Performing a ProteinPilot software search with the Mascot server enabled

For research use only. Not for use in diagnostic procedures.

Answer

ProteinPilot™ software 5.0.1 can perform searches using the Mascot server. To use the Mascot server, a license is required, and this must be purchased from Matrix Science. For an overview of the Matrix Science licensing requirements and how to get a quote, select this link: https://www.matrixscience.com/licensing.html .
 
To set up a search wtih ProteinPilot software and a Mascot server version 2.8, follow these steps: 
1) Install the ProteinPilot software 5.0.1 and activate its license to launch the software.
2) Purchase a Mascot server license.
3) Under the Add menu, select a wiff file.
4) Obtain the Mascot server name. Then open the ProteinPilot software and go to Configure.  
5) Select Mascot >Specify Mascot Server. Type in only the server name and not the entire URL. 

6) Select the Mascot method.
7) Add the new Mascot Method search parameters under Edit (see below).


8) Select Save As and provide a new name for the method. 


9) Select the green Process button to process your data. 
10) The analysis log will show the progress of the search. 
11) To open the Mascot search results from the Analysis Log window, double-click any result with Finished in the Status column. The results will open in a browser window.
12) To open the results of a previous Mascot search, navigate to the File menu. Select Open > Result or click Result in the Workflow Tasks. If necessary, navigate to the location of the results file. Mascot search results files have a .mrf file extension. Click the name of the results file and then click Open. The results will open in a browser window.
13) Scroll down in the Mascot results window to see each winner protein separately. 

14) Selecting the blue Winner protein name provides the protein sequence information and the matched peptide sequences in red.