Changing enzyme or no enzyme in the GUI

[dcan...@uw.edu]

Hello,

I'm attempting to sequence a peptide that was not digested by an enzyme. How can I change the settings to avoid the default trypsin? 

The wiki page had the following information:

            The type of digestion to consider: 
            0: Enzyme, 1: Unspecific or 2: Whole Protein. Default is 0.

            Enzyme, default is 'Trypsin'. 
            Available enzymes are listed in the GUI.
            Note: case sensitive.

 but I can't find the  enzyme list in the GUI, and my attempts in the command line have failed. 

Thanks. 

[Harald Barsnes]

Hi,

The enzyme does not have an impact on the de novo sequencing, as either the algorithm does not care about the enzyme when sequencing or it has been trained on a given enzyme (usually trypsin) and one would have to retrain it on a new enzyme (which can potentially be done, but only be contacting the algorithm developers directly). So you can safely ignore this setting for DeNovoGUI, the results should be fairly independent of the enzyme anyway. It is there in the settings only because we share the settings with out other tools. The full list of enzymes can however be found in SearchGUI or PeptideShaker.

Best regards,

Harald