Error when copy + pasting a peptide list into Skyline daily

Error when copy + pasting a peptide list into Skyline daily roberthardt  2020-08-28

Dear Skyline-Team,

if I want to insert peptides via "Edit - Insert - Peptides" in Skyline Daily (, 77dodc4a4) the software always freezes. In contrast, if I do exactly the same in the current public Skyline release (, a0e7323e3) it works without a glitch.



roberthardt responded:  2020-08-28

Additional info:

I also copied the list (Excel) to Notepad first before copying and pasting it into Skyline.



Brian Pratt responded:  2020-08-28

Hi Robert,

May we see the excel file in question?


Brian Pratt

roberthardt responded:  2020-08-31

Hi Pratt,

for some strange reason the error is gone this morning after my PC was shut down over the weekend. I can now copy & paste the peptide lists into both Skyline versions, regular and daily.



Brian Pratt responded:  2020-08-31

That is indeed strange. If the problem arises again please do provide a copy of the file(s) that are giving you trouble.


Brian Pratt

Nick Shulman responded:  2020-08-31

I have a couple of more questions:

1. Did you have a background proteome file? You can specify a Background Proteome at:
Settings > Peptide Settings > Digestion
and Skyline might use that in order to populate the Protein Description column in the Paste Peptides dialog
(although I would not expect this to be able to cause a hang like this).

2. In your screenshot, it looks like you were including extract stuff in the peptide sequence which would make Skyline reject it in the Paste Peptides dialog.
That is, one of your sequences for example looked like:
The "K." at the beginning and ".N" at the end are used elsewhere in Skyline to indicate the preceding and following amino acids in the protein sequence that the peptide came from. However, if you include that in the Paste Peptides dialog, Skyline will give you an error.

-- Nick