MS/MS Filtering is an extremely useful tool for both reducing search time and receiving more targeted results from a database search. It works by filtering the spectra searched to those with desired MS2 ions present in the spectra. Applications for this include oxonium ions for Glycan analysis and other PTMs with strong diagnostic ions. This feature has 3 settings to adjust:
Peak filters: lists the desired MS2 ions that you wish to have present in the final results. Such as oxonium ions from glycan fragmentation. Within the menu there is a list of common diagnostic ions used for this purpose:
You can also specify custom ions using the following notation: Peak label / Mass
m/z tolerance: Allows you to set the desired tolerance for selecting if the ions are present.
Required Number: Specifies the number of ions needed to be present in the spectra to utilize the scan in the search. For example if we list 4 common oxonium ions and set required number to 2 only spectra containing at least 2 of the specified diagnostic ions will be utilized in the search.