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147 <td><font size=5>PyMsXML</font></td>
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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 <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>
200 <ol>
201 <li> Download and install the latest version of <A href="http://www.activestate.com/Products/ActivePython/">ActiveState ActivePython</A> for Windows.
202 <P>
203 <li> Start the Pythonwin IDE (All Programs -> ActiveState ActivePython
204 2.4 -> Pythonwin IDE). From the Tools menu, select the "COM Makepy
205 utility" entry. In the popup window, select "ExploreDataObjects 1.0
206 Type Library (1.0)" to build a python interface to Analyst's COM
207 libraries for reading .wiff files, select "IDAExplorer 1.0 Type
208 Library (1.0)" to build a python interface to Data Explorer's COM
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
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
217 (copy-and-paste!) should elicit similar responses:<br>
218 <code>
219 >>> from win32com.client import Dispatch<br>
220 >>> Dispatch('Analyst.FMANSpecData')<br>
221 &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANSpecData instance at 0x14421558> <br>
222 >>> Dispatch('Analyst.FMANChromData')<br>
223 &lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANChromData instance at 0x14418408>
224 </code>
225 <P>
226 For Data Explorer, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br>
227 <code>
228 >>> from win32com.client import Dispatch, gencache<br>
229 >>> Dispatch('DataExplorer.Application',resultCLSID='{3FED40F1-D409-11D1-8B56-0060971CB54B}')<br>
230 &lt;COMObject DataExplorer.Application><br>
231 >>> gencache.EnsureModule('{06972F50-13F6-11D3-A5CB-0060971CB54B}',0,4,2)<br>
232 &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'>
233 </code>
234 <P>
235 <li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A
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.
240 </ol>
241 <P>
242 <h3>Usage</h3>
243 <P>
244 <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.
245 <dl>
246 <dt><b>pymsxml</b> [ options ] <i>raw-spectra-data-file</i></dt>
247 <P>
248 <dt>
249 Options:<P>
250 </dt>
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>, <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>.
258 <P>
259 <dt>-o <i>output-file</i>, --output <i>output-file</i></dt>
260 <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>.
261 <P>
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> <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>.
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>
286 <P>
287 <dt>-h, --help</dt>
288 <dd>Help.</dd>
289 </dl>
290 </dd>
291 </dl>
292 <P>
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 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>
303 <P>
304 The raw spectra data files for the MALDI spectra from Applied
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 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>.
312 <P>
313 The meta-data file is most easily constructed in Excel and saved as
314 tab-separated-values, but it can be formed by hand too, if
315 desired. Each line of the meta-data file specifies a record,
316 describing the MALDI plate, the plates' spots, and the scans acquired
317 from these spots. A short-cut record, that defines the plate and spot
318 naming convention is also provided.
319 <P>
320 The plate definition record consists of the word <tt>PLATE</tt> (case
321 insensitive) in the first column, followed by alternating key-value
322 pairs in subsequent columns. Particular key-value pairs do not need to
323 be specified in any particular order. The following keys must be
324 provided:
325 <tt>plateID</tt>, <tt>spotXCount</tt>, <tt>spotYCount</tt>,
326 <tt>plateManufacturer</tt>, and <tt>plateModel</tt>. The
327 <tt>plateID</tt> value is referenced by the spot and scan definition
328 records. The <tt>spotXCount</tt> is the number of MALDI spots in
329 the horizontal dimension (integer). The <tt>spotYCount</tt> is
330 the number of MALDI spots in the vertical dimension (integer). The
331 <tt>plateManufacturer</tt> and <tt>plateModel</tt> values are inserted verbatim in the output XML.
