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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> does no processing of the spectra, the output spectra
188 are as close to the raw profile data as is possible. In particular, no
189 peak detection is done for MS/MS spectra. This option may be added in
190 the future.
191 <P>
192 <b>PyMsXML</b> is <i>pre-beta</i> quality software - it may or may not
193 work reliably for you. In particular, the XML formats are in some
194 flux, and the output for ".t2d" and ".dat" files is missing much of
195 the meta-data required for fully compliant mzXML or mzData
196 XML. Further, the mzData XML format output is not as well tested as it
197 could be.
198 <P>
199 <h3>Installation</h3>
200 <P>
201 <ol>
202 <li> Download and install the latest version of <A href="http://www.activestate.com/Products/ActivePython/">ActiveState ActivePython</A> for Windows.
203 <P>
204 <li> Start the Pythonwin IDE (All Programs -> ActiveState ActivePython
205 2.4 -> Pythonwin IDE). From the Tools menu, select the "COM Makepy
206 utility" entry. In the popup window, select "ExploreDataObjects 1.0
207 Type Library (1.0)" to build a python interface to Analyst's COM
208 libraries for reading .wiff files, select "IDAExplorer 1.0 Type
209 Library (1.0)" to build a python interface to Data Explorer's COM
210 libraries for reading ".dat" and ".t2d" files. If you have both pieces
211 of software, repeat this step for each software package. Click OK.
212 <P>
213 <li> Check the installation of COM library interfaces. If any of these tests are unsuccessful, then <b>PyMsXML</b> will be unable to read the corresponding raw datafiles.
214 <P>
215 For Analyst, these commands at the Pythonwin IDE command-line (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>. Optional if <i>raw-spectra-data-file</i> ends in <tt>.wiff</tt> or <tt>.t2m</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>
264 <dd> Filter output scans by their meta-data. Filters are specified as a comma-separated list of filter tokens. Each filter token is specified as <i>field</i>.<i>comparison</i>.<i>value</i>. <i>field</i> must be an attribute of the scan object. <i>comparison</i> must be one of <tt>eq</tt>,<tt>ne</tt>,<tt>lt</tt>,<tt>le</tt>,<tt>gt</tt>, or <tt>ge</tt>, specifying =, !=, &lt;, &lt;=, &gt;, and &gt;= respectively.
265 <P>
266 <dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
267 <dd> Compress output file. Valid options <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>. <br>Note: PyMsXML will automatically detect input files with extension <tt>.gz</tt> as compressed with gzip.
268 <P>
269 <dt>-d, --debug</dt>
270 <dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd>
271 <P>
272 <dt>-h, --help</dt>
273 <dd>Help.</dd>
274 </dl>
275 </dd>
276 </dl>
277 <P>
278 <h3>Applied Biosystems Q-Star Spectra</h3>
279 <P>
280 The raw spectra data files for the ESI spectra from Applied
281 Biosystems' Q-Star instruments are usually
282 extracted as ".wiff" files. These can be opened using Applied
283 Biosystem's Analyst or BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries to extract profile mass spectra from these files.
284 <P>
285 <P>
286 <h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3>
287 <P>
288 The raw spectra data files for the MALDI spectra from Applied
289 Biosystems' Mariner, Voyager and 4700 instruments are usually
290 extracted as ".t2d" or ".dat" files. These can be opened using Applied
291 Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
292 support libraries to extract profile mass spectra from these
293 files. These file formats store very little meta-data in addition to
294 the mass spectrum. As such, additional information must be supplied in
295 a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
296 <P>
297 The meta-data file is most easily constructed in Excel and saved as
298 tab-separated-values, but it can be formed by hand too, if
299 desired. Each line of the meta-data file specifies a record,
300 describing the MALDI plate, the plates' spots, and the scans acquired
301 from these spots. A short-cut record, that defines the plate and spot
302 naming convention is also provided.
303 <P>
304 The plate definition record consists of the word <tt>PLATE</tt> (case
305 insensitive) in the first column, followed by alternating key-value
306 pairs in subsequent columns. Particular key-value pairs do not need to
307 be specified in any particular order. The following keys must be
308 provided:
309 <tt>plateID</tt>, <tt>spotXCount</tt>, <tt>spotYCount</tt>,
310 <tt>plateManufacturer</tt>, and <tt>plateModel</tt>. The
311 <tt>plateID</tt> value is referenced by the spot and scan definition
312 records. The <tt>spotXCount</tt> is the number of MALDI spots in
313 the horizontal dimension (integer). The <tt>spotYCount</tt> is
314 the number of MALDI spots in the vertical dimension (integer). The
315 <tt>plateManufacturer</tt> and <tt>plateModel</tt> values are inserted verbatim in the output XML.
