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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 nje01 1.5 <quote>
188     <b>NOTE!</b>
189     <P>
190     The vendor software (Analyst for .wiff
191     files, Data Explorer for .t2d files) be installed on the same computer
192     as <b>PyMsXML</b>. These binary formats cannot be read without the
193     vendor support libraries.
194     </quote>
195     <P>
196 nje01 1.1 <h3>Installation</h3>
197     <P>
198     <ol>
199     <li> Download and install the latest version of <A href="http://www.activestate.com/Products/ActivePython/">ActiveState ActivePython</A> for Windows.
200     <P>
201     <li> Start the Pythonwin IDE (All Programs -> ActiveState ActivePython
202     2.4 -> Pythonwin IDE). From the Tools menu, select the "COM Makepy
203     utility" entry. In the popup window, select "ExploreDataObjects 1.0
204     Type Library (1.0)" to build a python interface to Analyst's COM
205     libraries for reading .wiff files, select "IDAExplorer 1.0 Type
206     Library (1.0)" to build a python interface to Data Explorer's COM
207     libraries for reading ".dat" and ".t2d" files. If you have both pieces
208     of software, repeat this step for each software package. Click OK.
209     <P>
210 nje01 1.2 <li> Check the installation of COM library interfaces. If any of these
211     tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the
212     corresponding raw datafiles.
213 nje01 1.1 <P>
214 nje01 1.2 For Analyst, these commands at the Pythonwin IDE command-line
215     (copy-and-paste!) should elicit similar responses:<br>
216 nje01 1.1 <code>
217     >>> from win32com.client import Dispatch<br>
218     >>> Dispatch('Analyst.FMANSpecData')<br>
219     &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANSpecData instance at 0x14421558> <br>
220     >>> Dispatch('Analyst.FMANChromData')<br>
221     &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANChromData instance at 0x14418408>
222     </code>
223     <P>
224     For Data Explorer, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br>
225     <code>
226     >>> from win32com.client import Dispatch, gencache<br>
227     >>> Dispatch('DataExplorer.Application',resultCLSID='{3FED40F1-D409-11D1-8B56-0060971CB54B}')<br>
228     &lt;COMObject DataExplorer.Application><br>
229     >>> gencache.EnsureModule('{06972F50-13F6-11D3-A5CB-0060971CB54B}',0,4,2)<br>
230     &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'>
231     </code>
232     <P>
233     <li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A
234 nje01 1.5 href="http://www.umiacs.umd.edu/~nedwards/research/downloads/PyMsXML.zip">Download
235 nje01 1.1 <b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to
236     point to your Python installation (usually C:\Python24\python.exe)
237     and your <b>PyMsXML</b> installation.
238     </ol>
239     <P>
240     <h3>Usage</h3>
241     <P>
242     <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.
243     <dl>
244     <dt><b>pymsxml</b> [ options ] <i>raw-spectra-data-file</i></dt>
245     <P>
246     <dt>
247     Options:<P>
248     </dt>
249     <dd>
250     <dl>
251     <dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt>
252 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>.
253 nje01 1.1 <P>
254     <dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt>
255     <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>.
256     <P>
257     <dt>-o <i>output-file</i>, --output <i>output-file</i></dt>
258     <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>.
259     <P>
260     <dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt>
261     <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.
262     <P>
263 nje01 1.2 <dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <dd>
264     Filter output scans by their meta-data. Filters are specified as a
265     comma-separated list of filter tokens. Each filter token is specified
266     as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be
267     an attribute of the scan object. <i>comparison</i> must be one of
268     <tt>eq</tt>, <tt>ne</tt>, <tt>lt</tt>, <tt>le</tt>, <tt>gt</tt>, or
269     <tt>ge</tt>, specifying =, &ne;, &lt;, &le;, &gt;, and &ge;
270     respectively.
271 nje01 1.1 <P>
272     <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
273 nje01 1.5 <dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
274 nje01 1.1 <P>
275     <dt>-d, --debug</dt>
276     <dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd>
277     <P>
278     <dt>-h, --help</dt>
279     <dd>Help.</dd>
280     </dl>
281     </dd>
282     </dl>
283     <P>
284     <h3>Applied Biosystems Q-Star Spectra</h3>
285     <P>
286     The raw spectra data files for the ESI spectra from Applied
287 nje01 1.2 Biosystems' Q-Star instruments are usually extracted as ".wiff"
288     files. These can be opened using Applied Biosystem's Analyst or
289     BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries
290     to extract mass spectra from these files.
291 nje01 1.1 <P>
292     <P>
293     <h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3>
294     <P>
295     The raw spectra data files for the MALDI spectra from Applied
296     Biosystems' Mariner, Voyager and 4700 instruments are usually
297     extracted as ".t2d" or ".dat" files. These can be opened using Applied
298     Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
299 nje01 1.2 support libraries to extract mass spectra from these
300 nje01 1.1 files. These file formats store very little meta-data in addition to
301     the mass spectrum. As such, additional information must be supplied in
302     a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
303     <P>
304     The meta-data file is most easily constructed in Excel and saved as
305     tab-separated-values, but it can be formed by hand too, if
306     desired. Each line of the meta-data file specifies a record,
307     describing the MALDI plate, the plates' spots, and the scans acquired
308     from these spots. A short-cut record, that defines the plate and spot
309     naming convention is also provided.
