Background Proteome Problems -“Resolving protein details for background proteome not working” alena tierbach  2014-11-05 03:22
 
Hi Brendan,

I added the background proteome which consists of 29525 proteins. The fasta file for the background proteome is saved on C:
At the bottom of the screen it says “Resolving protein details for background proteome”, but the green bar is not moving at all and I cannot look at the unique peptides. A colleague of mine, who uses the same background proteome, has nearly the same problem. In her case the green bar needed more than 1.5 days to complete 1/2 of the way.
To see if the size of the fasta file may be the problem, I shortened the file by ½, but it did not help.
Any hints how this problem can be solved?
Thanks,
Alena

Wndows 7
Skyline2.6-64bit
 
 
Brian Pratt responded:  2014-11-05 09:06
Hi Alena,

I'm sorry the new protein lookup isn't working well for you. Could I possibly have a look at that fasta file?

For what it's worth, the lookup is a background process and you don't have to wait for it to complete to carry on with your Skyline work. But certainly something is amiss and I'd like to get that fixed.

Thanks,

Brian Pratt
 
alena tierbach responded:  2014-11-06 03:42
Thank you for the fast reply.
Here is the FASTA file of the background proteome that we are currently working with.
Cheers
Alena
 
Brian Pratt responded:  2014-11-06 08:03
Got the file, thanks. At first glance, it looks pretty normal. I won't be able to look into this properly until Monday, unfortunately.
 
alena tierbach responded:  2014-12-08 06:11
Hello,
I just wanted to ask if there are any news regarding my problem with the background proteome?
Cheers
Alena
 
Brian Pratt responded:  2014-12-08 09:23
First of all, I want to emphasize again that this is something you can ignore, even though it's extremely annoying. That said, I have identified the problem and hope to have a fix in the next Skyline-Daily release.

The problem, for what it's worth, is that when Skyline can't find a protein in Uniprot it then searches Entrez on the chance that it's an older style of protein description, something which Entrez handles well. If that succeeds, Skyline then uses the Entrez result to go back to Uniprot for the rest of the information. Interestingly the proteins in your data match at Entrez but the results don't have a match at Uniprot, something I hadn't seen before. The bug is that Skyline keeps trying when it should really just give up once it's apparent that things just aren't working out. I'll fix that.

Thanks for reporting the problem!

Brian