Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files.
Getting the Software
Comes with the current version of TPP.
Note: Though MzXML2Search's usage statement doesn't mention it, MzXML2Search can also convert mzML files.
MzXML2Search [options] *.mzXML
- -dta or -mgf or -pkl or -xdta or -odta or -ms2
- output format (default dta)
- where num is an int specifying the first scan
- where num is an int specifying the last scan
- "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)
- "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.
- where num is a float specifying minimum MH+ mass, default=600.0 Da
- where num is a float specifying maximum MH+ scan, default=4200.0 Da
- where num is an int specifying minimum peak count, default=5
- where num is a float specifying minimum threshold for peak intensity, default=0.01
- where n1 is an int specifying MS level to export (default=2) and n2 specifies an optional range of MS levels to export
- where str is the activation method, "CID" (default) or "ETD" if activation method not in scans of mzXML file, this option is ignored
- use hydrogen mass for charge ion (default is proton mass)
MzXML2Search -.mgf example.mzXML
MzXML2Search -.mgf example.mzML