The mzXML data files must be converted to Sequest .dta files to be accepted by the Sequest application. The MzXML2Search executable is used to convert the mzXML files and can also do some filtering of the scans that will be converted to .dta files. Arguments are passed to the MzXML2Search executable the same way that parameters are passed to Sequest. The available MzXML2Search parameters are:
| MzXML2Search argument | GROUP | NAME | Default | Notes |
| -F<num> | MzXML2Search | first scan | none | Where num is an int specifying the first scan |
| -L<num> | MzXML2Search | last scan | none | Where num is an int specifying the last scan |
| -C<n1>[-<n2>] | MzXML2Search | charge | 1,3 | Where n1 is an int specifying the precursor charge state to analyze and n2 is the end of a charge range (e.g. 1,3 will include charge states 1 thru 3). |
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