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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 <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 <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 <P>
205 For Analyst, these commands at the Pythonwin IDE command-line
206 (copy-and-paste!) should elicit similar responses:<br>
207 <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 href="http://bioinformatics.org/project/filelist.php?group_id=701">Download
226 <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 <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 </dd>
245 <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 </dd>
249 <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 </dd>
253 <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 </dd>
257 <P>
258 <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 </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 <P>
277 <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
278 <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 <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 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 <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 support libraries to extract mass spectra from these
306 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 -->
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