Help in getting started..

[Venugopal M R]

 Can anyone help me to get started with Abacus. I have the prot.xml and pep.xml.
I see that you need to have a combined file as well. Could you please tell me what should this combined file contain?
Also why do I need to combine the file?
And how do I combine it? is there a software that does it?

Thanks a lot

[dfermin]

Hello.

There are a few places to start. The first would be the Abacus Manual available for download on the SourceForge.net website for Abacus.  This not only provides a description of the data produced by ABACUS, but it also provides a walk through tutorial. The sample data is also available for download at the abacus website.

For more details about how the program works you could read the original publication in Proteomics:
http://onlinelibrary.wiley.com/doi/10.1002/pmic.201000650/abstract

As to your other questions:
You need a combined file because it will contain the least redundant list of proteins among all of your independent experiments which you are trying to run through Abacus.
You can generate a combined file through the TPP (the same software that created your prot.xml and pep.xml files).
 The easiest way I know of is to place all of your interact.pep.xml files into one folder and run the command:
ProteinProphet *.pep.xml interact-COMBINED.prot.xml

Depending upon your operating system there might be a GUI interface for doing this. You could ask the TPP developers at their forum on this point:
https://groups.google.com/forum/#!forum/spctools-discuss