Error when inserting cross-linked peptides into document

Error when inserting cross-linked peptides into document Juan C. Rojas E.  2022-06-09

Hi Skyline team,

So I am trying to insert a set of cross-linked peptides into Skyline through Edit -> Insert -> Peptides... by copying a list of crosslinked peptides that I parsed from a MeroX output into Skyline format. I loaded a .txt file (attached) with these sequences in Excel and attempted to copy-paste the whole list into the window in Skyline as I usually do for other "normal" peptides, but keep getting a "This peptide sequence contains invalid characters".

Strangely, when I click inside the cell of "Peptide Sequence" and paste a single sequence from the parsed list it accepts the entry. Any ideas what is going on?

Attached is also the Skyline document with the required mods and some pre-loaded peptides.

Hope ASMS was fun!
Juan C.

Nick Shulman responded:  2022-06-09
When you push the "Check for Errors" button in the Insert Peptides dialog, it will highlight the row that has the error.
Skyline actually ends up highlighting the last row which has an error in it.

Some of your peptide sequences really are invalid, for instance:
For that one, it looks like you intended to apply both a 214.1 and 16 modification to the same amino acid. That should have been written as:

Skyline is perfectly happy with the crosslinked peptide sequences in your list. It's those nested modifications which it is complaining about.
-- Nick
Juan C. Rojas E. responded:  2022-06-10
Thanks for the quick reply!

For whatever reason the workstation that I was using initially using only showed me the attached error which did not let me find the error easily. Where only the first entry is displayed and is not the one with the issue.

I just tried it in another pc (both with the same Skyline version and text editor) and I could troubleshoot it as you did. I have no idea what makes the difference. Anyway, thanks to you for pointing out the error I have fixed an error in the parser. The aimed dead-end sequence was actually the following:


Now I am trying to import the new list and it lets me import it, but when I try to insert or check for errors I get the attached error. I assume something with the aa locator, but I am not being able to pinpoint the error nor on which sequence; I have additionally report the error with the document.

Thanks for the help! Sincerely,

Juan C.