Software:MzXML2Search
From SPCTools
(Difference between revisions)
| Revision as of 18:24, 24 May 2010 Jesse j (Talk | contribs) (→Running) ← Previous diff |
Current revision Jesse j (Talk | contribs) (→Running) |
||
| Line 6: | Line 6: | ||
| ==Running== | ==Running== | ||
| + | Note: Though MzXML2Search's usage statement doesn't mention it, MzXML2Search can also convert mzML files. | ||
| <pre> | <pre> | ||
| MzXML2Search [options] *.mzXML | MzXML2Search [options] *.mzXML | ||
| </pre> | </pre> | ||
| - | Options are: | + | Options: |
| + | |||
| + | ;-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) | ||
| - | -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: | For example: | ||
| <pre> | <pre> | ||
| - | MzXML2Search .mgf example.mzXML | + | MzXML2Search -.mgf example.mzXML |
| + | </pre> | ||
| + | OR | ||
| + | <pre> | ||
| + | MzXML2Search -.mgf example.mzML | ||
| </pre> | </pre> | ||
Current revision
[edit]
Description
Converts mzXML files to SEQUEST dta, MASCOT mgf, and Micromass pkl files.
[edit]
Getting the Software
Comes with the current version of TPP.
[edit]
Running
Note: Though MzXML2Search's usage statement doesn't mention it, MzXML2Search can also convert mzML files.
MzXML2Search [options] *.mzXML
Options:
- -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
OR
MzXML2Search -.mgf example.mzML
