MudPIT scoring, an option for Mascot searches, is used for generating the protein score from data sets with large numbers of peptide matches, as in a complex proteome digest. Mascot stores 10 possible matches for each spectrum. The protein score is normally a sum of all possible matches. However, this might result in a high “protein” score that comprises numerous low-scoring erroneous matches. The Use MudPIT Scoring parameter prevents low-scoring peptide matches from contributing to a falsely reported high-scoring protein. For information about MudPIT scoring, refer to the Mascot Help.

Procedure

  1. From the application menu bar, select Administration > Configuration.
  2. Under Processing Settings, expand the Mascot folder.
  3. Select Mascot Protein Score.
  4. The configuration parameters for Protein Scoring Options appear. For information on these parameters, Mascot server configuration parameters</link>.
  5. You can review these parameter settings in the Protein Scorer section of the Consensus Workflow page of the Result Summaries. For information on the Result Summaries, see Using the Result Summaries.
  6. Specify whether to use MudPIT scoring or normal scoring by selecting one of the following:
  7. (Default) Automatic: Automatically determines whether to use MudPIT scoring.
  8. True: Always uses MudPIT scoring.
  9. False: Never uses MudPIT scoring.
  10. If you changed any settings of the Mascot protein-scoring configuration parameters, select Apply.
  11. Select OK in the administration message box.

  12. NOTE

    Select to return to the default values.