332 <P>
333 The spot definition record consists of the word <tt>SPOT</tt> (case
334 insensitive) in the first column, followed by alternating key-value
335 pairs in subsequent columns. Particular key-value pairs do not need to
336 be specified in any particular order. The following keys must be
337 provided:
338 <tt>plateID</tt>, <tt>spotID</tt>, <tt>spotXPosition</tt>,
339 <tt>spotYPosition</tt>, and <tt>maldiMatrix</tt>. The
340 <tt>plateID</tt> value must be defined by some plate definition
341 record. The <tt>spotID</tt> is referenced by the scan definition
342 records. The <tt>spotXPosition</tt> is the horizontal position of the
343 spot on the plate (integer). The <tt>spotYPosition</tt> is the
344 vertical position of the spot on the plate (integer). Spot positions
345 can be numbered beginning at 0 or 1. The
346 <tt>maldiMatrix</tt> value is inserted verbatim in the output XML.
347 <P>
348 The scan definition record consists of the word <tt>SCAN</tt> (case
349 insensitive) in the first column, followed by alternating key-value
350 pairs in subsequent columns. Particular key-value pairs do not need to
351 be specified in any particular order. The following keys must be
352 provided:
353 <tt>plateID</tt>, <tt>spotID</tt>, <tt>filename</tt>, and <tt>index</tt>.
354 The
355 <tt>plateID</tt> must be defined by some plate definition record. The
356 <tt>spotID</tt> must be defined by some spot definition record. The
357 <tt>filename</tt> is the name of the ".dat" or ".t2d" file containing
358 the corresponding scan's spectrum. The <tt>index</tt> is the ordinal
359 of the corresponding spectrum in the provided file. Spectra within
360 files should be referenced beginning at 1.
361 <P>
362 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
363 pairs in subsequent columns. Particular key-value pairs do not need to
364 be specified in any particular order. The following keys must be
365 provided:
366 <tt>plateID</tt>, <tt>plateManufacturer</tt>, <tt>plateModel</tt>, <tt>spotNaming</tt>, and <tt>maldiMatrix</tt>.
367 The
368 <tt>plateID</tt> value is referenced by the spot and scan definition
369 records. The <tt>plateManufacturer</tt> and <tt>plateModel</tt> are
370 used to identify the properties of the MALDI plate. Currently, only
371 the values <tt>ABI / SCIEX</tt> and <tt>01-192+06-BB</tt> are
372 recognized, but others are easily added on request. The "ABI / SCIEX
373 01-192+06-BB" plate consists of 8 rows of 24 spots (plus 6 calibration
374 spots). The <tt>spotNaming</tt> must be one of <tt>alpha</tt>,
375 <tt>parallel</tt>, or <tt>antiparallel</tt>. At this time, only
376 <tt>alpha</tt> is implemented. The <tt>alpha</tt> spot attribute
377 constructs <tt>spotID</tt> values for all spots on the plate with the
378 row specified by a letter from A to H, and the column specified by a
379 number from 1 to 24. The
380 <tt>maldiMatrix</tt> value is assumed the same for each spot and is
381 inserted verbatim in the output XML.
382 <P>
383 <b>NOTE:</b> The order of scan definition lines is important! MS/MS
384 spectra must appear immediately after the MS spectrum containing their
385 precursors.
386 <P>
387 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.
388 <P>
389 <h3>Examples</h3>
390 <P>
391 Convert the Q-Star <tt>example.wiff</tt> file to mzXML format, placing the output in the file <tt>qstar-example.xml</tt>.<P>
392 <code>
393 C:\PyMsXML\example\wiff> pymsxml.cmd -R wiff -X mzXML -o qstar-example.xml example.wiff<br>
394 </code>
395 <P>
396 Convert the Q-Star <tt>example.wiff</tt> file to mzData format, placing the output in the file <tt>example.mzData</tt>.<P>
397 <code>
398 C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
399 </code>
400 <P>
401 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>
402 <code>
403 C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>
404 </code>
405 <P>
406 <h3>Release Notes</h3>
407 <P>
408 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.
409 <P>
410 <h3>Credits</h3>
411 <P>
412 Development of <b>PyMsXML</b> was significantly helped by the
413 open-source Visual Basic source code from the MzStar program of the
414 ISB glossolalia project.
415 <P>
416 <!-- CONTENT ENDS HERE -->
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