Checking the boxes next to each ion type allows those ion types to be considered in matching the data to a sequence. Users can either choose to use the default ion types for a particular instrument or a user selected set.
Server administrators can modify the default instrument ion types or add new instrument selections.
Selection of fewer ion types will generally lead to fewer false positives, however ion masses corresponding to ion types not selected or unknown to the program will result in those ion masses NOT being matched. Furthermore, database entries frequently contain pre and pre-pro proteins, as well as gene fragments. The tolerances on both the parent ion and fragment ions should be set to be consistent with the mass accuracy of the instrument used to generate the data. Fragment mass accuracy is often better at lower mass than at higher mass. For PSD spectra this is particularly important.