316 <P>
317 The spot definition record consists of the word <tt>SPOT</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>spotID</tt>, <tt>spotXPosition</tt>,
323 <tt>spotYPosition</tt>, and <tt>maldiMatrix</tt>. The
324 <tt>plateID</tt> value must be defined by some plate definition
325 record. The <tt>spotID</tt> is referenced by the scan definition
326 records. The <tt>spotXPosition</tt> is the horizontal position of the
327 spot on the plate (integer). The <tt>spotYPosition</tt> is the
328 vertical position of the spot on the plate (integer). Spot positions
329 can be numbered beginning at 0 or 1. The
330 <tt>maldiMatrix</tt> value is inserted verbatim in the output XML.
331 <P>
332 The scan definition record consists of the word <tt>SCAN</tt> (case
333 insensitive) in the first column, followed by alternating key-value
334 pairs in subsequent columns. Particular key-value pairs do not need to
335 be specified in any particular order. The following keys must be
336 provided:
337 <tt>plateID</tt>, <tt>spotID</tt>, <tt>filename</tt>, and <tt>index</tt>.
338 The
339 <tt>plateID</tt> must be defined by some plate definition record. The
340 <tt>spotID</tt> must be defined by some spot definition record. The
341 <tt>filename</tt> is the name of the ".dat" or ".t2d" file containing
342 the corresponding scan's spectrum. The <tt>index</tt> is the ordinal
343 of the corresponding spectrum in the provided file. Spectra within
344 files should be referenced beginning at 1.
345 <P>
346 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
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>plateManufacturer</tt>, <tt>plateModel</tt>, <tt>spotNaming</tt>, and <tt>maldiMatrix</tt>.
351 The
352 <tt>plateID</tt> value is referenced by the spot and scan definition
353 records. The <tt>plateManufacturer</tt> and <tt>plateModel</tt> are
354 used to identify the properties of the MALDI plate. Currently, only
355 the values <tt>ABI / SCIEX</tt> and <tt>01-192+06-BB</tt> are
356 recognized, but others are easily added on request. The "ABI / SCIEX
357 01-192+06-BB" plate consists of 8 rows of 24 spots (plus 6 calibration
358 spots). The <tt>spotNaming</tt> must be one of <tt>alpha</tt>,
359 <tt>parallel</tt>, or <tt>antiparallel</tt>. At this time, only
360 <tt>alpha</tt> is implemented. The <tt>alpha</tt> spot attribute
361 constructs <tt>spotID</tt> values for all spots on the plate with the
362 row specified by a letter from A to H, and the column specified by a
363 number from 1 to 24. The
364 <tt>maldiMatrix</tt> value is assumed the same for each spot and is
365 inserted verbatim in the output XML.
366 <P>
367 <b>NOTE:</b> The order of scan definition lines is important! MS/MS
368 spectra must appear immediately after the MS spectrum containing their
369 precursors.
370 <P>
371 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.
372 <P>
373 <h3>Examples</h3>
374 <P>
375 Convert the Q-Star <tt>example.wiff</tt> file to mzXML format, placing the output in the file <tt>qstar-example.xml</tt>.<P>
376 <code>
377 C:\PyMsXML\example\wiff> pymsxml.cmd -R wiff -X mzXML -o qstar-example.xml example.wiff<br>
378 </code>
379 <P>
380 Convert the Q-Star <tt>example.wiff</tt> file to mzData format, placing the output in the file <tt>example.mzData</tt>.<P>
381 <code>
382 C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
383 </code>
384 <P>
385 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>
386 <code>
387 C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>
388 </code>
389 <P>
390 <h3>Release Notes</h3>
391 <P>
392 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.
393 <P>
394 <h3>Credits</h3>
395 <P>
396 Development of <b>PyMsXML</b> was significantly helped by the
397 open-source Visual Basic source code from the MzStar program of the
398 ISB glossolalia project.
399 <P>
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445 Original created by <a href="mailto:jfuetsch@umiacs.umd.edu">John Fuetsch</a><br>
446 Questions and comments to <a href="mailto:nedwards@umiacs.umd.edu">Nathan Edwards</a>
447 </font></td>
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