Exploring Data-Dependent Acquisition Strategies with the Instrument Control Libraries for the Thermo Scientific Instruments

摘要

The main advantage of interfacing directly with the on-board computer of the mass spectrometer during data collection is to be able to use the incoming information in real time to direct future decisions. At this point we have attempted several approaches to make additional decisions during data dependent acquisition. Intensity-based dynamic exclusion considers the change in the intensity of the target precursor ion peak in order to perform fragmentation near the peak’s maximum. On-the-fly isotopic envelope extraction from the full scan allows us to select only the monoisotopic ions for fragmentation. Full scan de-isotoping and selection of the monoisotopic species is a prerequisite for efficient permanent exclusion or permanent inclusion strategies because the overall fidelity of these strategies strongly depends not only on the mass accuracy of the instrument but also on the ability to exclude the heavy isotopes from being considered as targets for fragmentation in future runs.