Factors affecting the performance of a MALDI Time-of-Flight instrument for MS/MS of peptides are investigated. The instrument is designed to operate in both the post source decay (PSD) mode and the CID mode. A three stage gridless source gives the freedom to promote maximum PSD yield with high daughter ion resolution. Data will be presented on a number of well documented peptides illustrating resolution, sensitivity and mass accuracy. Spectra will be shown from peptides of a well characterized fragmentation pattern to compare the two processes. The compact focusing source coupled with a single stage reflectron keeps the calibration law for products a simple linear function which can be characterized by a known standard. The capability of the instrument to give isotope resolution on product ions reduces the ambiguity in identifying the fragment species produced by the PSD process. A Bradbury-Nielson ion gate allows precursor ion selection for true MS/MS capability. The ion gate also acts as an energy filter for the precursor which has the effect of increasing the resolution when operating the instrument in CID mode.
The application of delayed extraction to achieve higher resolution has been investigated. Wiley and McLaren in 1955 [1] showed that Time-Lag Focusing can be used to energy focus at the expense of spatial focusing. More recently Brown et al. [2] and Reilly et al. [3] showed that delayed extraction can be applied to a MALDI source to focus ions of differing velocities. In the delayed extraction mode ions are initially allowed to spread out in a zero electric field, the distance ions travel depends on their initial velocities. At the appropriate time an electric field is applied to the ions. Faster ions which have traveled further receive less potential energy from the applied electric field than the slower ions. In this way velocity focusing can be achieved. A two stage source coupled with the above instrument has been designed and built to achieve second order velocity focusing at the reflectron image. The main advantage of this technique apart from the resolution improvement is that the resolution is less dependent on laser intensity. Another consequence is that PSD can be partially suppressed when not required. This can result in improved high mass sensitivity, and can be used to enhance the contrast between CID and PSD spectra.