Software:Tandem2XML
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| Revision as of 18:03, 22 June 2007 Jtasman (Talk | contribs) (creating page) ← Previous diff |
Current revision Jeng (Talk | contribs) (→Converting X!Tandem results to TPP input files) |
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| + | '''Please see [[TPP:X!Tandem and the TPP|X!Tandem and the TPP]] for important general information about X!Tandem support.''' | ||
| - | Please see [[TPP:X!Tandem and the TPP|X!Tandem and the TPP]] | + | ==Getting the software== |
| + | '''This software is included in the current [[Software:TPP|TPP]] distribution.''' | ||
| + | |||
| + | ==In a nutshell== | ||
| + | Tandem2XML is part of the processing pipeline. This tool converts Tandem result files to pepXML files suitable for use in the TPP. | ||
| + | |||
| + | ==Running Tandem2XML== | ||
| + | |||
| + | ''Note: the TPP GUI does not yet support this program; you will have to run it manually on the command line.''' | ||
| + | |||
| + | ===Converting X!Tandem results to TPP input files=== | ||
| + | |||
| + | This example is based on Cygwin but behaves exactly the same under linux. | ||
| + | |||
| + | To run Tandem2XML open and cygwin terminal and run the command: | ||
| + | Tandem2XML /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/input/file /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/output/file | ||
| + | |||
| + | This will create a pepXML file called: | ||
| + | /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/output/file | ||
| + | |||
| + | |||
| + | When searching mzXML files directly, note that the following Tandem parameter should be set as shown in order for Tandem2XML to correctly report scan numbers attributes, required for quantitation tools like [http://tools.proteomecenter.org/wiki/index.php?title=Software:ASAPRatio ASAPRatio] or [http://tools.proteomecenter.org/wiki/index.php?title=Software:XPRESS XPRESS], in the resulting pepXML file: | ||
| + | <note type="input" label="output, spectra">yes</note> | ||
Current revision
Please see X!Tandem and the TPP for important general information about X!Tandem support.
Contents |
Getting the software
This software is included in the current TPP distribution.
In a nutshell
Tandem2XML is part of the processing pipeline. This tool converts Tandem result files to pepXML files suitable for use in the TPP.
Running Tandem2XML
Note: the TPP GUI does not yet support this program; you will have to run it manually on the command line.'
Converting X!Tandem results to TPP input files
This example is based on Cygwin but behaves exactly the same under linux.
To run Tandem2XML open and cygwin terminal and run the command:
Tandem2XML /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/input/file /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/output/file
This will create a pepXML file called: /cygdrive/c/Inetpub/wwwroot/ISB/data/full/path/to/output/file
When searching mzXML files directly, note that the following Tandem parameter should be set as shown in order for Tandem2XML to correctly report scan numbers attributes, required for quantitation tools like ASAPRatio or XPRESS, in the resulting pepXML file:
<note type="input" label="output, spectra">yes</note>
