Quick way to import hundreds of targeted proteins to Skyline? William  2018-11-22 13:17
 

Hi Skyline team,

I wonder if there is a quick way to import hundreds of targeted proteins withoout creat fasta file containing all those targets?

Thanks
 
 
Brendan MacLean responded:  2018-11-22 20:35

Short answer: yes.

Long answer: depends on your starting point. What do you have? A list of accession numbers? A spectral library with a bunch of peptides?

Give us a bit more info, and I am sure we can help.

—Brendan
 
William responded:  2018-11-22 20:40

Thank you Brendan, I have a list of accession numbers
 
Brendan MacLean responded:  2018-11-22 21:17

Then you would build a background proteome of the organism FASTA and use Edit > Inserts > Proteins. If you have the backing background proteome you can just paste into the Accession column. See the Targeted Method Editing tutorial for steps to build a background proteome.

Hope this helps.

—Brendan
 
Brendan MacLean responded:  2018-11-23 09:56

The creation of the Yeast background proteome starts here:

https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/MethodEdit-3_7.pdf#page=4

And the description of inserting a list of proteins by name starts here:

https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/MethodEdit-3_7.pdf#page=14

The example screenshot on this page hides the Accession column, but you can just as easily paste a line-separated list of accession numbers into this column as the tutorial walks you through pasting a line-separated list to the Name column. I think you can also do this in the Preferred Name column if you had a list of those.