Abacus is a tool for extracting adjusted spectral counts from the result XML files generated by the Trans-Proteomic Pipeline (TPP). Abacus outputs a tab-delimited file that can be used for label-free quantification or simply viewing proteomics results across multiple experimental runs.

A complete description of the algorithm can be found in our article in PROTEOMICS. If you use our program please cite this work.

The program is written in JAVA and designed to work on Windows, MacOS X, and Linux.

Please note that Abacus was developed and tested using Oracle's version of JAVA. We have not tested it on any of the open source flavors of JAVA. While we don't anticipate any problems using other JAVA flavors we cannot provide technical support if you are using one of them.

To download the latest version of Abacus, and/or other supporting files, go our Sourceforge site.

For technical support please post messages to the help forum.