Mascot configuration parameters - Proteome Discoverer Software - Mascot configuration parameters - Proteome Discoverer Software

Mascot configuration parameters - Proteome Discoverer Software - Mascot configuration parameters - Proteome Discoverer Software - Proteome Discoverer Software

Proteome Discoverer 3.1 User Guide

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Desktop Software > Proteome Discoverer Software

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User Guide

Software version

3.1

You can set configuration parameters for the Mascot server, the Mascot node, and Mascot’s protein-scoring calculation.

The following table lists the parameters that you can use to configure the Mascot server.

Mascot server configuration parameters
Parameter	Definition
Mascot Server
Max. MGF File Size [MB]	Specifies the maximum size, in megabytes, that the MGF file can be. This parameter splits the MGF file to avoid any potential file-size limitations on the web server. Range: 0–no maximum; Default: 500.
Mascot Server URL	Specifies the URL of the Mascot server that you use for Mascot searches.
Number of Attempts	Specifies the number of times that the application tries to submit the search when the Mascot server is busy. Range: 0–no maximum; Default: 20
Time Interval Between Attempts to Submit a Search [sec]	Specifies the interval of time, in seconds, that elapses between attempts to submit a search when the Mascot server is busy. Range: 20–no maximum; Default: 90
Mascot Server Authentication
Mascot User Name	Specifies your user name if you are accessing a Mascot server through your own network and security for that server is enforced.
Mascot Server Password	Specifies your password if you are accessing a Mascot server through your own network and security for that server is enforced.
Web Server Authentication
User Name	Specifies your user name if you are accessing a Mascot server through the web and if security for that server is enforced.
Password	Specifies your password if you are accessing a Mascot server through the web and if security for that server is enforced.

The following table lists the parameters that you can use to configure the Mascot node.

Mascot node configuration parameters
Parameter	Definition
Default Confidence Thresholds
Significance High	Specifies the thresholds for high-confidence peptides. The application automatically sets this value to the calculated relaxed significance when it performs a decoy search. Range: 0.0–1.0; default: 0.01
Significance Middle	Specifies the thresholds for medium-confidence peptides. The application automatically sets this value to the calculated relaxed significance when it performs a decoy search. Range: 0.0–1.0; default: 0.05

MudPIT scoring is an option 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 is composed of numerous low-scoring erroneous matches. The Use MudPIT Scoring option prevents low-scoring peptide matches from contributing to a falsely reported high-scoring protein.

The setting of this parameter is stored in the Result Summaries of the .pdResult file.

For more information, see Using the Result Summaries.

The following table describes the parameter that you can use to configure Mascot’s protein-scoring calculation, which is about the selection of MudPIT scoring.

Mascot protein score configuration parameters
Parameter	Definition
Protein Scoring Options
Use MudPIT Scoring	Determines whether to use MudPIT scoring or normal scoring. The parameter options are as follows: (Default) Automatic: Automatically determines whether to use MudPIT scoring. True: Always uses MudPIT scoring. False: Never uses MudPIT scoring. For information about MudPIT scoring, refer to the Mascot Help.