The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer

A new matrix-assisted laser desorption/ionization (MALDI) time-of-flight/ti me-of-flight (TOF/TOF) high-resolution tandem mass spectrometer is describe d for sequencing peptides, This instrument combines the advantages of high sensitivity for peptide analysis associated with MALDI and comprehensive fr agmentation information provided by high-energy collision-induced dissociat ion (CID). Unlike the postsource decay technique that is widely used with M ALDI-TOF instruments and typically combines as many as 10 separate spectra of different mass regions, this instrument allows complete fragment ion spe ctra to be obtained in a single acquisition at a fixed reflection voltage. To achieve optimum resolution and focusing over the whole mass range, it ma y be desirable to acquire and combine three separate sections. Different co mbinations of MALDI matrix and collision gas determine the amount of intern al energy deposited by the MALDI process and the CID process, which provide control over the extent and nature of the fragment ions observed. Examples of peptide sequencing are presented that identify sequence-dependent featu res and demonstrate the value of modifying the ionization and collision con ditions to optimize the spectral information.