Using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometer for combined in-source...

Mass spectrometric experiments with fragment ions have not yet been possible with a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometer because intense signals of fragment ions were rarely observed during continuous extraction and the mass resolution of in-source formed fragment ions has been low. This paper describes a combination of MALDI in-source decay and post-source decay experiments on a MALDI-TOF mass spectrometer equipped with delayed extraction. Fragment ions initially formed in the ion source were selected by the precursor ion gate and investigated by post-source decay. The in-source formed fragment ions were sufficiently excited to undergo further metastable decay. The new method was applied to linear peptides, the cyclic peptide gramicidin S and a pentasaccharide, leading to unambiguous structural information.