Software:MzXML2Search

From SPCTools

Description

Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files.

Getting the Software

Comes with the current version of TPP.

Running

MzXML2Search [options] *.mzXML

Options are:

-dta or -mgf or -pkl or -xdta or -odta or -ms2 output format (default dta)
-F<num>      where num is an int specifying the first scan
-L<num>      where num is an int specifying the last scan
-C<n1>[-<n2>]     "force charge(s)": where n1 is an integer specifying the precursor charge state (or possible charge range from n1 to n2 inclusive) to use; this option forces input scans to be output with the user-specified charge (or charge range)
-c<n1>[-<n2>]     "suggest charge(s)": for scans which do not have a precursor charge (or charge range) already determined in the input file, use the user-specified charge (or charge range) for those scans.  Input scans which already have defined charge (or charge range) are output with their original, unchanged values.
-B<num>      where num is a float specifying minimum MH+ mass, default=600.0 Da
-T<num>      where num is a float specifying maximum MH+ scan, default=4200.0 Da
-P<num>      where num is an int specifying minimum peak count, default=5
-I<num>      where num is a float specifying minimum threshold for peak intensity, default=0.01
-M<n1>[-<n2>]where n1 is an int specifying MS level to export (default=2) and n2 specifies an optional range of MS levels to export
-A<str>      where str is the activation method, "CID" (default) or "ETD" if activation method not in scans of mzXML file, this option is ignored
-h           use hydrogen mass for charge ion (default is proton mass)

For example:

MzXML2Search .mgf example.mzXML