typing sequence name

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typing sequence name gabriele philipps  2020-11-09
 

Hello,

when I paste an entire amino acid sequence into the left pane in order to identify peptides according to my peptide settings, I am always struggling with filling in the sequence name, i.e. replacing the "sequence 1" name with my protein name. By some strange reason the name flips back to "sequence 1" after some seconds and I have to type my protein name a second time an then it will remain.
Is there any trick to keep already the first entry?

Thanks a lot for your help!
Gabriele

 
 
Brendan MacLean responded:  2020-11-10

Hi Gabriele,
I just tried it and I don't see the behavior you mention. So, likely we will need your Skyline document and exact steps to reproduce the issue. You can attach a small Skyline document to your next post.

I will also note that you can use the Edit > Insert > Peptides form to insert multiple peptides at a time and specify their protein names, which may be easier than typing directly into the Targets view, if you are doing a lot of adding.

Thanks for letting us know that you have encountered this issue. If you can help us reproduce it, we would definitely like to fix it for you and all Skyline users.

--Brendan

 
gabriele philipps responded:  2020-11-10

Dear Brendan,

thanks for your answer and your willingness to help.
I am currently using Skyline 20.1.0.31 (if that is relevant). My colleague seems to have the same problem (I think he has a slightly newer version - so I think it is Skyline version independent).
The procedure I am following is copying the entire protein sequence from the program clone manager or Notepad and pasting it into the left pane from Skyline (peptide settings are at ~ 6-14 aa after tryptic digest). Then the 11 peptides appear (here for the ampicilline resistance protein as an example) and the sequence name is shown as sequence 1. Then I try to rename the sequence as "bla" and it will switch back to sequence 1 after some seconds ( I counted ~ 4-8 seconds). after a second try of renaming it, it will remain.

I tried your second option (Edit > Insert > Peptides), except that I used "> Protein" which seemed fine for the moment, but than I recognized, that when pasting the sequence into the sequence column, than I get only the peptides for the first 60 amino acids (that seems to be a result from copying it from the clone manager program as it generates some kind of break after every 60 aa - when I paste it into notepad or word than I can remove the "enter" signs and I can paste the entire sequence into the grid. In that case the sequence name remains, but again more steps are necessary)

I attached a picture of the pasted sequence in skyline, the protein sequence and the *.sky file.

I am curious if you will see the same. effect

Best regards,

Gabriele