Before using the Mascot search engine, set the parameters that configure the Mascot server, the Mascot node, and the Mascot protein-scoring calculation.

Procedure

  1. From the application menu bar, select Administration > Configuration.
  2. Under Processing Settings, expand the Mascot folder.
  3. Select Mascot Server to open the parameters.
  4. The Proteome Discoverer application generates an MGF file that contains the search settings and all mass spectral information. It submits this file to the Mascot server through a web server, which might have a file size limitation. A search that generates large amounts of data—for example, a search with multiple raw data files—could create an MGF file that exceeds this limitation. The Max. MGF File Size [MB] parameter avoids this limitation by performing several separate Mascot searches and merging the results.
  5. Under Mascot Server, do the following:
  6. To split the MGF file and avoid any potential file-size limitations on the web server, enter the maximum size (in MB) that the MGF file can be in the Max. MGF File Size [MB] box.

  7. NOTE

    Make sure the size is less than the file size permitted by the web server. For information on these parameters, Mascot server configuration parameters</link>.

  9. In the Number of Attempts to Submit the Search box, specify the number of times that the application tries to submit the search when the Mascot server is busy.
  10. In the Time Interval Between Attempts to Submit a Search [sec] box, specify the interval of time, in seconds, that elapses between attempts to submit a search when the Mascot server is busy.
  11. When you are accessing a Mascot server through your own network and security for that server is enforced, enter your username and password in the corresponding boxes under Mascot Server Authentication.
  12. When you are accessing a Mascot server through the web and security for that server is enforced, enter your username and password in the corresponding boxes under Web Server Authentication.
  13. If you changed any settings of the Mascot server configuration parameters, select Apply.
  14. Select OK in the administration message box.

  15. NOTE

    Select to return to the default values.