If you're looking for a powerful and user-friendly search engine for proteomics data, SearchGUI is the perfect solution. Developed by the PeptideShaker Team, this software is designed to help you easily search, visualize, and analyze large quantities of data. With its intuitive interface and advanced algorithms, SearchGUI makes it easy to identify proteins, peptides, and other important molecules. Whether you're a research scientist, a bioinformatics expert, or just someone who needs to process complex data quickly and effectively, SearchGUI is the ideal tool for the job. Download it today and see for yourself how easy it is to get the most out of your proteomics data!

SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines and de novo sequencing algorithms, currently supporting X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA, Novor and DirecTag. To start using SearchGUI, unzip the downloaded file, and double-click the SearchGUI-X.Y.Z.jar file. No additional installation required! The main purpose of SearchGUI is to make it simpler to use multiple search engines at the same time. We believe that a graphical user interface would be the best choice for most users, and therefore made SearchGUI with a graphical user interface. However, it can sometimes be easier to perform a search from the command line. For example when incorporating the search into some sort of pipeline. With this in mind we have therefore included the option of using SearchGUI as a command line tool.

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