SearchGUI

SearchGUI can help you identify proteins, using the Open Mass Spectrometry Search Algorithm (OMSSA), as well other proteomics identification search engines, including X!Tandem, Andromeda, Comet and more. As its name suggests, the software is essentially a graphical user interface for various search engines. It provides a wide range of useful configuration options, to help you search analyze and process your data in a comfortable manner.

SearchGUI is a Java-based application, so you can use it on Windows, Mac OS X and Linux. It is distributed under the Apache2 license, which means that it is free. The software's components come in a ZIP archive, so you only need to extract them and run a .jar file, instead of going through an installation process.

Identifying proteins can be a straightforward process. You can just load your spectrum files, edit your search settings, choose an output folder and click a button to begin. However, the software lets you make many other fine adjustments. For example you can choose which search engines to use, by clicking their corresponding check boxes, on the same window. Furthermore, you can set up three operational stages, if you want more refined data.

Besides proteomics identification search engines, the program works in tandem with other useful utilities as well, which are displayed just like the search engines, on the same interface and separated, to make them easier to spot. In addition to the aforementioned operation, the program can go through pre-processing and post-processing stages.

For the pre-processing stage, you can use ProteoWizard to convert raw data, after which the program will use the selected search engines to identify proteins. Finally, SearchGUI can use PeptideShaker to interpret the data and to present it in an efficient and easy to understand manner.

When it comes to proteomics identification, SearchGUI will definitely meet all your expectations.