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.