To create a new search parameter definition click on the button for the algorithm of interest and complete the form. Or click Import to import an existing search parameter XML file. Search parameters complex and slight changes in some settings can have large impacts on search performance and output. Descriptions of most X! search parameters are available here. Links to the specific parameter help pages are available in the search form. For OMSSA, tooltips are available to describe specific search parameters. When defining search parameters use the taxon field to specify the organisms to be searched. Simply start typing the species names and an auto-complete list of names will appear. These names are derived from the UniProt taxonomies. All UniProt organisms are available for search and are updated monthly.

The search parameters table lists the name of each parameter definition, the algorithm defined (use the XML link to download), the Uniprot libraries defined and dates specifying creation, last use and last modification. Click the search parameters name to edit the parameters.