![]() ![]() comet_folder The folder where Comet is installed, defaults to the provided version for the given OS. omssa_folder The folder where OMSSA is installed, defaults to the provided version for the given OS. msgf_folder The folder where MS - GF + is installed. ms_amanda_folder The folder where MS Amanda is installed, defaults to the provided version for the given OS. ![]() myrimatch_folder The folder where MyriMatch is installed, defaults to the provided version for the given OS. xtandem_folder The folder where X ! Tandem is installed, defaults to the provided version for the given OS. In distributed setups, we recommend keeping a clean copy of SearchGUI, and distribute it to the different workers prior to execution. It is thus important to use a single instance of SearchCLI at a time. Please note that the search engines use indexes and temporary files stored locally in their folders. We recommend redirecting temporary folders and logs when running SearchGUI on the command line. Alternatively, the parameters can be passed directly to SearchCLI by using the command line arguments of the IdentificationParametersCLI. Identification parameter files are in the json format and can be created in the graphical user interface, using the IdentificationParametersCLI, or using third party tools. Identification parameters for use in SearchCLI can be provided as a file. SearchCLI searches spectrum files according to search parameters using X! Tandem, MyriMatch, MS Amanda, MS-GF+, OMSSA, Comet, Tide, Andromeda, MetaMorpheus, Novor and DirecTag. The command line interface to SearchGUI, referred to as SearchCLI, makes it possible to run all search engines and de novo algorithms supported by SearchGUI using a single command line. To further research, users can also mold the different algorithms to their needs: spectrum annotation, sequence matching, peptide variants, fraction analysis, and other such algorithms and methods can be modified to better fit your workflow.SearchCLI SearchGUI Command Line Interface What's more, the Spectrum Maching menu allows one to input their proteomics modifications: fixed and variable modifications can be added, and you'll also have to input additional data under the Protease & Fragmentation section. Users can go very in-depth with the Enzyme alterations, too, as they can designate the cleavage rules that best meet their demands. Users are able to modify the search engines' settings: specify minimum and maximum values for peptide lengths and precursor masses, select your preferred fragmentation method, change the output format, and more. You'll first have to set up some search settings: first, input a name, then select the relevant Spectrum and Database files, as well as an output folder for exporting. Of course, a user not in tune with some knowledge related to proteomics will be a confused user: from being able to tweak the search engines and algorithms, to the managing of the Enzyme and Modifications menus, there's plenty of versatility to the program. ![]() Though a first impression might give one the feeling that the program is deceptively simple, the truth is that there's a lot of to tap into. In an effort to provide a means to streamline proteomics research, SearchGUI comes in the form of an interface capable of offering users a place where one can identify anything proteomics-related, such as peptides and proteins, through the combined work of several search engines and de novo algorithms. ![]() When conducting research on specialized topics that are harder to access by the general population, dedicated tools designed to help with such endeavors exist to proper research further, as well as provide an environment for those looking to study and deepen their knowledge on the matter. ![]()
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