Abacus is a TPP compatible spectral counting tool developed by the Nesvizshkii lab at the University of Michigan. Here are instructions on how to run it on the command line on our linux systems.
Otherwise you would run some command like the following for each of your files:
xinteract -OAp -Nfile1 file1.pep.xml
xinteract -OAp -Nfile2 file2.pep.xml
xinteract -OAp -Nfile3 file3.pep.xml
xinteract -OAp -Nfile4 file4.pep.xml
Next, you need to generate a combined ProteinProphet file using all of the
interact-*.pep.xml files as input. Use this command to do this:
ProteinProphet interact*.pep.xml interact-COMBINED.prot.xml
At this point you should have a set of interact-*.pep.xml, interact-*.prot.xml,
and an interact-COMBINED.prot.xml files. For some reason, Abacus will attempt to load
every file in the directory, including the non-interact pep.xml files and I don't
know if this is detrimental or not. In order to keep it from loading the base search
files (e.g. file1.pep.xml, file2.pep.xml in the examples above), move those away
temporarily into a "bak" subdirectory. Even if these files aren't detrimental,
a nice side effect of doing this is reducing the run time by not loading useless files.
mv file1.pep.xml file2.pep.xml file3.pep.xml file4.pep.xml bak/
This parameters file is set to run Abacus with default settings using NSAF. Hopefully you can figure out how to edit the parameters as needed. If you need help understanding the settings, here's the Abacus support forum. You will need to edit the line entries for:
Now cross your fingers that you did everything right and run Abacus:
java -Xmx16g -jar /net/pr/vol1/ProteomicsResource/bin/abacus.jar -p Abacus_parameters.txt
We can undo step 3 above now:
mv bak/* .
That's it. Hopefully you now have an "ABACUS_output.tsv" (or whatever you named the output file in step 4) in your search directory.