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Adding (glycan) modifications as a list

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Adding (glycan) modifications as a list Erik de Graaf  2018-02-06 08:03
 
Hi Skyline Team,


I have generated list of all glycans I could expect like this:
Name    Mol Formula
H5N2    C46O35H76N2
H6N2    C63O49H103N3
H7N2    C80O63H130N4
H8N2    C97O77H157N5
H9N2    C114O91H184N6
... ...


Is it possible to add a lot of modifications like this list to the Mod table, just by simply copy/pasting into a Skyline config file?

This would help the glycoproteomics field a lot.

Thank you,

Erik
 
 
Erik de Graaf responded:  2018-02-06 08:29
Hi again,

I actually forgot about my previous thread:
https://skyline.ms/announcements/home/support/thread.view?entityId=b374a594-562f-1034-87f8-da20258210fe&_docid=thread%3Ab374a594-562f-1034-87f8-da20258210fe

I concatenated/converted the list into a list with entries like this:
 
<static_modification name="H5N2" aminoacid="N" variable="true" formula="C46O35H76N2" />

This does work! Partially... It shows up in the modification table of this .sky file. However, I want the peptide list to look like:

SEQUENCE
SEQUEN[MOD1]CE
SEQUEN[MOD2]CE
...


Oh wait maybe I can do this with the import peptides list...
 
Brendan MacLean responded:  2018-02-09 22:18
Hi Erik,
It might be helpful to others if you could save your settings with these modifications added as either a .skys file (Settings > Save - give them a name, Settings > Share) or just a blank (targetless) .sky file.

We would be happy to post this to the Skyline website under Tips, which would make it easier for anyone else to get these 142 modifications.

Are there also charged losses that go with these that might get added to the Transition Settings - Filter tab under Special ions?

Thanks for posting this information to the Skyline support board. Glad to hear you are finding ways to get what you need.

--Brendan