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 |
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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 |
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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. |
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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 |
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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 |
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