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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>
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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>
# Line 231 | Line 233
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.
# Line 249 | Line 251
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>.
# Line 260 | Line 262
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 =, !=, &lt;, &lt;=, &gt;, and &gt;= 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 =, &ne;, &lt;, &le;, &gt;, and &ge;
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>
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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>
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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,
# Line 382 | Line 402
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>

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