Automatic function switching and its usefulness in peptide and protein analysis using direct infusion microspray quadrupole time-of-flight mass spectrometry

Automatic function switching has been investigated for high-throughput prot ein identification and sequencing of peptides using direct infusion of tryp tic digests on a quadrupole time-of-flight instrument. The increase in spee d and the high quality of data make it a favourable technique for tandem ma ss spectrometry when compared to manual selection of each precursor ion; th ese advantages are not restricted to combined LC/MS/MS analyses for which t he automatic function-switching mode was originally developed. This mode wa s compared to analyses performed using a slow scan of the quadrupole analyz er with repeated recording of product ion spectra. For the specific purpose of generating product ion data for sequence determination (as opposed to s urveying all precursors of a selected product ion), the automatic function- switching mode was, as expected, markedly superior with respect to speed of analysis and quality of data. Furthermore, the automatic function-switchin g mode provides greater versatility with respect to selection of optimal co llision energies. Copyright (C) 2001 John Wiley & Sons, Ltd.