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<h3>Introduction</h3>
<P>
<b>PyMsXML</b> is a python script for converting vendor specific mass
spectrometry data files for Applied Biosystems' Q-Star, 4700, Mariner,
and Voyager mass spectrometers from their raw binary form, to either
of the emerging XML file formats for mass spectra: mzXML, from the
Sashimi Glossolalia project of the Institute for Systems Biology (ISB);
and mzData, from the Proteome Standardization Initiative (PSI) project
of the Human Proteome Organization (HUPO).
<P>
<b>PyMsXML</b> uses installed vendor software under Windows to access the
proprietary raw mass spectra file format, interfacing to the vendor
supplied libraries via the supplied COM interface. Unlike other
software solutions that use this approach, <b>PyMsXML</b> is written in a
free, open-source language called Python. As such, no installation of
Microsoft Visual C++ or Visual Basic is necessary to use, alter, or
improve the <b>PyMsXML</b> script.
<P>
<b>PyMsXML</b> is easily extended for new instruments and vendor software,
and for new, or changed, XML file formats. The code that interfaces to
the vendor software is decomposed from the code that formats the data
as XML, as such, the addition of new instrument capability need not
re-write the XML data format code. Similarly, as new XML file formats
emerge, the code that interfaces with the instrument software need not
change. 
<P>
<h3>Installation</h3>
<P>
<ol>
<li> Download and install the latest version of <A href="http://www.activestate.com/Products/ActivePython/">ActiveState ActivePython</A> for Windows.
<P>
<li> Start the Pythonwin IDE (All Programs -> ActiveState ActivePython
2.4 -> Pythonwin IDE). From the Tools menu, select the "COM Makepy
utility" entry. In the popup window, select "ExploreDataObjects 1.0
Type Library (1.0)" to build a python interface to Analyst's COM
libraries for reading .wiff files, select "IDAExplorer 1.0 Type
Library (1.0)" to build a python interface to Data Explorer's COM
libraries for reading ".dat" and ".t2d" files. If you have both pieces
of software, repeat this step for each software package. Click OK.
<P>
<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.
<P>
For Analyst, these commands at the Pythonwin IDE command-line
(copy-and-paste!) should elicit similar responses:<br>
<code>
>>> from win32com.client import Dispatch<br>
>>> Dispatch('Analyst.FMANSpecData')<br>
&lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANSpecData instance at 0x14421558> <br>
>>> Dispatch('Analyst.FMANChromData')<br>
&lt;win32com.gen_py.ExploreDataObjects 1.0 Type Library.IFMANChromData instance at 0x14418408>
</code>
<P>
For Data Explorer, these commands at the Pythonwin IDE command-line (copy-and-paste!) should elicit similar responses:<br>
<code>
>>> from win32com.client import Dispatch, gencache<br>
>>> Dispatch('DataExplorer.Application',resultCLSID='{3FED40F1-D409-11D1-8B56-0060971CB54B}')<br>
&lt;COMObject DataExplorer.Application><br>
>>> gencache.EnsureModule('{06972F50-13F6-11D3-A5CB-0060971CB54B}',0,4,2)<br>
&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'>
</code>
<P>
<li> Download and unpack the <b>PyMsXML</b> scripts and examples. <A
href="http://bioinformatics.org/project/filelist.php?group_id=701">Download
<b>PyMsXML</b></A>. After unzipping <b>PyMsXML</b>, edit the file pymsxml.cmd to
point to your Python installation (usually C:\Python24\python.exe)
and your <b>PyMsXML</b> installation.
</ol>
<P>
<h3>Usage</h3>
<P>
<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.
<dl>
<dt><b>pymsxml</b> [ options ] <i>raw-spectra-data-file</i></dt>
<P>
<dt>
Options:<P>
</dt>
<dd>
<dl>
<dt>-R <i>raw-format</i>, --rawdata <i>raw-format</i></dt>
<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>. 
<P>
<dt>-X <i>xml-format</i>, --xmlformat <i>xml-format</i></dt>
<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>.
<P>
<dt>-o <i>output-file</i>, --output <i>output-file</i></dt>
<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>.
<P>
<dt>-p <i>ms-levels</i>, --peaks <i>ms-levels</i></dt>
<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.
<P>
<dt>-f <i>filter-spec</i>, --filter <i>filter-spec</i></dt> <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 =, &ne;, &lt;, &le;, &gt;, and &ge;
respectively.
<P>
<dt>-Z <i>compress-format</i>, --compress <i>compress-format</i></dt>
<dd> Compress output file. Valid options: <tt>gz</tt>. Default: None, unless output file ends with <tt>.gz</tt>, then <tt>gz</tt>.
<P>
<dt>-d, --debug</dt>
<dd>Debug. Output XML for first 10 spectra only. Truncate spectral data, too. Useful to verify that the output is formatted correctly.</dd>
<P>
<dt>-h, --help</dt>
<dd>Help.</dd>
</dl>
</dd>
</dl>
<P>
<h3>Applied Biosystems Q-Star Spectra</h3>
<P>
The raw spectra data files for the ESI spectra from Applied
Biosystems' Q-Star instruments are usually extracted as ".wiff"
files. These can be opened using Applied Biosystem's Analyst or
BioAnalyst programs. <b>PyMsXML</b> uses Analyst's support libraries
to extract mass spectra from these files.
