Software:Tandem2XML

From SPCTools

Please see X!Tandem and the TPP for important general information about X!Tandem support.

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>