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147     <td><font size=5>PyMsXML</font></td>
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158    
159     <!-- CONTENT STARTS HERE -->
160    
161     <h3>Introduction</h3>
162     <P>
163     <b>PyMsXML</b> is a python script for converting vendor specific mass
164     spectrometry data files for Applied Biosystems' Q-Star, 4700, Mariner,
165     and Voyager mass spectrometers from their raw binary form, to either
166     of the emerging XML file formats for mass spectra: mzXML, from the
167     Sashimi Glossolalia project of the Institute for Systems Biology (ISB);
168     and mzData, from the Proteome Standardization Initiative (PSI) project
169     of the Human Proteome Organization (HUPO).
170     <P>
171     <b>PyMsXML</b> uses installed vendor software under Windows to access the
172     proprietary raw mass spectra file format, interfacing to the vendor
173     supplied libraries via the supplied COM interface. Unlike other
174     software solutions that use this approach, <b>PyMsXML</b> is written in a
175     free, open-source language called Python. As such, no installation of
176     Microsoft Visual C++ or Visual Basic is necessary to use, alter, or
177     improve the <b>PyMsXML</b> script.
178     <P>
179     <b>PyMsXML</b> is easily extended for new instruments and vendor software,
180     and for new, or changed, XML file formats. The code that interfaces to
181     the vendor software is decomposed from the code that formats the data
182     as XML, as such, the addition of new instrument capability need not
183     re-write the XML data format code. Similarly, as new XML file formats
184     emerge, the code that interfaces with the instrument software need not
185     change.
186     <P>
187     <h3>Installation</h3>
188     <P>
189     <ol>
190     <li> Download and install the latest version of <A href="http://www.activestate.com/Products/ActivePython/">ActiveState ActivePython</A> for Windows.
191     <P>
192     <li> Start the Pythonwin IDE (All Programs -> ActiveState ActivePython
193     2.4 -> Pythonwin IDE). From the Tools menu, select the "COM Makepy
194     utility" entry. In the popup window, select "ExploreDataObjects 1.0
195     Type Library (1.0)" to build a python interface to Analyst's COM
196     libraries for reading .wiff files, select "IDAExplorer 1.0 Type
197     Library (1.0)" to build a python interface to Data Explorer's COM
198     libraries for reading ".dat" and ".t2d" files. If you have both pieces
199     of software, repeat this step for each software package. Click OK.
200     <P>
201 nje01 1.2 <li> Check the installation of COM library interfaces. If any of these
202     tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the
203     corresponding raw datafiles.
204 nje01 1.1 <P>
205 nje01 1.2 For Analyst, these commands at the Pythonwin IDE command-line
206     (copy-and-paste!) should elicit similar responses:<br>
207 nje01 1.1 <code>
208     >>> from win32com.client import Dispatch<br>
209     >>> Dispatch('Analyst.FMANSpecData')<br>
210     &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANSpecData instance at 0x14421558> <br>
211     >>> Dispatch('Analyst.FMANChromData')<br>
212     &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANChromData instance at 0x14418408>
213     </code>
214     <P>
215     For Data Explorer, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br>
216     <code>
217     >>> from win32com.client import Dispatch, gencache<br>
218     >>> Dispatch('DataExplorer.Application',resultCLSID='{3FED40F1-D409-11D1-8B56-0060971CB54B}')<br>
219     &lt;COMObject DataExplorer.Application><br>
220     >>> gencache.EnsureModule('{06972F50-13F6-11D3-A5CB-0060971CB54B}',0,4,2)<br>
221     &lt;module 'win32com.gen_py.06972F50-13F6-11D3-A5CB-0060971CB54Bx0x4x2' from 'C:\Python24\lib\site-packages\win32com\gen_py \06972F50-13F6-11D3-A5CB-0060971CB54Bx0x4x2.py'>
222     </code>
223     <P>
224     <li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A
225 nje01 1.3 href="http://bioinformatics.org/project/filelist.php?group_id=701">Download
226 nje01 1.1 <b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to
227     point to your Python installation (usually C:\Python24\python.exe)
228     and your <b>PyMsXML</b> installation.
229     </ol>
230     <P>
231     <h3>Usage</h3>
232     <P>
233     <b>PyMsXML</b> consists of a single python script. A windows cmd file wrapper is provided, to take care of calling the python interpretor appropriately.
234     <dl>
235     <dt><b>pymsxml</b> [ options ] <i>raw-spectra-data-file</i></dt>
236     <P>
237     <dt>
238     Options:<P>
239     </dt>
240     <dd>
241     <dl>
242     <dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt>
243 nje01 1.2 <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>.
