| 184 |
|
emerge, the code that interfaces with the instrument software need not |
| 185 |
|
change. |
| 186 |
|
<P> |
| 187 |
< |
<b>PyMsXML</b> does no processing of the spectra, the output spectra |
| 188 |
< |
are as close to the raw profile data as is possible. In particular, no |
| 189 |
< |
peak detection is done for MS/MS spectra. This option may be added in |
| 190 |
< |
the future. |
| 191 |
< |
<P> |
| 192 |
< |
<b>PyMsXML</b> is <i>pre-beta</i> quality software - it may or may not |
| 193 |
< |
work reliably for you. In particular, the XML formats are in some |
| 194 |
< |
flux, and the output for ".t2d" and ".dat" files is missing much of |
| 195 |
< |
the meta-data required for fully compliant mzXML or mzData |
| 196 |
< |
XML. Further, the mzData XML format output is not as well tested as it |
| 197 |
< |
could be. |
| 187 |
> |
<b>PyMsXML</b> is hosted at <a href="http://bioinformatics.org/project/?group_id=701">bioinformatics.org</a>. |
| 188 |
> |
<P> |
| 189 |
> |
<quote> |
| 190 |
> |
<b>NOTE!</b> |
| 191 |
> |
<P> |
| 192 |
> |
The vendor software (Analyst for .wiff |
| 193 |
> |
files, Data Explorer for .t2d files) be installed on the same computer |
| 194 |
> |
as <b>PyMsXML</b>. These binary formats cannot be read without the |
| 195 |
> |
vendor support libraries. |
| 196 |
> |
</quote> |
| 197 |
|
<P> |
| 198 |
|
<h3>Installation</h3> |
| 199 |
|
<P> |
| 209 |
|
libraries for reading ".dat" and ".t2d" files. If you have both pieces |
| 210 |
|
of software, repeat this step for each software package. Click OK. |
| 211 |
|
<P> |
| 212 |
< |
<li> Check the installation of COM library interfaces. If any of these tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the corresponding raw datafiles. |
| 212 |
> |
<li> Check the installation of COM library interfaces. If any of these |
| 213 |
> |
tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the |
| 214 |
> |
corresponding raw datafiles. |
| 215 |
|
<P> |
| 216 |
< |
For Analyst, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br> |
| 216 |
> |
For Analyst, these commands at the Pythonwin IDE command-line |
| 217 |
> |
(copy-and-paste!) should elicit similar responses:<br> |
| 218 |
|
<code> |
| 219 |
|
>>> from win32com.client import Dispatch<br> |
| 220 |
|
>>> Dispatch('Analyst.FMANSpecData')<br> |
| 233 |
|
</code> |
| 234 |
|
<P> |
| 235 |
|
<li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A |
| 236 |
< |
href="http://www.umiacs.umd.edu/~nedwards/research/downloads/PyMsXML.zip">Download |
| 236 |
> |
href="http://bioinformatics.org/project/filelist.php?group_id=701">Download |
| 237 |
|
<b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to |
| 238 |
|
point to your Python installation (usually C:\Python24\python.exe) |
| 239 |
|
and your <b>PyMsXML</b> installation. |
| 251 |
|
<dd> |
| 252 |
|
<dl> |
| 253 |
|
<dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt> |
| 254 |
< |
<dd>Valid <i>raw-format</i> values: <tt>wiff</tt>, <tt>qstar</tt>, <tt>t2d</tt>, <tt>ab4700</tt>, <tt>voyager</tt>, <tt>mariner</tt>. Optional if <i>raw-spectra-data-file</i> ends in <tt>.wiff</tt> or <tt>.t2m</tt>. |
| 254 |
> |
<dd>Valid <i>raw-format</i> values: <tt>wiff</tt>, <tt>qstar</tt>, <tt>t2d</tt>, <tt>ab4700</tt>, <tt>voyager</tt>, <tt>mariner</tt>, <tt>mzXML</tt>. Optional if <i>raw-spectra-data-file</i> ends in <tt>.wiff</tt>, <tt>.t2m</tt>, or <tt>.mzXML</tt>. |
| 255 |
|
<P> |
| 256 |
|
<dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt> |
| 257 |
|
<dd>Valid <i>xml-format</i> values: <tt>mzXML</tt> (ISB), <tt>mzData</tt> (HUPO). Optional if <i>output-file</i> ends in <tt>.mzXML</tt> or <tt>.mzData</TT>. |
| 262 |
|
<dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt> |
| 263 |
|
<dd> Apply (vendor library) peak detetion to spectra with level in <i>ms-levels</i> (comma separated). QStar (MS/MS spectra only) raw format, 4700 raw format only. Default: 2. |
| 264 |
|
<P> |
| 265 |
< |
<dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> |
| 266 |
< |
<dd> Filter output scans by their meta-data. Filters are specified as a comma-separated list of filter tokens. Each filter token is specified as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be an attribute of the scan object. <i>comparison</i> must be one of <tt>eq</tt>,<tt>ne</tt>,<tt>lt</tt>,<tt>le</tt>,<tt>gt</tt>, or <tt>ge</tt>, specifying =, !=, <, <=, >, and >= respectively. |
| 265 |
> |
<dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <dd> |
| 266 |
> |
