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