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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>.
308 > support libraries to extract mass spectra from these files. These file
309 > formats store very little meta-data in addition to the mass
310 > spectrum. If you do not care whether or not the output data-file
311 > contains valid spot, matrix, and plate meta-data; and if your spectra
312 > are all contained in one raw datafile, then the datafile can be
313 > supplied on the command-line as <i>raw-spectra-data-file</i>. However, if you have many .dat or .t2d files, each corresponding to a MALDI spot, or if you wish to have spot, matrix, or plate meta-data populated into the output file, then see the next set of instructions.
314   <P>
315 + Plate, matrix, and spot meta-data must be supplied in
316 + a meta-data text file, which is supplied on the command-line as <i>raw-spectra-data-file</i>.
317   The meta-data file is most easily constructed in Excel and saved as
318   tab-separated-values, but it can be formed by hand too, if
319   desired. Each line of the meta-data file specifies a record,
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402   C:\PyMsXML\example\wiff> pymsxml.cmd -X mzData example.wiff<br>
403   </code>
404   <P>
405 + Convert the Mariner ESI-CE-MALDI spectra in <tt>example3.dat</tt> to mzXML format, placing the output in the file <tt>example3.mzXML.gz</tt> (automatically gzipped):
406 + <code>
407 + C:\PyMsXML\example\dat> pymsxml.cmd -R mariner -o example3.mzXML.gz example3.dat<br>
408 + </code>
409 + <P>
410   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>
411   <code>
412   C:\PyMsXML\example\t2d> pymsxml.cmd -X mzXML example*.t2m<br>

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