Filter output scans by their meta-data. Filters are specified as a |
| 267 |
> |
comma-separated list of filter tokens. Each filter token is specified |
| 268 |
> |
as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be |
| 269 |
> |
an attribute of the scan object. <i>comparison</i> must be one of |
| 270 |
> |
<tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or |
| 271 |
> |
<tt>ge</tt>, specifying =, ≠, <, ≤, >, and ≥ |
| 272 |
> |
respectively. |
| 273 |
> |
<P> |
| 274 |
> |
<dt>-V <i>version</i>, --version <i>version</i></dt><dd> |
| 275 |
> |
XML version. mzXML only. Valid options |
| 276 |
> |
<tt>2.1</tt>,<tt>2.2</tt>,<tt>3.0</tt>. Default: <tt>3.0</tt>. |
| 277 |
> |
<P> |
| 278 |
> |
<dt>-z, --compress_peaks</dt> |
| 279 |
> |
<dd>Compress mzXML peak data using zlib. Default: No compression of peak data. Requires mzXML version 3.0.</dd> |
| 280 |
|
<P> |
| 281 |
|
<dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt> |
| 282 |
< |
<dd> Compress output file. Valid options <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>. <br>Note: PyMsXML will automatically detect input files with extension <tt>.gz</tt> as compressed with gzip. |
| 282 |
> |
<dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>. |
| 283 |
|
<P> |
| 284 |
|
<dt>-d, --debug</dt> |
| 285 |
|
<dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd> |
| 293 |
|
<h3>Applied Biosystems Q-Star Spectra</h3> |
| 294 |
|
<P> |
| 295 |
|
The raw spectra data files for the ESI spectra from Applied |
| 296 |
< |
Biosystems' Q-Star instruments are usually |
| 297 |
< |
extracted as ".wiff" files. These can be opened using Applied |
| 298 |
< |
Biosystem's Analyst or BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries to extract profile mass spectra from these files. |
| 296 |
> |
Biosystems' Q-Star instruments are usually extracted as ".wiff" |
| 297 |
> |
files. These can be opened using Applied Biosystem's Analyst or |
| 298 |
> |
BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries |
| 299 |
> |
to extract mass spectra from these files. |
| 300 |
|
<P> |
| 301 |
|
<P> |
| 302 |
|
<h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3> |
| 305 |
|
Biosystems' Mariner, Voyager and 4700 instruments are usually |
| 306 |
|
extracted as ".t2d" or ".dat" files. These can be opened using Applied |
| 307 |
|
Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's |
| 308 |
< |
support libraries to extract profile mass spectra from these |
| 309 |
< |
files. These file formats store very little meta-data in addition to |
| 310 |
< |
the mass spectrum. As such, additional information must be supplied in |
| 311 |
< |
a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>. |
| 308 |
> |
support libraries to extract mass spectra from these files. These file |
| 309 |
> |
formats store very little meta-data in addition to the mass |
| 310 |
> |
spectrum. If you do not care whether or not the output data-file |
| 311 |
> |
contains valid spot, matrix, and plate meta-data; and if your spectra |
| 312 |
> |
are all contained in one raw datafile, then the datafile can be |
| 313 |
> |
supplied on the command-line as <i>raw-spectra-data-file</i>. However, if you have many .dat or .t2d files, each corresponding to a MALDI spot, or if you wish to have spot, matrix, or plate meta-data populated into the output file, then see the next set of instructions. |
| 314 |
|
<P> |
| 315 |
+ |
Plate, matrix, and spot meta-data must be supplied in |
| 316 |
+ |
a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>. |
| 317 |
|
The meta-data file is most easily constructed in Excel and saved as |
| 318 |
|
tab-separated-values, but it can be formed by hand too, if |
| 319 |
|
desired. Each line of the meta-data file specifies a record, |
| 402 |
|
C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br> |
| 403 |
|
</code> |
| 404 |
|
<P> |
| 405 |
+ |
Convert the Mariner ESI-CE-MALDI spectra in <tt>example3.dat</tt> to mzXML format, placing the output in the file <tt>example3.mzXML.gz</tt> (automatically gzipped): |
| 406 |
+ |
<code> |
| 407 |
+ |
C:\PyMsXML\example\dat> pymsxml.cmd -R mariner -o example3.mzXML.gz example3.dat<br> |
| 408 |
+ |
</code> |
| 409 |
+ |
<P> |
| 410 |
|
Convert the AB4700 spectra listed in <tt>example1.t2m</tt> and <tt>example2.t2m</tt> to mzXML format, placing the output in the files <tt>example1.mzXML</tt> and <tt>example2.mzXML</tt>.<P> |
| 411 |
|
<code> |
| 412 |
|
C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br> |
