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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 <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 <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 <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 <P>
214 For Analyst, these commands at the Pythonwin IDE command-line
215 (copy-and-paste!) should elicit similar responses:<br>
216 <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 href="http://www.umiacs.umd.edu/~nedwards/research/downloads/PyMsXML.zip">Download
235 <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 <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 <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 <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 <P>
272 <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
273 <dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
274 <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 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 <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 support libraries to extract mass spectra from these
300 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 -->
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448 <td valign="middle"><a href="http://www.umd.edu/"><img src="../images/maryland_small.gif" width=185 height=32 alt="University of Maryland" border=0></a></td>
449 <td>&nbsp; &nbsp;</td>
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451 <a href="http://www.umd.edu/">UM Home</a> | <a href="http://www.umd.edu/whoswho.html">Directories</a> | <a href="http://www.search.umd.edu/">Search</a> | <a href="http://www.umd.edu/prospective/">Admissions</a> | <a href="http://www.umd.edu/calendar/today/">Calendar</a><br>
452 Original created by <a href="mailto:jfuetsch@umiacs.umd.edu">John Fuetsch</a><br>
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460
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