Hi Kristen,
You can post modification annotated peptide sequences in to the Skyline document directly or into the Edit > Insert > Peptides form. These look like either:

AFC[+57]AVPWQGTM[+16]TLSK

or

S[Phospho (ST)]LLYFVYVAPGIVNT[Phospho (ST)]YLFMMQAQGILIR

Even if you don't have these particular modifications defined in Skyline, it will attempt to match whatever you have between the brackets with Unimod modifications.

You can also explicitly specify heavy modifications to help Skyline understand what you mean, but this is also not required.

A{+1}E{+1}I{+1}D{+1}M{+1}[+16]L{+1}D{+1}I{+1}R

For 15N labeling with an oxidized Methionine.

Hope that helps. Good luck with your method design.

--Brendan

Hi,

It would be useful if this were possible in batches. Any plans to implement a batch modified peptide import?

Best,

Michael

Hi Michael,
I don't yet understand your request. Are you asking for a way to do this from the command line with SkylineRunner? Or something else.

I'll need to understand the request before I can give you a time-frame for when it might happen.

Thanks for using Skyline in your research.

--Brendan

Hi,

1) If I follow the instructions above (7/12/13) I can manually enter modified peptide sequences.
2) If I have a large number of sequences to import manual entry becomes a chore.
3) I already have my sequences in the required format for manual entry.
4) The ability to import my list of peptides would save me some time and eliminate a possible source of error.

Does that help clarify my request? Thanks for your help.

Michael

Hi Michael,
Sorry for not giving clear enough instructions. You can paste a large list of peptides in this format either directly into the Edit > Insert > Peptides form, or directly into your Skyline document with Edit > Paste.

Both forms of pasting are covered in the Targeted Method Editing tutorial:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_method_edit

Though, modified sequences are not explicitly mentioned, as they were implemented after the tutorial was written.

--Brendan

Follow up question regarding peptide list, anyway to include peptide charge information with list as well ? Ie. I have a list of hundreds of peptides with mods and different overall charges . Would it be something like xxxS[+80]xxx +4 ? Thanks.

Tanveer

Hi Tanveer,
Not yet possible, but seems like a good suggestion. I have posted a TODO issue for it to the issues list:

https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=262

Can't promise when it might get done, but it doesn't seem like it would be that difficult. So, maybe for the next release after v2.1.

Thanks for the feedback.

--Brendan