310     <P>
311     The plate definition record consists of the word <tt>PLATE</tt> (case
312     insensitive) in the first column, followed by alternating key-value
313     pairs in subsequent columns. Particular key-value pairs do not need to
314     be specified in any particular order. The following keys must be
315     provided:
316     <tt>plateID</tt>, <tt>spotXCount</tt>, <tt>spotYCount</tt>,
317     <tt>plateManufacturer</tt>, and <tt>plateModel</tt>. The
318     <tt>plateID</tt> value is referenced by the spot and scan definition
319     records. The <tt>spotXCount</tt> is the number of MALDI spots in
320     the horizontal dimension (integer). The <tt>spotYCount</tt> is
321     the number of MALDI spots in the vertical dimension (integer). The
322     <tt>plateManufacturer</tt> and <tt>plateModel</tt> values are inserted verbatim in the output XML.
323     <P>
324     The spot definition record consists of the word <tt>SPOT</tt> (case
325     insensitive) in the first column, followed by alternating key-value
326     pairs in subsequent columns. Particular key-value pairs do not need to
327     be specified in any particular order. The following keys must be
328     provided:
329     <tt>plateID</tt>, <tt>spotID</tt>, <tt>spotXPosition</tt>,
330     <tt>spotYPosition</tt>, and <tt>maldiMatrix</tt>. The
331     <tt>plateID</tt> value must be defined by some plate definition
332     record. The <tt>spotID</tt> is referenced by the scan definition
333     records. The <tt>spotXPosition</tt> is the horizontal position of the
334     spot on the plate (integer). The <tt>spotYPosition</tt> is the
335     vertical position of the spot on the plate (integer). Spot positions
336     can be numbered beginning at 0 or 1. The
337     <tt>maldiMatrix</tt> value is inserted verbatim in the output XML.
338     <P>
339     The scan definition record consists of the word <tt>SCAN</tt> (case
340     insensitive) in the first column, followed by alternating key-value
341     pairs in subsequent columns. Particular key-value pairs do not need to
342     be specified in any particular order. The following keys must be
343     provided:
344     <tt>plateID</tt>, <tt>spotID</tt>, <tt>filename</tt>, and <tt>index</tt>.
345     The
346     <tt>plateID</tt> must be defined by some plate definition record. The
347     <tt>spotID</tt> must be defined by some spot definition record. The
348     <tt>filename</tt> is the name of the ".dat" or ".t2d" file containing
349     the corresponding scan's spectrum. The <tt>index</tt> is the ordinal
350     of the corresponding spectrum in the provided file. Spectra within
351     files should be referenced beginning at 1.
352     <P>
353     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
354     pairs in subsequent columns. Particular key-value pairs do not need to
355     be specified in any particular order. The following keys must be
356     provided:
357     <tt>plateID</tt>, <tt>plateManufacturer</tt>, <tt>plateModel</tt>, <tt>spotNaming</tt>, and <tt>maldiMatrix</tt>.
358     The
359     <tt>plateID</tt> value is referenced by the spot and scan definition
360     records. The <tt>plateManufacturer</tt> and <tt>plateModel</tt> are
361     used to identify the properties of the MALDI plate. Currently, only
362     the values <tt>ABI / SCIEX</tt> and <tt>01-192+06-BB</tt> are
363     recognized, but others are easily added on request. The "ABI / SCIEX
364     01-192+06-BB" plate consists of 8 rows of 24 spots (plus 6 calibration
365     spots). The <tt>spotNaming</tt> must be one of <tt>alpha</tt>,
366     <tt>parallel</tt>, or <tt>antiparallel</tt>. At this time, only
367     <tt>alpha</tt> is implemented. The <tt>alpha</tt> spot attribute
368     constructs <tt>spotID</tt> values for all spots on the plate with the
369     row specified by a letter from A to H, and the column specified by a
370     number from 1 to 24. The
371     <tt>maldiMatrix</tt> value is assumed the same for each spot and is
372     inserted verbatim in the output XML.
373     <P>
374     <b>NOTE:</b> The order of scan definition lines is important! MS/MS
375     spectra must appear immediately after the MS spectrum containing their
376     precursors.
377     <P>
378     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.
379     <P>
380     <h3>Examples</h3>
381     <P>
382     Convert the Q-Star <tt>example.wiff</tt> file to mzXML format, placing the output in the file <tt>qstar-example.xml</tt>.<P>
383     <code>
384     C:\PyMsXML\example\wiff> pymsxml.cmd -R wiff -X mzXML -o qstar-example.xml example.wiff<br>
385     </code>
386     <P>
387     Convert the Q-Star <tt>example.wiff</tt> file to mzData format, placing the output in the file <tt>example.mzData</tt>.<P>
388     <code>
389     C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
390     </code>
391     <P>
392     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>
393     <code>
394     C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>
395     </code>
396     <P>
397     <h3>Release Notes</h3>
398     <P>
399     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.
400     <P>
401     <h3>Credits</h3>
402     <P>
403     Development of <b>PyMsXML</b> was significantly helped by the
404     open-source Visual Basic source code from the MzStar program of the
405     ISB glossolalia project.
406     <P>
407     <!-- CONTENT ENDS HERE -->
408     </td>
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444     <!-- UNIVERSITY OF MARYLAND FOOTER BEGINS HERE -->
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452     Original created by <a href="mailto:jfuetsch@umiacs.umd.edu">John Fuetsch</a><br>
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