Sequential product‐ion spectra (MS³ and MS⁴) with array detection and reaction‐intermediate scanning on a four‐sector mass spectrometer

Frangmentation yields during high‐energy collisionally activated decomposition (CAD) tandem mass spectrometie experiments are often low, due in part to the short time‐period available for the fragmentations. Consequently, attempts at multi‐stage mass spectrometry undeer high‐energy CAD conditions can give unsatisfactory result when a conventional point detector is used. Arry detection dramatically improves the detection of ion currents of low abundance; we therefore incorporated arry detection in a variety of sequential product‐ion ‘scanning’ experiments, including MS³ and MS⁴, using a BEBE instrument. The corresponding experiments were previously established on a BEqQ hybrid instrument. where the final stage of decomposition occurred under low‐energy CAD conditions. The results from the hybrid were used as a basis of comparison for the results under high‐energy CAD with array detection. On the BEBE instrument, the use of the array greatly enhanced the signal‐to background ratio for second‐and third‐generation product‐ion spectra, as compared to the use of the point detector on the instrument in several instances, the use of the array was criticaL to the success of the experiment on the four‐sector instrument. For the peptides analyzed, the fragmentation patterns observed in the sequential product spectra were similar on the four‐sector instrument and on the hybrid instrument, although the relative abundances differed between the high‐and low energy CAD regimes. Reaction‐intermediate scanning, involving two sequential decomposition step occurring on the microsecond high energy time scale, has also been implemented on the BEBE instrument. A New mode of reaction‐intermediate scanning has also been implemented on the BEqQ hybrid instrument, permitting it to access sequential fragmentation when both occur under high‐energy CAD conditions.