Spectrum Library with specific modifications

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Spectrum Library with specific modifications sophie lagache  2017-09-25 06:33
 
Hi Skyline team,
I have a quick question regarding the spectrum library ... how the modifications are coded by mass difference or by mass adduct ?
I would like to look at the citrullination modifications on the Arginine which were identified on my sptxt file library but after adding in Skyline it seems to be disappeared !!! Is it because it is not a modification existing in your list, or do I have to do something special to see it ...
Thanks in advance,
Sophie
 
 
Nick Shulman responded:  2017-09-25 12:28
I do not know the answer to your question, but if you send us your files we can probably figure it out.
In Skyline, you can use the menu item:
File > Share > (Complete)
to create a .zip file containing your Skyline document and supporting files, including spectral libraries.

You can upload that .zip file here:
https://skyline.ms/files.url
 
sophie lagache responded:  2017-09-26 00:57
Ok Skyline document is uploaded :-)

Thanks
 
Nick Shulman responded:  2017-09-26 11:46
Thank you for sending us your files.
I am a little confused because your original post mentioned the sptxt file, but you did not send us one.
You can use an .sptxt file as a spectral library in Skyline. You do this by going to:
Settings > Peptide Settings > Library
and pressing the "Edit List", and then "Add" buttons. You then browse for the .sptxt file.

This is different from the way that you use peptide search results. With peptide search result, you Build a .blib file, which is what you seem to have done with your msms.txt file.

The thing about sptxt files is that we have in the Skyline source code a list of a few dozen named modifications. If you want to refer to a modification that is not in the list, you just need to send us your .sptxt file, and we will figure out how to add it. Also, if Skyline is just ignoring your modification and not telling you about that, we should fix that too.

I am not sure what I should be looking at with the files that you did send us. Can you tell us what you are seeing and what you expect to see?
 
sophie lagache responded:  2017-09-27 06:36
Yes you are right it was confusing ... I forgot to tell you that I tested 2 libraries (one from MaxQuan building it, and one from our pipeline adding it ;-) and both failed) and sent you the one from MaxQuan.
Anyway I downloaded now the .sptxt and if you could work on both, it would be awsome!!!

I am expected to see citrullination modification on R (it's like a deamidation ) and be able to insert my protein with peptides with Citrullination and no Citrullination. Does it make sense?

Thanks in advance

Sophie
 
sophie lagache responded:  2017-10-09 05:44
Hi Nick,
sorry to bother you, but do you have any good news for my library?
thank you
Sophie
 
Kaipo Tamura responded:  2017-10-09 15:21
Hi Sophie,
Sorry for the delay - we are looking into fixing these bugs.

Thanks,
Kaipo
 
Kaipo Tamura responded:  2017-10-09 15:53
Hi Sophie,
You will be able to use the MaxQuant results files with the correct modifications, if you have your modifications.xml file in the same directory as the msms.txt file when you build the library. The modifications.xml file must contain the citrullination modification in it, i.e.:

<modification title="Arg-&gt;Citrullin" ...>
...
</modification>

We are still looking into the issue with the sptxt library.

Thanks,
Kaipo