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