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'Protein BestName' and gi numbers

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'Protein BestName' and gi numbers edwin.lowe  2009-10-08 23:27
Status: Closed
 
I have an issue that I strike every now and then with the way that LabKey reports Protein names. It may or may not be a LabKey issue (perhaps I should use a different database).

Quite often I have some users who want to do a comparison that uses the 'Protein' name (which with my databases is a gi number) rather than the 'Protein Best' name. However, when I add the 'Protein' name to the comparison view it is actually displaying the 'Protein BestName' not the 'Protein' name that appears in the standard 'ShowRun' MS2 Dashboard view.

EXCEPT, the Spectral Count comparison shows the 'Protein' name, not the ProteinBest name.

The reason why is is an issue is that in a database like NR sometimes the protein name will be a SwisProt name (if its there) and sometimes a gi number. I've tried playing with setting the protein best name for the database but unfortunately that doesn't fix it completely. Any tips on how I can get the system to not use the ProteinBest name on the comparison views would be much appreciated.
 
 
jeckels responded:  2009-10-16 16:21
Hi Edwin,

Yes, protein naming can cause quite a headache. Unfortunately I don't have any great recommendations for how to do this with 9.2.

I just made a small change to 9.3, due out in a few weeks, to help you out - in the ProteinProphet (Query) and Spectra Count comparison views you'll be able to specifically request the GI number for a protein. It will show up as an option like the Swiss Prot Name and IPI names when you expand the Protein node in Customize View.

Additionally, on a FASTA-by-FASTA basis you'll be able to set the GI number (if available) as the protein's "Best" Name in the protein admin page, which should help out in the other comparison views.

Thanks,
Josh
 
edwin.lowe responded:  2009-10-29 17:56
Hi Josh,

That sounds like just what I need!

Edwin