Download SearchGUI 4.1.21 (Mac) – Download Free

Search GUI is an open source project that serves as a common interface for proteomics search and de novo engines, allowing you to configure and run multiple engines simultaneously. It supports X! Tandem, MS Amanda, MyriMatch, MS-GF+, OMSSA, Tide, Comet, Andromeda, Novor, MetaMorpheus and DirecTag.

Designed to simplify the task of using multiple search engines simultaneously through a graphical user interface, SearchGUI is also available from the command line and can be added to various analysis pipelines. The program is Java based and available for Mac, Windows and Linux.

As far as input formats are concerned, the software supports mzML and mgf files as data sources. ThermoRawFileParser is built in and allows you to easily convert Thermo raw files to mzML or mgf.

From the main user interface, you can load spectrum files and search settings, then set the preferred output folder. Optionally run preprocessing and postprocessing. Finally, you can choose which search engines to use and configure them independently. Note that some engines are only available on certain operating systems.

Once results are provided, they can be viewed and interpreted using specialized applications such as PeptideShaker.