PeptideShaker

PeptideShaker can be used to process the search results from OMSSA, X!Tandem and Mascot and combine the identifications into a single result. For details on PeptideShaker please the the PeptideShaker home page.

In order to use PeptideShaker from SearchGUI you first have to download and unzip PeptideShaker. When this is done all you have to do is to click the Edit button next to the PeptideShaker location field in this dialog and locate the PeptideShaker jar file. You only have to do this the first time you want to use PeptideShaker.

Next you provide some information about the project: project name, sample name and replicate number. These are used for referring to the project at later stages of the analysis.

Finally you select the output file where you want the PeptideShaker results to be saved. Note that the results will be automatically opened in PeptideShaker when the processing has completed.

You also have the opportunity of linking the SearchGUI results with Mascot results. Note that the Mascot results have to be compatible with the SearchGUI results, i.e., the Mascot searches have to be run the exact same spectrum files and database, and with the same search settings. For details on how to carry out the Mascot searches see Mascot Support and Database Help.

It is also possible to tailor the processing parameters and the import filters at this stage.