| LC-QTOF tandem mass spectrometers behave according to user controlled switching parameters, duty-cycle and repetition rate, which guide the selection of peptides and the timing of their fragmentation. Using a novel algorithm which analyses all spectra simultaneously, it has been found that the majority of available peptides are not fragmented with the current switching scheme. Unfortunately, it is not practical to experiment with the mass spectrometer to determine optimal switching parameters. In this study, simulation coupled with intensity surface analysis was used as a method of evaluating mass spectrometer performance. Algorithms that mimic the mass spectrometer were created in order to simulate its response to various data sets. The simulations resulted in operating curves displaying the trade-off between quality and quantity of fragment spectra. The optimal operating curve demonstrated that the current switching scheme is sub-optimal, and that new switching parameters with fewer duty cycles and fewer repetitions should be selected. |
