Abacus

Abacus is a free and open-source Java-based software application that allows you to extract spectral count data for label-free quantitative proteomic analysis.

There is no setup pack involved. Provided that you have Java installed, you can just click the JAR file to run Abacus.

Another possibility is to save the app to a pen drive in order to launch it on any computer with minimum effort. What's more, it does not modify Windows registry settings or create extra files on the disk without your approval, thus leaving no traces behind after its removal.

The GUI is user-friendly, consisting of a regular window with a plain and simple structure that shows all available options. You can specify the Abacus database name, decoy tag, source directory, FASTA file, Gene map, along with the combined and output directory.

There are several presets available for the output type, namely Gene, Peptide, QSpec Prot, and Qspec Gene. Alternatively, you can customize each file. Before saving and running the project, it is possible to ask Abacus to preserve the database and to generate verbose results.

There were no kind of issues in our testing, since the app did not hang, crash or pop up error messages. It runs on low CPU and RAM, so it shouldn't affect the overall performance of the computer. Abacus serves its purpose.