The Main Window 3: Set search parameters
On this page, and its four subpages, you define parameters and cutoff values for your search.
Although there are four pages worth of parameters, mostly just one or two of these are generally changed between standard searches.

Here you can set the protease(s) used in your search. Trypsin is selected by default with two missed cleavages.

Here you also set the mass tolerance on MS and MS/MS levels in PPM or Da. The default values are shown below

You can also limit the result output to include only identifications above a certain MassAI score. Default is 10.

If you selected "Custom fragmentation" when selecting datafiles, this is where you include fragment ions to search for. If you selected standard
CID/HCD/ETD fragmentation, you do not need to make any changes here, but you can optionally override the standard search if you wish to
include more exotic fragment ions.
On the second sub-page, you can restrict the number of proteins that are forwarded from the initial fast mass-based identification to the in-depth
fragment based validation. These values can be adjusted if you work with very large search spaces in order to cut down on search time and memory
load, but have little or no impact on smaller search spaces.
Subpages 3 and 4 are for advanced users, and will be described in a later chapter.

You should now turn to page 4 of the main window.