244 nje01 1.4 </dd>
245 nje01 1.1 <P>
246     <dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt>
247     <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>.
248 nje01 1.4 </dd>
249 nje01 1.1 <P>
250     <dt>-o <i>output-file</i>, --output <i>output-file</i></dt>
251     <dd>Name of output file. If omitted, and <i>xml-format</i> is supplied, then the output file is inferred by changing the file extention of <i>raw-spectra-data-file</i> to <i>xml-format</i>.
252 nje01 1.4 </dd>
253 nje01 1.1 <P>
254     <dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt>
255     <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.
256 nje01 1.4 </dd>
257 nje01 1.1 <P>
258 nje01 1.2 <dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <dd>
259     Filter output scans by their meta-data. Filters are specified as a
260     comma-separated list of filter tokens. Each filter token is specified
261     as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be
262     an attribute of the scan object. <i>comparison</i> must be one of
263     <tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or
264     <tt>ge</tt>, specifying =, &ne;, &lt;, &le;, &gt;, and &ge;
265     respectively.
266 nje01 1.4 </dd>
267     <P>
268     <dt>-V <i>xml-version</i>, --version <i>xml-version</i></dt>
269     <dd>
270     XML version. mzXML only. Valid values: <tt>2.1</tt>, <tt>2.2</tt>, and <tt>3.0</tt>. Default: <tt>3.0</tt>
271     </dd>
272     <P>
273     <dt>-z, --compress_peaks</dt>
274     <dd> Compress mzXML peaks data using zlib. mzXML version &ge; 3.0 only. Default: False.
275     </dd>
276 nje01 1.1 <P>
277     <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
278 nje01 1.4 <dd> Compress output file. Valid values: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
279     </dd>
280 nje01 1.1 <P>
281     <dt>-d, --debug</dt>
282     <dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd>
283     <P>
284     <dt>-h, --help</dt>
285     <dd>Help.</dd>
286     </dl>
287     </dd>
288     </dl>
289     <P>
290     <h3>Applied Biosystems Q-Star Spectra</h3>
291     <P>
292     The raw spectra data files for the ESI spectra from Applied
293 nje01 1.2 Biosystems' Q-Star instruments are usually extracted as ".wiff"
294     files. These can be opened using Applied Biosystem's Analyst or
295     BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries
296     to extract mass spectra from these files.
297 nje01 1.1 <P>
298     <P>
299     <h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3>
300     <P>
301     The raw spectra data files for the MALDI spectra from Applied
302     Biosystems' Mariner, Voyager and 4700 instruments are usually
303     extracted as ".t2d" or ".dat" files. These can be opened using Applied
304     Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
305 nje01 1.2 support libraries to extract mass spectra from these
306 nje01 1.1 files. These file formats store very little meta-data in addition to
307     the mass spectrum. As such, additional information must be supplied in
308     a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
309     <P>
310     The meta-data file is most easily constructed in Excel and saved as
311     tab-separated-values, but it can be formed by hand too, if
312     desired. Each line of the meta-data file specifies a record,
313     describing the MALDI plate, the plates' spots, and the scans acquired
314     from these spots. A short-cut record, that defines the plate and spot
315     naming convention is also provided.
316     <P>
317     The plate definition record consists of the word <tt>PLATE</tt> (case
318     insensitive) in the first column, followed by alternating key-value
319     pairs in subsequent columns. Particular key-value pairs do not need to
320     be specified in any particular order. The following keys must be
321     provided:
322     <tt>plateID</tt>, <tt>spotXCount</tt>, <tt>spotYCount</tt>,
323     <tt>plateManufacturer</tt>, and <tt>plateModel</tt>. The
324     <tt>plateID</tt> value is referenced by the spot and scan definition
325     records. The <tt>spotXCount</tt> is the number of MALDI spots in
326     the horizontal dimension (integer). The <tt>spotYCount</tt> is
327     the number of MALDI spots in the vertical dimension (integer). The
328     <tt>plateManufacturer</tt> and <tt>plateModel</tt> values are inserted verbatim in the output XML.
