Characterization of a new in-line SID mode and comparison with high energy CID

A new mode of operation for an in-line surface induced dissociation device in a tandem four sector instrument was developed based on SIMION ion trajectory calculations. The calculations predict that a double deflection mode of operation provides a more focused precursor ion beam at the target electrode compared to a single deflection mode and suggests improved SID efficiencies might be obtained. Characterization of the double deflection mode of operation was accomplished by examining standard compounds commonly used for SID experiments. Ion/surface reactions using a hydrocarbon surface and a surface coated with a perfluoropolyether revealed that the correct target was indeed being bombarded. Efficiency measurements were made by measuring precursor ion intensities prior to the collision region and product ion intensities after MS-2. Efficiencies were compared for a variety of precursor ions between single deflection mode, double deflection mode, and high energy CID in the four sector instrument. Efficiency values ranging from 3.2 to 15.4% indicated that, for most ions, double deflection mode was 2-10 fold more efficient than single deflection mode or CID. The most dramatic differences in efficiencies were observed for peptide precursor ions. (C) 1998 Elsevier Science B.V.