<P>
<P>
<h3>Applied Biosystems Mariner, Voyager, 4700 Spectra</h3>
<P>
The raw spectra data files for the MALDI spectra from Applied
Biosystems' Mariner, Voyager and 4700 instruments are usually
extracted as ".t2d" or ".dat" files. These can be opened using Applied
Biosystem's Data Explorer program. <b>PyMsXML</b> uses Data Explorer's
support libraries to extract mass spectra from these
files. These file formats store very little meta-data in addition to
the mass spectrum. As such, additional information must be supplied in
a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
<P>
The meta-data file is most easily constructed in Excel and saved as
tab-separated-values, but it can be formed by hand too, if
desired. Each line of the meta-data file specifies a record,
describing the MALDI plate, the plates' spots, and the scans acquired
from these spots. A short-cut record, that defines the plate and spot 
naming convention is also provided. 
<P>
The plate definition record consists of the word <tt>PLATE</tt> (case
insensitive) in the first column, followed by alternating key-value
pairs in subsequent columns. Particular key-value pairs do not need to
be specified in any particular order. The following keys must be
provided:
<tt>plateID</tt>, <tt>spotXCount</tt>, <tt>spotYCount</tt>,
<tt>plateManufacturer</tt>, and <tt>plateModel</tt>. The
<tt>plateID</tt> value is referenced by the spot and scan definition
records. The <tt>spotXCount</tt> is the number of MALDI spots in
the horizontal dimension (integer). The <tt>spotYCount</tt> is
the number of MALDI spots in the vertical dimension (integer). The
<tt>plateManufacturer</tt> and <tt>plateModel</tt> values are inserted verbatim in the output XML.
<P>
The spot definition record consists of the word <tt>SPOT</tt> (case
insensitive) in the first column, followed by alternating key-value
pairs in subsequent columns. Particular key-value pairs do not need to
be specified in any particular order. The following keys must be
provided:
<tt>plateID</tt>, <tt>spotID</tt>, <tt>spotXPosition</tt>,
<tt>spotYPosition</tt>, and <tt>maldiMatrix</tt>.  The
<tt>plateID</tt> value must be defined by some plate definition
record. The <tt>spotID</tt> is referenced by the scan definition
records. The <tt>spotXPosition</tt> is the horizontal position of the
spot on the plate (integer). The <tt>spotYPosition</tt> is the
vertical position of the spot on the plate (integer). Spot positions
can be numbered beginning at 0 or 1. The
<tt>maldiMatrix</tt> value is inserted verbatim in the output XML.
<P>
The scan definition record consists of the word <tt>SCAN</tt> (case
insensitive) in the first column, followed by alternating key-value
pairs in subsequent columns. Particular key-value pairs do not need to
be specified in any particular order. The following keys must be
provided:
<tt>plateID</tt>, <tt>spotID</tt>, <tt>filename</tt>, and <tt>index</tt>.
The
<tt>plateID</tt> must be defined by some plate definition record. The
<tt>spotID</tt> must be defined by some spot definition record. The
<tt>filename</tt> is the name of the ".dat" or ".t2d" file containing
the corresponding scan's spectrum. The <tt>index</tt> is the ordinal
of the corresponding spectrum in the provided file. Spectra within
files should be referenced beginning at 1.
<P>
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
pairs in subsequent columns. Particular key-value pairs do not need to
be specified in any particular order. The following keys must be
provided:
<tt>plateID</tt>, <tt>plateManufacturer</tt>, <tt>plateModel</tt>, <tt>spotNaming</tt>, and <tt>maldiMatrix</tt>. 
The
<tt>plateID</tt> value is referenced by the spot and scan definition
records. The <tt>plateManufacturer</tt> and <tt>plateModel</tt> are
used to identify the properties of the MALDI plate. Currently, only
the values <tt>ABI / SCIEX</tt> and <tt>01-192+06-BB</tt> are
recognized, but others are easily added on request. The "ABI / SCIEX
01-192+06-BB" plate consists of 8 rows of 24 spots (plus 6 calibration
spots). The <tt>spotNaming</tt> must be one of <tt>alpha</tt>,
<tt>parallel</tt>, or <tt>antiparallel</tt>. At this time, only
<tt>alpha</tt> is implemented. The <tt>alpha</tt> spot attribute
constructs <tt>spotID</tt> values for all spots on the plate with the
row specified by a letter from A to H, and the column specified by a
number from 1 to 24. The
<tt>maldiMatrix</tt> value is assumed the same for each spot and is
inserted verbatim in the output XML.
<P>
<b>NOTE:</b> The order of scan definition lines is important! MS/MS
spectra must appear immediately after the MS spectrum containing their
precursors. 
<P>
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.
<P>
<h3>Examples</h3>
<P>
Convert the Q-Star <tt>example.wiff</tt> file to mzXML format, placing the output in the file <tt>qstar-example.xml</tt>.<P>
<code>
C:\PyMsXML\example\wiff> pymsxml.cmd -R wiff -X mzXML -o qstar-example.xml example.wiff<br>
</code>
<P>
Convert the Q-Star <tt>example.wiff</tt> file to mzData format, placing the output in the file <tt>example.mzData</tt>.<P>
<code>
C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
</code>
<P>
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>
<code>
C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>
</code>
<P>
<h3>Release Notes</h3>
<P>
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.
<P>
<h3>Credits</h3>
<P>
Development of <b>PyMsXML</b> was significantly helped by the
open-source Visual Basic source code from the MzStar program of the
ISB glossolalia project.
<P>
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