SearchGUI

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.

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.

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. 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.

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.

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. Users can go very in-depth with the Enzyme alterations, too, as they can designate the cleavage rules that best meet their demands.

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. 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.

SearchGUI is a tool intended for the ones researching proteomics: though admittedly very specialized, the tool nevertheless manages to marry all the numerous functions on offer within a relatively compact interface