Generating reproducible fragmentation patterns is a problem in electrospray ionization mass
spectrometry. Two generations of quadrupole time-of-flight(Q-TOF) instruments were selected to evaluate
the reproducibility of tandem mass spectrometry(MS/MS) spectra:an old- and a new-generation instrument.
Ninety-four MS/MS and MS/MS/MS spectra with information-rich product ions were obtained in
positive- or negative-ion mode with two different-generation Q-TOF instruments, BioTOF-Q and micrOTOF-
Q. Two principles were selected to optimize the collision energy. On the one hand, maximal structural information is
obtained when the collision energy is increased; on the other hand, when most product ions show relative abundance of
more than 10%, the lowest collision energy should be selected. The Paired-Samples T Test method was used to analysis
these paired-spectra. We found that most product ions were the same and the profiles of the product ions were similar with
both Q-TOF instruments. Interestingly, at the low signal to-noise ratio (S/N) of the precursor ion (ion intensity low to 180
counts), the profile of the MS/MS spectrum is very similar to that at a high S/N. Furthermore, when spectra were generated
with micrOTOF-Q even before and after a four-year interval, the profiles and product ions were virtually identical. In
summary, databases built with different-generation Q-TOF instruments may be universally applicable.