329     <P>
330     The spot definition record consists of the word <tt>SPOT</tt> (case
331     insensitive) in the first column, followed by alternating key-value
332     pairs in subsequent columns. Particular key-value pairs do not need to
333     be specified in any particular order. The following keys must be
334     provided:
335     <tt>plateID</tt>, <tt>spotID</tt>, <tt>spotXPosition</tt>,
336     <tt>spotYPosition</tt>, and <tt>maldiMatrix</tt>. The
337     <tt>plateID</tt> value must be defined by some plate definition
338     record. The <tt>spotID</tt> is referenced by the scan definition
339     records. The <tt>spotXPosition</tt> is the horizontal position of the
340     spot on the plate (integer). The <tt>spotYPosition</tt> is the
341     vertical position of the spot on the plate (integer). Spot positions
342     can be numbered beginning at 0 or 1. The
343     <tt>maldiMatrix</tt> value is inserted verbatim in the output XML.
344     <P>
345     The scan definition record consists of the word <tt>SCAN</tt> (case
346     insensitive) in the first column, followed by alternating key-value
347     pairs in subsequent columns. Particular key-value pairs do not need to
348     be specified in any particular order. The following keys must be
349     provided:
350     <tt>plateID</tt>, <tt>spotID</tt>, <tt>filename</tt>, and <tt>index</tt>.
351     The
352     <tt>plateID</tt> must be defined by some plate definition record. The
353     <tt>spotID</tt> must be defined by some spot definition record. The
354     <tt>filename</tt> is the name of the ".dat" or ".t2d" file containing
355     the corresponding scan's spectrum. The <tt>index</tt> is the ordinal
356     of the corresponding spectrum in the provided file. Spectra within
357     files should be referenced beginning at 1.
358     <P>
359     To alleviate some of the tedium with specifying the spot definition records, a shortcut plate definition record is provided. The platedef definition record consists of the word <tt>PLATEDEF</tt> (case insensitive) in the first column, followed by alternating key-value
360     pairs in subsequent columns. Particular key-value pairs do not need to
361     be specified in any particular order. The following keys must be
362     provided:
363     <tt>plateID</tt>, <tt>plateManufacturer</tt>, <tt>plateModel</tt>, <tt>spotNaming</tt>, and <tt>maldiMatrix</tt>.
364     The
365     <tt>plateID</tt> value is referenced by the spot and scan definition
366     records. The <tt>plateManufacturer</tt> and <tt>plateModel</tt> are
367     used to identify the properties of the MALDI plate. Currently, only
368     the values <tt>ABI / SCIEX</tt> and <tt>01-192+06-BB</tt> are
369     recognized, but others are easily added on request. The "ABI / SCIEX
370     01-192+06-BB" plate consists of 8 rows of 24 spots (plus 6 calibration
371     spots). The <tt>spotNaming</tt> must be one of <tt>alpha</tt>,
372     <tt>parallel</tt>, or <tt>antiparallel</tt>. At this time, only
373     <tt>alpha</tt> is implemented. The <tt>alpha</tt> spot attribute
374     constructs <tt>spotID</tt> values for all spots on the plate with the
375     row specified by a letter from A to H, and the column specified by a
376     number from 1 to 24. The
377     <tt>maldiMatrix</tt> value is assumed the same for each spot and is
378     inserted verbatim in the output XML.
379     <P>
380     <b>NOTE:</b> The order of scan definition lines is important! MS/MS
381     spectra must appear immediately after the MS spectrum containing their
382     precursors.
383     <P>
384     Example meta-data files are provided in the distribution. <tt>example1.t2m</tt> explicitly defines the MALDI plate, spots and scans. <tt>example2.t2m</tt> is equivalent, but uses the platedef keyword shortcut.
385     <P>
386     <h3>Examples</h3>
387     <P>
388     Convert the Q-Star <tt>example.wiff</tt> file to mzXML format, placing the output in the file <tt>qstar-example.xml</tt>.<P>
389     <code>
390     C:\PyMsXML\example\wiff> pymsxml.cmd -R wiff -X mzXML -o qstar-example.xml example.wiff<br>
391     </code>
392     <P>
393     Convert the Q-Star <tt>example.wiff</tt> file to mzData format, placing the output in the file <tt>example.mzData</tt>.<P>
394     <code>
395     C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
396     </code>
397     <P>
398     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>
399     <code>
400     C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>
401     </code>
402     <P>
403     <h3>Release Notes</h3>
404     <P>
405     The Analyst COM libraries seem to have trouble with long pathnames. If you consistently have trouble getting PyMsXML to read ".wiff" files, try moving the files to a shorter directory path.
406     <P>
407     <h3>Credits</h3>
408     <P>
409     Development of <b>PyMsXML</b> was significantly helped by the
410     open-source Visual Basic source code from the MzStar program of the
411     ISB glossolalia project.
412     <P>
413     <!-- CONTENT ENDS HERE -->
414     </td>
415     </tr>
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