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Batch XML Conversion of X!Tanem Output Files (Windows)

This post is going to be a short one . When you run X!tandem search on linux, you get output files with .t.xml extension. This file can be open on gpm-web site to see the models.  It can be also opened in PeptideShaker. But if you want to use IDPicker to look at the results, you need to convert the file to xml file that is compatible with the software. The utility software for conversion is called Tandem2XML.exe, and it is one of tools used in TPP.  If you have already installed TPP on your PC, you can find the program in the following directory.

C:\Inetpub\tpp-bin\

You can also download it from here (may not be fast). To use this in the command line, you can type

>Tandem2XML.exe [FILE_PATH\INPUT_FILE_NAME.t.xml] [FILE_PATH\OUTPUT_FILE_NAME.xml]

Once the file is converted to xml file (pepXML), you can import it to IDPicker. This utility is simply to use, but typing file path and name for multiple files is pretty cumbersome. So I wrote a script which will find all .t.xml files in a specified directory and automatically convert to .xml.

>ECHO OFF
>set msfd=”C:\FILE_PATH_FOR_THE_TANDEM_RESULTS_DIRECTORY”
>:: read file names from the directory and create a new file with all file names
>echo %msfd%
>dir -F %msfd%\*.t.xml /a:-d /b>file_name.txt
>for /f “tokens=*” %%l in (file_name.txt) do Tandem2XML.exe %msfd%\%%l %msfd%\%%l.xml

You can save this script as AutoTandem2XML.bat and place the Tandem2XML.exe in the same directory as this program.

To use, just change the second line for the directory containing .t.xml files.  When you execute either by double clicking the program or running in the command line, first it creates a file file_name.txt which contains the file names ending with .t.xml.

output_tandem2xml

Then it will convert the .t.xml to IDPicker compatible xml file in the same directory.  You may see some error messages like  output files will not contain retention time. But the output files still works in IDPicker.

error_tandem2xml

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