Error message when trying to copy and paste phospho peptides from one file into another file

Error message when trying to copy and paste phospho peptides from one file into another file rschoenh  2018-11-08


we're sometimes having trouble copying and pasting phospho peptides from one Skyline file into another Skyline file. Skyline basically doesn't let us do the pasting, but instead we get an error message saying "The modification Phospho (ST) already exists with a different definition." As far as we can tell, we have the same definitions in both Skyline files. Thanks very much in advance for your help!


Brendan MacLean responded:  2018-11-08

Hi Regine,
We will need documents that allow us to reproduce the issue, which you can provide us by using File > Share - Complete and posting the files to:

Then just the steps, e.g. copy this peptide from document A to document B. Once we can reproduce the error ourselves, I am sure we can fix the problem, or at least explain how to avoid it or give you a temporary workaround until we can fix it.

Thanks for reporting this issue.


Nick Shulman responded:  2018-11-08
Can you send us your two Skyline documents?
In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files.

If those .zip files are less than 50MB then you can attach them to this support request.
Otherwise, you can upload them here:

Let me know which peptide you were having trouble pasting.
-- Nick
rschoenh responded:  2018-11-08
Hi Brendan and Nick,

thanks for your quick responses. We're attaching two files with one and two peptides, respectively; copying the peptides from either file to the other does not work for us. Please let us know if you need any other info.

Thanks so much!
Nick Shulman responded:  2018-11-08

It looks like that modifications in the "" were originally added in 2014, before Skyline added the feature of being able to specify a short name for Unimod modifications. Because of this, Skyline thinks that the modification you have is different than what it is in documents created later than that. This is a bug, but it might be tricky for us to figure out how to fix it.

The easiest way to fix this would be for you to open up that first .sky file in a text editor (such as Notepad). Towards the top of the file, there's a line that looks like this:
<static_modification name="Phospho (ST)" aminoacid="S, T" formula="HO3P" explicit_decl="true" unimod_id="21">
you just need to insert short_name="Pho" so that it looks like this:
<static_modification name="Phospho (ST)" aminoacid="S, T" formula="HO3P" explicit_decl="true" unimod_id="21" short_name="Pho">

If you have any trouble with that, you should send us your Skyline document and we will fix it for you and send it back.
-- Nick

rschoenh responded:  2018-11-08

Hi Nick,

thanks for your help; that fixed the issue!

Have a great rest of your day!


rschoenh responded:  2021-05-07

Hello all,

hope you are doing fine! We've come across a similar issue as the one in the thread above, but this time your work-around unfortunately didn't fix it (we've used it successfully in the past), or we somehow didn't do it correctly. This time, we have a Skyline file with ~70 peptides, copied and pasted together from a few different Skyline files, not just one or two files, so maybe that messed something up...

I think it might be best if I send you the file. Would you let me know what the best way is to get the file to you securely and confidentially (not sure if the way described above is still applicable)?

Thanks so much,

Nick Shulman responded:  2021-05-07
I will send you an email message directly.
-- Nick