail cyclization to form cyclic-peptide isomers [32,40]. Further evidence supporting the conclusion that b ions have the protonated oxazolone structure is that the major dissociation products of b ions (a n and b nϪ1 ions) have product ion analogs in the MS/MS spectra of synthesized oxazolone compounds [37].Although formation of a n ions via the b n ¡ a n pathway is well understood [41], the actual mechanism of b nϪ1 formation is less clear. Two major mechanisms were considered here, the direct b n ¡ b nϪ1 [36] and indirect b n ¡ a n ¡ b nϪ1 [42] pathways. Metastable ion studies indicate that a n ions are formed with substantial release of kinetic energy (KER). On the other hand b nϪ1 fragments are formed from b n parents with small KER values [36,37]. This finding suggests that a direct b n ¡ b nϪ1 mechanism is preferred. Additionally, doubleresonance experimen...

Thermally assisted collision-induced dissociation (TA-CID) provides increased dissociation in comparison with CID performed at ambient temperature in a quadrupole ion trap mass spectrometer. Heating the bath/collision gas during CID increases the initial internal energy of the ions and reduces the collisional cooling rate. Thus, using the same CID parameters, the parent ion can be activated to higher levels of internal energy, increasing the efficiency of dissociation and the number of dissociation pathways. The increase in the number of dissociation pathways can provide additional structural information. A consequence of the increase in initial internal energy is the ability to use less power to effect collisional activation. This allows lower q(z) values to be used and, thus, a greater mass range of product ions to be observed. TA-CID alleviates the problems associated with traditional CID and results in more available information than traditional CID.

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