The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics

Comparative MS/MS studies of singly and doubly charged electrospray ionizat ion (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been e valuated with particular emphasis on the data quality for subsequent data p rocessing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of c ollision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closel y spectra obtained by matrix-assisted laser desorption/ionization post-sour ce decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other h and, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MAL DI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionizat ion event. Since MALDI ions are predominantly formed as singly charged spec ies and ESI ions as doubly charged, the associated difference in the spectr al quality of MS/MS spectra as described here imposes direct consequences o n data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed. Copyright (C) 2001 John Wiley & Sons, Ltd.