Quick way to import hundreds of targeted proteins to Skyline?

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

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?


Brendan MacLean responded:  2018-11-22

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.


William responded:  2018-11-22

Thank you Brendan, I have a list of accession numbers

Brendan MacLean responded:  2018-11-22

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 MacLean responded:  2018-11-23

The creation of the Yeast background proteome starts here:


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


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.